ROMMIE E. AMARO Professor and Endowed Chair

Department of Chemistry and Biochemistry University of California, San Diego

3234 Urey Hall, 9500 Gilman Drive MC-0340, La Jolla, CA 92093-0340 858-534-9629 (office); 773-490-6063 (cell)

ramaro@ucsd.edu amarolab.ucsd.edu; nbcr.ucsd.edu; drugdesigndata.org; biochemcore.ucsd.edu; vmcc.ucsd.edu

EDUCATION 1999 B.S. High Distinction, University of Illinois, Urbana- Champaign, IL Major: Chemical Engineering Dissertation Title: Structure Prediction of HisH in the Context of Structural

Genomics; Advisors: Z. Luthey-Schulten and C. Zukoski 2005 Ph.D., High Distinction, University of Illinois, Urbana- Champaign, IL Major: Chemistry Dissertation Title: Investigating the Structure and Function of IGP Synthase

Advisor: Z. Luthey-Schulten 2005 – 2009 Postdoctoral Fellow — NIH NSRA Ruth Kirschstein Fellow, UC San Diego Advisor: J. Andrew McCammon PROFESSIONAL POSITIONS 2019 – present Endowed Chair, Distinguished Professorship in Theoretical and Computational

Chemistry, Department of Chemistry and Biochemistry, UC San Diego 2017 – present Department Vice Chair, Department of Chemistry and Biochemistry, UC San Diego 2017 – present Section Chair, Biochemistry and Physics, Department of Chemistry and Biochemistry,

UC San Diego 2017 – 2018 Member, Advisory Board for the Task Force on the Status of Women in the Division

of Physical Sciences, UC San Diego 2017 – 2018 Academic Senate System-wide Representative for UCADDE, UC San Diego 2017 – 2018 Chair, Academic Senate Committee for Diversity and Equity, UC San Diego 2016 – 2019 Shuler Scholar, Department of Chemistry and Biochemistry, UC San Diego 2016 – present Professor, Department of Chemistry and Biochemistry, UC San Diego 2015 – present Co-Director, Visible Molecular Cell Consortium, UC San Diego 2015 – present Co-Director, UCSD Center for Translational Drug Discovery, UC San Diego 2014 – present Co-Director, Drug Design Data Resource, UC San Diego 2014 – 2016 Associate Professor, Department of Chemistry and Biochemistry, UC San Diego 2013 – 2020 Director, National Biomedical Computation Resource, UC San Diego 2012 – 2014 Assistant Professor, Department of Chemistry and Biochemistry, UC San Diego 2010 – 2011 Assistant Professor, Department of Chemistry, UC Irvine 2009 – 2011 Assistant Professor, Department of Computer Science, UC Irvine 2009 – 2011 Assistant Professor, Department of Pharmaceutical Sciences, UC Irvine 2005 – 2009 Postdoctoral Fellow, UC San Diego 2001 – 2005 Graduate Research Fellow, Luthey-Schulten Group, University of Illinois, Urbana-

Champaign, IL 2000 – 2001 Associate Research Engineer II, Research and Development, Kraft Foods, Inc.,

Glenview, IL 1998 – 1999 Undergraduate Research Fellow, Wolynes Group, University of Illinois, Urbana-

Champaign, IL

1998 US Lubes and Marketing Research Intern, Mobil Oil Corp., Cicero, IL AWARDS AND HONORS 01/2019 Lattimer Fellowship from the Division of Physical Sciences, UC San Diego 01/2018 UC San Diego Faculty Research Lecturer Award 12/2017 DE Shaw Research Distinguished Lecture 10/2017 NIH Stetten Lecturer 10/2017 University of Minnesota, Department of Med Chem, Distinguished Lecture 09/2016 Corwin Hansch Award, Hansch-Fujita Society 07/2016 Gordon Research Conference Computational Chemistry Keynote Lecture Spring 2016 ACS Kavli Emerging Leader in Chemistry National Lecturer 06/2015 Work featured on cover of Biophysical Journal 03/2015 Work featured on cover of ACS Biochemistry 2015 San Diego 78th District Woman of the Year, awarded by the Speaker of the California

State Assembly, Toni Atkins, 78th District Representative 2015 Invited Speaker, Burroughs Wellcome “Future of Biophysics” Symposium, 59th

Annual International Biophysical Society Meeting, Baltimore, Maryland 04/2014 Work featured on cover of Current Opinion in Structural Biology 2014 NVIDIA Women Who CUDA Awardee 2014 Athena Pinnacle Award Nominee 2014 NVIDIA Compute-the-Cure Awardee 2013 ACS ChemLuminary Award for “Innovation and Outstanding Service to Members of

a Division” for the Teach-Discover-Treat Initiative 2013 ACS COMP Open Eye Outstanding Junior Faculty Award 01/2013 Chu Lectureship, Idaho State University 2012 Hellman Fellow 2010 Presidential Early Career Award for Scientists and Engineers (received October 2011) 2010 – 2015 NIH Director's New Innovator Award, National Institutes of Health 09/2009 UC Irvine Nominee for the Searle Scholar Award Program 2006 – 2009 NIH NRSA Ruth Kirschstein Postdoctoral Fellow, National Institutes of Health 2008 UC San Diego Nominee for the Burroughs Wellcome Career Award at the Scientific

Interface 03/2008 Work featured on the cover of Chemical Biology & Drug Design 08/2007 Awarded “Best Demo” at PRAGMA-13, Urbana-Champaign, IL 08/2007 Elected Alternate Councilor, American Chemical Society COMP Division 07/2007 Computer-Aided Drug Design Gordon Research Conference Fellowship Recipient 01/2007 Keystone Symposia Scholarship Recipient 2005 Selected as a Student Facilitator at the Council for Chemical Research Annual

Meeting 2005 Work featured as cover story of NCSA Access Magazine 07/2005 Work featured on cover of Biophysical Journal 2001 – 2004 University of Illinois Urbana-Champaign, Department of Chemistry Graduate

Fellowship, Graduate College MAPP Fellow 2002 NCSA Performance Capability Champion Award 2000 Above and Beyond Call of Duty Award, Kraft Foods 2000 DNA Spark Award, Kraft Foods for “Diligence, Dedication, and Enthusiasm” 1999 Alpha Delta Gamma “Outstanding Teacher of Freshmen”, All-Campus Teaching

Award

1995 – 1999 Ameritech Minority Engineering Scholarship, MChEP Air Products Scholar, Chancellor’s Scholar, President’s Scholar, Unofficial List of Excellent Teachers (4 times)

ADVISORY BOARD MEMBERSHIPS 2014 – present Advisory Board Member, NIH Program, Illuminating the Druggable Genome 2012 – present User Advisory Committee, NSF XSEDE (Extreme Science and Engineering

Discovery Environment) 2014 Resource Advisory Committee Member, NIH Research Resource, National Resource

for Automated Molecular Microscopy (NRAMM) PROFESSIONAL MEMBERSHIPS 2012 – 2013 Alternate Councilor American Chemical Society, Elected 2010 – 2011 Alternate Councilor American Chemical Society, Elected 2010 – present AAAS 2008 – 2009 President, Tau Chapter, Graduate Women in Science 2007 – 2009 Alternate Councilor American Chemical Society 2005 – present American Chemical Society 2005 – present Biophysical Society 2005 – 2011 Council for Chemical Research PROFESSIONAL SERVICE 2017 – present NIH HIVE Advisory Board 2016 – present American Chemical Society, National Awards Committee Member 2015 – present NIH Illuminating the Druggable Genome, Phase I and Phase II Advisory Board

Member 2012 – 2014 American Chemical Society COMP Division, Alternate Councilor, Elected 2008 – present Protein Society, Member 2005 – 2012 Council for Chemical Research, Member 2004 – present American Chemical Society and Biophysical Society, Member 2010 – 2012 American Chemical Society COMP Division, Alternate Councilor, Elected 2008 – 2009 Graduate Women in Science, Tau Chapter, President, Elected 2007 – 2009 American Chemical Society COMP Division, Alternate Councilor, Elected 2007 – 2008 Graduate Women in Science, Tau Chapter, Vice President, Elected REVIEWER SERVICE 2018 – present Journal of Chemical Physics, International 2018 – present Nature Catalysis, International 2016 – present Science, International 2016 – present eLife, International 2015 – present ACS Chemical Biology, International 2012 – present Nature Communications, International 2012 – present Biophysical Journal, Reviewer, International 2011 – present Journal of Medicinal Chemistry, Reviewer, International 2011 – present Journal of the American Chemical Society, Reviewer, International 2011 – present Journal of Medicinal Chemistry, Reviewer, International 08/2010 – present Journal of Computational Chemistry, Reviewer, International

08/2010 – present Journal of Molecular Biology, Reviewer, International 07/2010 – present Journal of Biological Physics, Reviewer, International 07/2010 – present Journal of Physical Chemistry (American Chemical Society), Reviewer 07/2010 – present Molecular Pharmacology, Reviewer, International 07/2010 – present Nature, Reviewer, International 07/2010 – present Proteins: Structure, Function, and Bioinformatics, Reviewer, International 2010 – present Biochemistry, Reviewer, International 2010 – present Journal of Theoretical and Computational Chemistry, Reviewer 2010 – present PLOS Computational Biology, Reviewer 2008 – present Chemical Biology and Drug Discovery, Reviewer 2008 – present Journal of Chemical Information and Modeling, Reviewer 2008 – present Journal of Computer Aided Molecular Design, Reviewer 2008 – present Journal of Molecular Graphics and Modeling, Reviewer UNIVERSITY SERVICE 2017 – 2018 Member of the Advisory Board for the Task Force on the Status of Women in the

Division of Physical Sciences, UC San Diego 2017 – 2018 Academic Senate System-wide Rep for UCADDE for UC San Diego 2017 – 2018 Chair, Academic Senate Committee for Diversity and Equity, UC San Diego 2017 – 2018 Vice Chair, Department of Chemistry and Biochemistry, UC San Diego 2017 – 2018 Section Chair, Biochemistry and Biophysics Section, Department of Chemistry and

Biochemistry, UC San Diego 2016 – 2017 Academic Senate System-wide Rep for UCADDE for UC San Diego 2016 – 2017 Academic Senate Committee for Diversity and Equity, UC San Diego 2015 – 2016 Diversity Committee, Department of Chemistry and Biochemistry, UC San Diego 2015 – 2016 Head of the Division of Physical Chemistry, Department of Chemistry and

Biochemistry, UC San Diego 2014 – 2016 Campus-wide, Leader of the Task Force to Establish a New Alliance with The Scripps

Research Institute, UC San Diego 2015 – 2016 Department of Chemistry and Biochemistry, Physical Chemistry Council

Representative, UC San Diego 2015 – 2016 Department of Chemistry and Biochemistry, Physical Chemistry Seminar Committee,

UC San Diego 2015 – 2016 School of Medicine, OMICS Search Committee, UC San Diego 2014 – 2015 Campus-wide, PDB Search Committee, UC San Diego 2014 – 2015 Department of Chemistry and Biochemistry, Super Search Committee, UC San Diego 2014 – 2015 Department of Chemistry and Biochemistry, Crick Chair Search Committee, UC San

Diego 2014 – 2015 Department of Chemistry and Biochemistry, Physical Chemistry Seminar Committee,

UC San Diego 2014 – 2015 Department of Chemistry and Biochemistry, Admissions and Recruitment – Member-

at-Large, UC San Diego 2013 – 2014 Department of Chemistry and Biochemistry, Diversity and Outreach Committee, UC

San Diego 2013 – 2014 Department of Chemistry and Biochemistry, Admissions and Recruitment – Member-

at-Large, UC San Diego 2013 – 2014 Department of Chemistry and Biochemistry, Diversity and Outreach Committee, UC

San Diego Spring 2013 Conversations about Diversity, UC San Diego

2012 – 2013 Department of Chemistry and Biochemistry, Junior Chemical Biology Search Committee, UC San Diego

2012 – 2013 Department of Chemistry and Biochemistry, Physical Chemistry Seminar Committee, UC San Diego

2012 – 2013 Department of Chemistry and Biochemistry, Graduate Affairs Committee, Physical Chemistry Representative and First-year Advisor for incoming Physical Chemistry Graduate Students, UC San Diego

2012 – 2013 Department of Chemistry and Biochemistry, Diversity and Outreach Committee, UC San Diego

Summer 2012 Department of Chemistry and Biochemistry, Leading the renovation of the Urey Hall Keck II Facility, UC San Diego

Spring 2012 Department of Chemistry and Biochemistry, LPSOE Search Committee, UC San Diego

Spring 2011 Department of Pharmaceutical Sciences Committee to develop a new assessment of undergraduate education, UC Irvine

02/2010 – 11/2011 Member, Mathematical, Computational, and Systems Biology (MCB) Admissions Committee, UC Irvine 01/2010 – 11/2011 Member, MCP Admissions Committee, UC Irvine EDITORIAL BOARD DUTIES 2019 – present Associate Editor, ACS Journal of Chemical Information and Modeling 2017 – present Editorial Board Member, Quarterly Reviews of Biophysics 2016 – present Editorial Committee Member, Annual Review of Physical Chemistry 2016 – present Editorial Advisory Board Member, Journal of Chemical Theory and Computation 2016 – present Editorial Advisory Board Member, Journal of Chemical Information and Modeling 2012 – 2019 Senior Editor, Chemical Biology and Drug Design http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1747-0285 2010 Associate Editor, PLOS Computational Biology GRANT REVIEWS 2018 Humboldt Young Investigator Group Award, Reviewer 2017 European Research Council, Ad Hoc Reviewer 01/2017 – present Stanford Linear Coherent Light Source (LCLS) Beamline Review Panel, Standing

Member 2016 – 2022 NIH Standing Study Section Member, Macromolecular Structure and Function,

Section D (MSFD) 11/2015 NIH Special Emphasis Panel, Reviewer 09/2015 DOE/NSF INCITE Computational Allocations Panel, Reviewer 11/2014 NIH P41 Study Section, Reviewer 03/2014 NIH R01/R21 MSFD Study Section, Ad Hoc Member 07/2012 – present NSF XSEDE Allocations Committee, Reviewer, Quarterly 06/2012 NIH SBIR Panel, Reviewer 03/2012 NSF Division of Chemistry, Chemistry of Life Program, Reviewer 09/2011 NIH SBIR Panel, Reviewer OTHER PROFESSIONAL ACTIVITIES 2016 – present LCLS X-ray XFEL Proposal Review Panel 2016 – present NIH MSFD Study Section Standing Member

2016 NIH P41 Review Panel 2016 INCITE Review Panel 2016 – present NIH MSFD Study Section Member 2014 – 2015 ACS National Meeting Spring 2016 Presidential Symposia Organizing Committee,

Computer-Aided Drug Design Subgroup 2015 INCITE Review Panel 2014 NIH P41 Review Panel 2012 – present BioChemCoRe Outreach and Mentoring Program http://biochemcore.ucsd.edu 2011 – present Teach – Discover – Treat Initiative Co-Founder and Steering Committee Member http://www.teach-discover-treat.org LECTURES AND SEMINARS (Invited Plenary), Gordon Research Conference: Computer Aided Drug Design, “Deriving Dynamics from CryoEM”, Mt Snow, VT. (July 2019) (Invited Plenary), OneChemistry Symposium: Molecular Machinery of Life, “Predicting Chemistry in a Cellular Context”, Johns Hopkins University, Baltimore, MD. (April 2019) (Invited Plenary), Biophysical Society Annual Meeting: Proteins: Dynamics and Allostery, “Protein Dynamics in a Cellular Context”, Baltimore, MD. (March 2019) (Student Invited), Yale University, Raymond and Beverly Sackler Institute Seminar, “Multiscale Dynamics: Molecules to Cells”, New Haven, CT. (November 2018) (Invited Plenary), NSF Center for Aerosol Impacts on the Chemistry of the Environment, “Integrating Computation and Experiment for Biotransformations”, La Jolla, CA. (November 2018) (Invited Keynote), Scialog Conference: Chemistry of the Cell, “Predicting Chemistry in a Cellular Context”, Tucson, AZ. (October 2018) (Invited Talk), National Cancer Institute, A3B Reverse Site Visit, “Computational Models and Predictions for APOBEC3B”, Bethesda, MD. (August 2018) (Invited Plenary), EMSL Integration at Pacific Northwest National Lab, “Molecular Simulation at the Mesoscale”, Richland, WA. (August 2018) (Invited Lecture), Telluride Workshop: Challenges in Large-Scale Biomolecular Simulation, “Molecular Simulation at the Mesoscale,” Telluride, CO. (June 2018) (Invited Plenary Representing the Whole of Molecular Biophysics), Blue Waters Annual Symposium, “Computational Biophysics in the Petascale Computing Era,” Sun River, OR. (June 2018) (Opening Plenary), CCP5/ CCP-BioSim Multiscale Modelling Conference, “Multiscale Dynamics: Molecules to Cells,” Manchester, England. (May 2018) (Invited Lecture), Brownian Dynamics and Biological Diffusion Brainstorm 4, “Multiscale Estimation of Ligand Binding Kinetics,” Heidelberg, Germany. (April 2018)

National Science Foundation, Center for Aerosol Impacts on Climate and the Environment Reverse Site Visit, Alexandria, VA. (March 2018) (Invited Lecture), “Computer Aided Drug Design,” The Scripps Research Institute, La Jolla, CA. (March 2018) (Opening Plenary), Drug Design Data Resource Face-to-Face Workshop, “Drug Design Data Resource,” La Jolla, CA. (February 2018) (Academic Senate Faculty Research Award Lecture), “Computing Cures: Discovery through the Lens of a Computational Microscope,” UC San Diego, La Jolla, CA. (January 2018) (Distinguished Lecture), DE Shaw Research, “Computing Cures: Discovery through the Lens of a Computational Microscope,” New York City, NY. (December 2017) (Invited Lecture), “Computing Cures: Discovery through the Lens of a Computational Microscope,” Stanford University, Department of Chemistry, Palo Alto, CA. (November 2017) (Invited Plenary Lecture), Supercomputing ’17 (SC17), “Molecular Simulation at the Mesoscale,” Salt Lake City, UT. (November 2017) (Invited Talk), Klaus Schulten Memorial Symposium, “Molecular Simulation at the Mesoscale,” Urbana, IL. (November 2017) National Institutes of Health, Stetten DeWitt Award Lectureship, NIH Director’s Series, “Computing Cures: Discovery through the Lens of a Computational Microscope,” (October 2017) (Invited Talk), National Institute of Standards and Technology (NIST), “Molecular Modeling at the Mesoscale,” Gaithersburg, MD. (October 2017) (Distinguished Lecture), “Computing Cures: Discovery through the Lens of a Computational Microscope,” University of Minnesota, Department of Medicinal Chemistry, Minneapolis, MN. (October 2017) (Invited Talk), Kinetics for Drug Discovery (K4DD) Closing Symposium, “Multiscale Estimation of Drug Binding Kinetics,” Berlin, Germany. (October 2017) (Invited Talk), Structure Based Drug Design Conference, “Multiscale Estimation of Drug Binding Kinetics,” Lausanne, Switzerland. (September 2017) (Invited Talk), American Conference on Theoretical Chemistry, “Multiscale Dynamics: Molecules to Cells,” Boston, MA. (July 2017) (Opening Plenary Keynote), Bio-IT World Expo 2017, “Computing Cures: Enabling Chemical Discovery through the Lens of a Computational Microscope,” Cambridge, MA. (May 2017) (Chancellor’s Associates Invited Lecture), “Computing Cures: Enabling Chemical Discovery through the Lens of a Computational Microscope,” UC San Diego, La Jolla, CA. (May 2017)

American Chemical Society National Meeting, Spring 2017, “Allostery and Regulation of Complex Biomolecular Systems through the Lens of a Computational Microscope,” San Francisco, CA. (April 2017) (Keynote Lecture), USHUPO National Conference, “Bringing Molecular Modeling Into the Mesoscale,” San Diego, CA. (March 2017) (Invited Lecture), DaVinci Convergent Science Symposium, “Multiscale Dynamics: Molecules to Cells,” USC Michelson Center for Convergent Bioscience, Bridge Institute, Los Angeles, CA. (March 2017) (Invited Lecture), Department of Energy Workshop, “Multiscale Dynamics: Molecules to Cells,” Washington, DC. (February 2017) (Invited Webinar Lecture), Pfizer, Inc., “Multiscale Dynamics: Molecules to Cells,” (January 2017) (Invited Webinar Lecture), National Institutes of Health, The Big Data 2 Knowledge (BD2K) Guide to the Fundamentals of Data Science, “Workflows and Pipelines in Biomedical Research,” (January 2017) National Science Foundation, National Strategic Computing Initiative (NCSI) Series, “Multiscale Dynamics: Molecules to Cells,” Alexandria, VA. (October 2016) (Invited Lecture), “Multiscale Dynamics: Molecules to Cells,” UC Riverside, Department of Bioengineering, Riverside, CA. (September 2016) (Invited Lecture), Department of Energy Workshop, “Multiscale Dynamics: Molecules to Cells,” Washington, DC. (September 2016) (Corwin Hansch Award Lecture), EuroQSAR International Conference, “Multiscale Structure Based Drug Design,” Verona, Italy. (September 2016) (Invited Lecture), “Multiscale Dynamics: Molecules to Cells,” University of Queensland (Australia) / Monash University. (September 2016) (Invited Keynote Lecture), Computational Chemistry Gordon Research Conference (GRC), “Multiscale Dynamics: Molecules to Cells,” Girona, Spain. (July 2016) (Invited National Plenary Lecture), International Conference on Computational Science (ICCS), “Discovery through the Lens of a Computational Microscope,” San Diego, CA. (June 2016) (Invited Lecture), Southern California Theoretical Chemistry Symposium, “Multiscale Dynamics: Molecules to Cells,” UC San Diego, La Jolla, CA. (June 2016) (Invited Lecture), Theoretical and Computational Biophysics Group, “Multiscale Dynamics: Molecules to Cells,” University of Illinois, Champaign, IL. (April 2016) (Invited Lectureship), University of Kentucky Naff Symposium, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Lexington, KY. (April 2016) American Physical Society National Meeting, “Enabling Biophysical Discovery through the Lens of a Computational Microscope,” Baltimore, MD. (March 2016)

ACS National Meeting, MPPG Division, “Allostery through the lens of a computational microscope: Conformational selection in a canonical signaling domain,” San Diego, CA. (March 2016) (National Plenary Lecture), ACS National Meeting, ACS Kavli Emerging Leader in Chemistry, “Computing Cures: Enabling Chemical Discovery through the Lens of a Computational Microscope,” San Diego, CA. (March 2016) ACS National Meeting, UNDERGRADUATE Division, “Seeing the Unseen: Chemical Discovery through the Lens of a Computational Microscope,” San Diego, CA. (March 2016) ACS National Meeting, PHYS Division, “Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics, and Milestoning,” San Diego, CA. (March 2016) National Institutes of Health, P41 Director’s Meeting, “Multiscale Dynamics: Molecules to Cells,” Bethesda, MD. (March 2016) PacifiChem Symposium, “Chemical discovery through a computational lens,” Honolulu, HI. (December 2015) Departmental Colloquium, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” UC San Diego, LA Jolla, CA. (October 2015) Simula Summer School, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” UC San Diego, La Jolla, CA. (August 2015) Discovery Lecture, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” UC San Diego, La Jolla, CA. (July 2015) (Invited Speaker), Gordon Research Conference: Enzymes, Co-Enzymes, and Metabolic Pathways, “Allostery through the Lens of a Computational Microscope,” Waterville Valley, NH. (July 15, 2015) (Invited Speaker), Telluride Conference: Challenges in Large Scale Biomolecular Simulations, “Crossing Scales in Biomolecular Simulations,” Telluride, CO. (June 17, 2015) (Invited Speaker), Albany 2015: The 19th Albany Conversation, “Multiscale Estimation of Binding Kinetics Using Molecular Dynamics, Brownian Dynamics, and Milestoning,” Albany, NY. (June 11, 2015) (Invited Speaker), Integrated Digital Infrastructure Showcase, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” UC San Diego, La Jolla, CA. (May 6, 2015) (Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” University of Utah, Department of Medicinal Chemistry, Salt Lake City, UT. (April 23, 2015) (Invited Speaker), SDCSB's Cytoscape and Network Analysis Workshop, “Allosteric Networks through the Lens of a Computational Microscope,” La Jolla, CA. (April 17, 2015) (Invited Speaker), National Institutes of Health, National Cancer Institute, “Taming of the Mutator: Breaking Resistance in Cancer through APOBEC,” Rockville, MD. (April 8, 2015)

(Invited Speaker), NVIDIA GTC Annual Conference, “Accelerating the Cure: GPU-Driven Drug Discovery for Targets in Cancer,” San Jose, CA. (March 18, 2015) (Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Mira Costa Community College, Oceanside, CA. (March 4, 2015) 59

th Annual International Biophysical Society Meeting, Burroughs Wellcome Future of Biophysics Symposium: “Enabling Biophysical Discovery through the Lens of a Computational Microscope,” Baltimore, MD. (February 2015) (Invited Speaker), UT Austin, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Indianapolis, IN. (January 19, 2015) (Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Indiana University – Purdue University at Indianapolis, Indianapolis, IN. (December 10, 2014) (Invited Speaker), International Society for Quantum Biology and Pharmacology International Meeting, “Simulation-Based Discovery: Celebrations, Challenges, and Conversations About a New Way Forward,” La Jolla, CA. (June 2014) (Invited Speaker), NOBBChE Annual Meeting, “Enabling Biophysical Discovery through the Lens of a Computational Microscope,” La Jolla, CA. (March 2014) (Invited Speaker), American Association of Pharmaceutical Scientists (AAPS) Annual Meeting and Exposition, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” San Antonio, TX. (November 11, 2013) (Invited Speaker), American Chemical Society National Meeting, 20 Years of PME: Symposium in Honor of Tom Darden, Lee G. Pedersen, and Darrin York, “Pocket full of promise: Simulation-based discovery against p53,” Indianapolis, IN. (September 2013) (Invited Speaker), American Chemical Society National Meeting, Emerging Science Frontiers: Young Investigators, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Indianapolis, IN. (September 2013) (Invited Speaker), Snowmass Free Energy Conference, Free Energy Calculations: Three decades of adventure in chemistry and biophysics, “Towards exploiting the functional free energy landscapes of proteins,” (July 16, 2013) (Invited Speaker), Telluride Conference, Chemistry and Dynamics in Complex Environments, “Investigating Chemistry and Dynamics in Complex Environments…. Through the Lens of a Computational Microscope,” (June 27, 2013) (Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” University of Minnesota, Department of Biochemistry, Molecular Biology, and Biophysics, Minneapolis, MN. (May 1, 2013) (Invited Speaker), CHI Drug Discovery Conference, Fragment-based Drug Design Session, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” San Diego, CA. (April 17, 2013)

(Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Johns Hopkins University, Department of Biophysics, Baltimore, MD. (April 1 2013) (Invited Speaker), National Institutes of Health, Structural Biology Laboratory, “Enabling Chemical and Biophysical Discovery through the Lens of a Computational Microscope,” Bethesda, MD. (March 19, 2013) (Invited Speaker), “Enabling Chemical Discovery through the Lens of a Computational Microscope,” University of Tennessee, Knoxville, Knoxville, TN. (February 13, 2013) (Invited Keynote Speaker), First Inaugural Chu Lectureship, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Idaho State University, Pocatello, ID. (January 29, 2013) (Invited Speaker), MBTG Symposium, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” Scripps Institute of Oceanography, La Jolla, CA. (January 2013) (Invited Speaker), The 4th Seminar & Workshop on Computer-Aided Drug Design CADD2012 – Malaysia, “Enabling Chemical Discovery through the Lens of a Computational Microscope,” University of UiTM Puncak Alam, Malaysia. (December 2012) (Invited Speaker), Center for Theoretical Biological Physics, “Computational Biophysics and Drug Discovery,” Pacific Hall, UC San Diego, La Jolla, CA. (October 5, 2012) (Invited Speaker), National Biomedical Computation Resource (NBCR) Summer Institute, “CADD Pipeline: Enabling routine ensemble- based drug discovery,” Fung Auditorium, UC San Diego, La Jolla, CA. (July 30, 2012) (Invited Speaker), 15th UCSD MedChem Symposium, “Tackling receptor flexibility in computer-aided drug design,” Price Center, UC San Diego, La Jolla, CA. (July 13, 2012) (Invited Speaker), 6th Drug Design and Medicinal Chemistry Conference, “Tackling receptor flexibility in computer-aided drug design,” Hilton San Diego Resort and Spa, San Diego, CA. (June 8, 2012) (Invited Speaker), Department of Bioengineering Seminar Series, “Computational Biophysics and Drug Discovery: where the rubber meets the road,” UC San Diego, La Jolla, CA. (June 1, 2012) (Invited Speaker), 2012 Workshop on Free Energy Methods in Drug Design, “Small Molecule Membrane Permeability,” Vertex Pharmaceuticals, Cambridge, MA. (May 22, 2012) (Invited Speaker), Schrodinger User Group Meeting, “Predicting Small Molecule Membrane Permeability,” Hyatt Regency, La Jolla at Aventine, La Jolla, CA. (April 16, 2012) (Invited Speaker), American Chemical Society National Meeting, Symposium Honoring J. Andrew McCammon, “Tales from the Trenches: Explorations at the interface of computational biophysics and drug discovery,” San Diego Convention Center, San Diego, CA. (March 26, 2012) (Invited Speaker), Allostery Workshop, “Computational Biophysics and Drug Discovery: where the rubber meets the road,” UC San Diego, La Jolla, CA. (March 10, 2012)

(Invited Speaker), Department of Biological Chemistry Seminar Series, “Tackling receptor flexibility in computer-aided drug design,” UC Irvine, Irvine, CA. (October 19, 2011) (Invited Speaker), The 3rd International Young Researcher Seminar for Zoonosis Control, 2011, "Unlocking clues to influenza antiviral evasion through computational investigations of neuraminidase," Hokkaido University, Sapporo, Japan. (September 17, 2011) (Invited Speaker), Influenza 2011, “Mechanism of 150-cavity formation in influenza neuraminidase,” Oxford University, Oxford, England. (September 7, 2011) PSWRCE Annual Meeting, “Investigating proteins of the rip operon,” Honolulu, HI. (August 2, 2011) TeraGrid 2011, “Mechanism of 150-cavity formation in influenza neuraminidase,” Salt Lake City, UT. (July 19, 2011) 7th International Conference on Biological Physics, "Applications to Drug Discovery," Center for Theoretical Biological Physics & the UC San Diego, La Jolla, CA. (June 19, 2011) Electrostatics in Molecular Biology, "Electrostatics of the Influenza Glycoproteins," Clemson University, Clemson, SC. (April 5, 2011) "Tackling receptor flexibility in computation-guided pharmaceutical discovery: where the rubber meets the road," UC San Diego, Department of Chemistry and Biochemistry, La Jolla, CA. (January 2011) (Plenary Lecturer), SACNAS National Conference 2010, "Pushing the Limits of Computer- Aided Drug Design to Sustain Discovery of Next-generation Pharmaceuticals," SACNAS, Anaheim, CA. (October 1, 2010) (Keynote Speaker), National Biomedical Computation Resource (NBCR) Summer Institute 2010, "Tackling receptor flexibility in computer-aided drug design: where the rubber hits the road," National Biomedical Computation Resource, NIH, UC San Diego, La Jolla, CA. (August 2010) (Plenary Lecturer), Biophysics Summer School, "Tackling receptor flexibility in computer- aided drug design," University of Tennessee / Oak Ridge National Laboratory, Knoxville, TN. (July 2010) Theoretical and Computational Biophysics Group: Hands-On Computational Workshop, "National Biomedical Computation Resource CADD Pipeline," The Scripps Research Institute, La Jolla, CA. (July 2010) (Keynote Speaker), Point Loma Perspectives On Science Conference, "Towards Developing New Influenza Therapeutics Using Computer-aided Drug Design," Point Loma Nazarene University, San Diego, CA. (October 2009) MERCURY Conference, "Tackling Receptor Flexibility in Computer-Aided Drug Design: How to hit a moving target," Hamilton, NY. (August 2009) Kinetoplastid Molecular Cell Biology III, "Discovery of drug-like inhibitors of an essential RNA editing ligase in T. brucei," Woods Hole, MA. selected from abstracts. (April 2009) Sanibel Symposium, "Remarkable Loop Flexibility in Avian Influenza Neuraminidase and its Implications for Antiviral Drug Design," St. Simon’s Island, GA. (February 2009)

Schrodinger User Meeting, "Tackling Receptor Flexibility in Computer-Aided Drug Design: Investigations of Avian Influenza Neuraminidase," San Diego, CA. (November 2008) EChemInfo Meeting, "Comparative Studies Using Explicit and Generalized Born Molecular Dynamics Simulations of Avian Influenza Neuraminidase," Bryn Mawr, PA. (October 2008) National Biomedical Computation Resource Mini-symposium, "Tackling Receptor Flexibility in Computer-Aided Drug Design," UC San Diego, La Jolla, CA. (August 2008) "Tackling Receptor Flexibility in Computer-Aided Drug Design," UC Irvine; Department of Pharmaceutical Sciences, Invine, CA. (February 2008) International Conference on Avian Influenza, "Avian Flu Grid: International Collaborative Environment for Team Science on Avian Influenza," Bangkok, Thailand. selected from abstracts. (January 2008) American Chemical Society National Meeting, "Accommodating Receptor Flexibility in the Search for Inhibitors Against an Essential RNA Editing Ligase in Trypanosoma brucei," Chicago, IL. (March 2007) Inaugural Annual Chemical Biology Interface Symposium, "Investigating the Structure and Function of IGP Synthase," UIUC, Urbana, IL. (August 2005) Great Lakes Regional Meeting of the American Chemical Society, "Further Insights into the Reaction Mechanism of IGP Synthase," Peoria, IL. (October 2004) NIH/NSF Theoretical and Computational Biophysics Workshop, "Methods and Applications of Parameterization," Perth, Australia. (June 2004) NSF Theoretical and Computational Biophysics Summer School, "Methods of Parameterization," Urbana, IL. (June 2003) Cell & Molecular Biology & Molecular Biophysics Research Symposium, "Developing and Energy Landscape for the Novel Function of a (β/α)8 Barrel Ammonia Conduction Through HisF," Urbana, IL. (October 2002) Colgate-Palmolive Biotechnology Conference, "Structure Prediction of HisH in the Context of Structural Genomics," Urbana, IL. (April 2000) JOURNAL ARTICLES, PEER-REVIEWED

136. Luo, M. Wauer, N.A., Angle, K.J., Dommer, A.C., Song, M., Nowak, C.M., Amaro, R.E., Grassian, V.H., “Insights into the behavior of nonanoic acid and it’s conjugate base a the air/water interface through a combined experimental and theoretical approach”, Chem. Sci., 2020, Advance Article. doi: 10.1039/D0SC02354J

135. Ahn, S., Jagger, B.R., Amaro, R.E., “Ranking of Ligand Binding Kinetics Using a Weighted Ensemble Approach and Comparison with a Multiscale Milestoning Approach”, J. Chem. Inf. Model. doi: 10.1021/acs.jcim.9b00968 (2020).

134. Amaro, R.E., Mulholland, A.J. “A Community Letter Regarding Sharing Biomolecular Simulation Data for COVID-19”, J. Chem. Inf. Model., doi: 10.1021/acs.jcim.0c00319 (2020).

133. Lee, C.T., Laughlin, J.G., Angliviel de La Beaumelle, N., Amaro, R.E., McCammon, J.A., Ramamoorthi, R., Holst, M., Rangamani, P. “3D mesh processing using GAMer 2 to enable

reaction-diffusion simulations in realistic cellular geometries”, PLOS Comp Bio I, doi: 10.1371/journal.pcbi.1007756 (2020).

132. Parks, C.D., Gaieb, Z., Chiu, M., Yang, H., Shao, C., Walters, W.P., Jansen, J.M., McGaughey, G., Lewis, R.A., Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Burley, S.K., Amaro, R.E., Gilson, M.K. “D3R Grand Challenge 4: Blind Prediction of Protein-Ligand Poses, Affinity Rankings, and Relative Binding Free Energies”, J Comput Aided Mol Des, doi: 10.1007/s10822-020-00289-y (2020).

131. Lee, C.T., Laughlin, J.G., Moody, J.B., Amaro, R.E., McCammon, J.A., Holst, M., Rangamani, P. “An Open-Source Mesh Generation Platform for Biophysical Modeling Using Realistic Cellular Geometries”, Biophysical Journal, doi: 10.1016/j.bpj.2019.11.3400 (2020).

130. Jagger, B.R., Kochanek, S.E., Haldar, S., Amaro, R.E., Mulholland, A.J. “Multiscale simulatons approaches to modeling drug-protein bindng”, Current Opinion n Structural Biology, doi: 10.1016/j.sbi.2020.01.014 (2020).

129. Durrant, J.D., Kochanek, S.E., Casalino, L., Ieong, P.U., Dommer, A.C., Amaro, R.E., “Mesoscale All-Atom Influenza Virus Simulations Suggest New Substrate Binding Mechanisma”, ACS Cent Sci, doi: 10.1021/acscentsci (2020).

128. Shi, K., Demir, O. Carpenter, M.A., Banerjee, S., Harki, D.A, Amaro, R.E., Harris, R.S., Aihara, H., “Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3”, FASEB BioAdvances, doi: 10.1096/fba.2019-00068 (2020).

127. Le, K.P., Do, P-C., Amaro, R.E. and Le, L., “Molecular Docking of Broad-Spectrum Antibodies on Hemagglutinins of Influenza A Virus”, Evolutionary Bioinformatics, doi: 10.1177/1176934319876938 (2019).

126. Bernetti, M., Masetti, M., Recanatini, M. Amaro, R.E., Cavalli, A., “An Integrated Markov State Model and Path Metadynamics Approach to Characterize Drug Binding Processes”, J. Chem. Theory Comput., Vol. 15, Issue 10, doi: 10.1021/acs.jctc.9b00450 (2019).

125. Barros, E.P., Schiffer, J.M., Vorobieva, A., Dou, J., Baker, D., Amaro, R.E., “Improving the Efficiency of Ligand-Binding Protein Design with Molecular Dynamics Simulations”, J. Chem. Theory Comput., Vol. 15, Issue 10, doi: 10.1021/acs.jctc.9b00483 (2019).

124. Lee, C.T., Moody, J.B., Amaro, R.E., McCammon, J.A., Holst, M.J., “The Implementation of the Colored Abstract Simplicial Complex and Its Application to Mesh Generation”, ACM Trans. Math. Soft., Vol. 45, Issue 3, doi: 10.1145/3321515 (2019).

123. Wagner, J.R., Churas, C.P., Liu, S., Swift, R.V., Chiu, M., Shao, C., Feher, V.A., Burley, S.K., Gilson, M.K., Amaro, R.E., “Continuous Evaluation of Ligand Protein Predictions: A Weekly Community Challenge for Drug Docking”, Structure, Vol. 27, Issue 8, pp 1326-1335.e4. doi: 10.1016/j.str.2019.05.012 (2019).

122. Palermo, G., Sugita, Y., Wriggers, W., Amaro, R.E., “Frontiers in CryoEM Modeling”, J. Chem. Inf. Model., doi: 10.1021/acs.jcim.9b00412 (2019).

121. Luo, M., Dommer, A.C., Schiffer, J.M., Rez, D.J., Mitchell, A.R., Amaro, R.E., Grassian, V.H., Surfactant Charge Modulates Structure and Stability of Lipase-Embedded Monolayers at marine-Relevant Aerosol Surfaces”, Langmuir, doi: 10.1021/acs.langmuir.9b00689 (2019).

120. Taylor, B.C., Lee, C.T., Amaro, R.E., Structural basis for ligand modulation of the CCR2 conformational landscape”, PNAS, doi: 10.1073/pnas.1814131116 (2019).

119. Altman, M.O., Angel, M., Košík, I., Trovão, N.S., Zost, S.J., Gibbs, J.S., Casalino, L., Amaro, R.E., Hensley, S.E., Nelson, M.I., Yewdell, J.W. “Human Influenza A Virus Hemagglutinin Glycan Evolution Follows a Temporal Pattern to a Glycan Limit”, mBio, 10(2):e00204-19, doi: 10.1128/mBio.00204-19 (2019).

118. Amaro, R.E. “Will the Real Cryptic Pocket Please Stand Out”, Biophy J, 116(5):753-754, doi: 10.1016/j.bpj.2019.01.018 (2019).

117. Shi, K., Demir, O., Carpenter, M.A, Banerjee, S, Harki, D.A., Amaro, R.E., Harris, R.S., Aihara, H. “Active site plasticity and possible modes of chemical inhibition of the human DNA deaminase APOBEC3B”, bioRXiv, doi: 10.1101/513366 (2019).

116. Feher, V.A., Schiffer, J.M., Mermelstein, D.J., Mih, N., Pierce, L.C.T., McCammon, J.A., Amaro, R.E., “Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant”, Biophy J, 116(2):205-214, doi: 10.1016/j.bpj.2018.09.035 (2019).

115. Gaieb, Z., Parks, C.D., Chiu, M., Yang, H. Shao, C., Walters, W.P., Lambert, M.H., Nevins, N., Bembenek, S.D., Ameriks, M.K., Mirzadegan, T., Burley, S.K., Amaro, R.E., Gilson, M.K., “D3R Grand Challenge 3: Blind prediction of protein-ligand poses and affinity rankings”, J Comput Aided Mol Des, PMCID: PMC6472484; PMID: 30632055; doi: 10.1007/s10822-018-0180-4 (2019).

114. Schiffer, J.M., Mael, L.E., Prather, K.A., Amaro, R.E., Grassian, V.H., “Sea Spray Aerosol: Where Marine Biology Meets Atmospheric Chemistry”, ACS Central Science, Article ASAP, doi: 10.1021/acscentsci.8b00674 (2018).

113. Wagner JR, Demir Ö, Carpenter MA, Aihara H, Harki DA, Harris RS, Amaro RE. “Determinants of Oligonucleotide Selectivity of APOBEC3B”, J Chem Inf Model. Epub ahead of print, doi: 10.1021/acs.jcim.8b00427 (2018).

112. Amaro, R.E., Ieong, P.U., Huber, G., Dommer, A., Steven, A.C., Bush, R.M., Durrant, J.D., Votapka, L.W., “A Computational Assay that Explores the Hemagglutinin/Neuraminidase Functional Balance Reveals the Neuraminidase Secondary Site as a Novel Anti-Influenza Target”, ACS Central Science, 4(11):1570-1577. doi: 10.1021/acscentsci.8b00666 (2018).

111. Castro-Falcón, G., Seiler, G. Demir, O., Rathinaswamy, M., Hamelin, D., Hoffmann, R.M., Makowski, S., Letzel, A-C., Field, S., Burke, J., Amaro, R.E., and Hughes, C.C., “Neolymphostin A is a Covalent Phosphoinositide-3-kinase (P13-K)/Mammalian Target of Rapamycin (mTOR) Dual Inhibitor that Employs an Unusual Electrophilic Vinylogous Ester”, J. Med. Chem., 61(23):10463-10472. doi: 10.1021/acs.jmedchem.8b00975 (2018).

110. Offutt, T., Ieong, P.U., Demir, O., and Amaro, R.E., “Dynamics and Molecular Mechanisms of p53 Transcriptional Activation”, Biochemistry, 57(46):6528-6537. doi: 10.1021/acs.biochem.8b01005 (2018).

109. Wahab, H., Amaro, R.E., Cournia, Z., “Women in Computational Chemistry”, J. Chem. Inf. Model, Article ASAP, doi: 10.1021/acs.jcim.8b00642 (2018).

108. Gaieb, Z., Parks, C.D., Chiu, M. Yang, H., Shao, C., Walters, P.W., Lambert, M., Nevins, N., Bembenek, S.D., Burley, S.K., Amaro, R.E., and Gilson, M.K., “D3R Grand Challenge 3: Blind Prediction of Protein-Ligand Poses and Affinity Rankings”, ChemRxiv, doi:10.26434/chemrxiv.6752831 (2018).

107. Jagger, B. R., Lee, C. T. and Amaro, R.E., “Quantitative Ranking of Ligand Binding Kinetics with a Multiscale Milestoning Simulation Approach”, J Phys Chem Lett, 9: 4941-4948; PMCID: PMC6443090; doi: 10.1021/acs.jpclett.8b02047 (2018).

106. Salamango, D., Becker, J.T., McCann, J.L., Cheng, A.Z., Demir, O., Amaro, R.E., Brown, W., Shaban, N.M., and Harris, R.S., “APOBEC3H Subcellular Localization Determinants Define Zipcode for Targeting HIV-1 for Restriction”, Molecular and Cellular Biology; doi: 10.1128/MCB.00356-18 (2018).

105. Lee, C. T. and Amaro, R. E., “Exascale Computing: A New Dawn for Computational Biology”, Comput. Sci. Eng., PMCID: PMC6458592; doi:10.1109/MCSE.2018.05329812 (2018).

104. Schiffer, J.M., Luo, M., Dommer, A.C., Thoron, G., Pendergraft, M., Santander, M.V., Lucero, D., Pecora de Barros, E., Prather, K.A., Grassian, V.H., Amaro, R.E., “Impacts of Lipase Enzyme on the Surface Properties of Marine Aerosols”, The Journal of Physical Chemistry Letters doi: 10.1021/acs.jpclett.8b01363 (2018).

103. Salamango, D.J., McCann, J.L., Demir, O., Brown, W.L., Amaro, R.E., Harris, R.S. “APOBEC3B Nuclear Localization Requires Two Distinct N-Terminal Domain Surfaces”, Journal of Molecular Biology, doi: 10.1016/j.jmb.2018.04.044 (2018).

102. Mulero, M.C., Shahabi, S., Ko, M.S., Schiffer, J.M., Huang, D., Wang, V. Y-F., Amaro, R.E., Huxford, T., Ghosh, G., “Protein co-factors are essential for high affinity DNA binding by the nuclear factor κB RelA subunit”, Biochemistry, 57(20):2943-2957. doi: 10.1021/acs.biochem.8b00158 (2018).

101. Bohl, T.E., Ieong, P., Lee, J.K., Lee, T., Kankanala, J. Shi, K., Demir, Ö., Kurahashi, K., Amaro, R.E., Wang, Z., Aihara, H., “The substrate-binding cap of the UDP-diacylglucosamine pyrophosphatase LpxH is highly flexible, enabling facile substrate binding and product release”, Journal of Biological Chemistry, 293(21). PMCID: PMC5971466; doi: 10.1074/jbc.RA118.002503 (2018).

100. Amaro, R.E. and Mulholland, A.J., “Multiscale methods in drug design bridge chemical and biological complexity in the search for cures”, Nature Reviews Chemistry. 2: 0148; PMCID: PMC6445369; doi: 10.1038/s41570-018-0148 (2018).

99. Amaro, R.E., Baudry, J.,Chodera, J., Demir, Ö., McCammon, J.A., Miao, Y., and Smith, J., “Ensemble Docking in Drug Discovery”, Biophysical Journal. 114(10):2271-2278. PMCID:PMC6129458; doi: 10.1016/j.bpj.2018.02.038 (2018).

98. Prabhu, L., Chen, L., Wei, H., Demir, Ö., Safa, A., Zeng, L.-F., Amaro, R.E., O’Neil, B., Zhang, Z.-Y., Lu, T., “Development of AlphaLISA high throughput technique to screen for small molecule inhibitors targeting protein arginine methyltransferases”, Mol. Biosyst.201713(12) 2509-2520, doi: 10.1039/c7mb00391a (2017).

97. Shi, K., Demir, O., Carpenter, M.A., Wagner, J.R., Kurahashi, K., Harris, R.S., Amaro, R.E., Aihara, H., “Conformational Switch Regulates the DNA Cytosiine Deaminase Activity of Human APOBEC3B”, Nat Sci Rep doi: 10.1038/s41598-017-17694-3 (2017).

96. Grogan, F., Holst, M., Lindblom, L., Amaro, R. E., “Reliability assessment for large-scale molecular dynamics approximations”, J Chem Phys, doi: 10.1063/1.5009431 (2017).

95. Amaro, R.E., “Toward Understanding the Ways of Allosteric Drugs”, ACS Central Science, doi: 10.1021/acscentsci.7b00396 (2017).

94. Amaro, R.E., Villa, E., Luthey-Schulten, Z., “Biography of Klaus Schulten”, J Phys Chem B., doi: 10.1021/acs.jpcb.7b02141 (2017).

93. Gaieb, Z., Liu, S., Gathiaka, S., Chiu, M., Yang, H., Shao, C., Feher, V.A., Walters, W.P., Kuhn, B., Rudolph, M. G., Burley, S. K., Gilson, M.K. Amaro, R.E., “D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies”, J Comput Aided Mol Des., doi: 10.1007/s10822-017-0088-4 (2017).

92. Wagner, J.R., Sorensen, J., Hensley, N., Wong, C., Zhu, C., Perison, T., and Amaro, R.E., “POVME 3.0: Software for Mapping Binding Pocket Flexibility”, J Chem Theory Comput., doi: 10.1021/acs.jctc.7b00500 (2017).

91. Hirakis, S.P., Malmstrom, R.D., and Amaro, R.E., “Molecular Simulations Reveal an Unresolved Conformation of the Type IA Protein Kinase A Regulatory Subunit and Suggest Its Role in the cAMP Regulatory Mechanism”, Biochemistry, doi: 10.1021/acs.biochem.7b00461 (2017).

90. Cheng, K.J., Demir, O., and Amaro, R.E., “A Comparative Study of the Structural Dynamics of Four Terminal Uridylyl Transferases”, Genes (Basel), doi: 10.3390/genes8060166 (2017).

89. Purawat, S., Ieong, P.U., Malmstrom, R.D., Chan, G.J., Yeung, A.K., Walker, R.C., Altintas, I., and Amaro, R.E., “A Kepler Workflow Tool for Reproducible AMBER GPU Molecular Dynamics”, Biophys J., doi: 10.1016/j.bpj.2017.04.055 (2017).

88. Demir, Ö., Ieong, P., and Amaro, R. “Full-length p53 tetramer bound to DNA and its quaternary dynamics”, Oncogene, 36(10) 1451-1460; doi: 10.1038/onc.2016.321 (2017).

87. Votapka, L.W., Jagger B.R., Heyneman A.L., and Amaro R.E., “SEEKR: Simulation Enabled Estimation of Kinetic Rates, A Computational Tool to Estimate Molecular Kinetics and Its Application to Trypsin-Benzamidine Binding”, J Phys Chem B., doi: 10.1021/acs.jpcb.6b09388 (2017).

86. Prabhu L., Wei H., Chen L., Demir O., Sandusky G., Sun E., Wang J., Mo J., Zeng L., Fishel M., Safa A., Amaro R.E., Korc M., Zhang Z.Y., Lu T., “Adapting AlphaLISA high throughput screen to discover a novel small-molecule inhibitor targeting protein arginine methyltransferase 5 in pancreatic and colorectal cancers”, Oncotarget, doi: 10.18632/oncotarget.18102 (2017).

85. Pecora de Barros, E., Malmstrom, R.D., Nourbakhsh, K., Del Rio, J.C., Kornev, A.P., Taylor, S.S., Amaro, R.E., “Electrostatic Interactions as Mediators in the Allosteric Activation of Protein Kinase A RIα”, Biochemistry, 56(10):1536-45, doi: 10.1021/acs.biochem.6b01152 (2017).

84. Amaro, R.E. “A Reflection on Klaus Schulten”, Journal of Chemical Theory and Computation, 13 (1) 1-2; doi: 10.1021/acs.jctc.6b01111 (2016).

83. Shi, K., Carpenter, M.A., Banerjee, S., Shaban, N.M., Kurahashi, K., Salamango, D.J., McCann, J.L., Starrett, G.J., Duffy, J.V., Demir, O., Amaro, R.E., Harki, D.A., Harris, R.S., Aihara, H., “Structural basis

for targeted DNA cytosine deamination and mutagenesis by APOBEC3A and APOBEC3B”, Nat Struct Mol Biol., doi: 10.1038/nsmb.3344 (2016).

82. Amaro, R.E., Madura, J., Wong, C.F., “Tribute to J. Andrew McCammon”, The Journal of Physical Chemistry B, 120(33) 8055-8056; doi: 10.1021/acs.jpcb.6b07015 (2016).

81. Amaro, R.E., “Drug Discovery Gets a Boost from Data Science”, Structure, 2(8) 1225-1226; doi: 10.1016/j.str.2016.07.003 (2016).

80. Schiffer J.M., Feher V.A., Malmstrom R.D., Sida R., Amaro R.E., “Capturing Invisible Motions in the Transition from Ground to Rare Excited States of T4 Lysozyme L99A”, Biophys J. 2016;111(8):1631-40, doi: 10.1016/j.bpj.2016.08.041 (2016).

79. Rajappa-Titu, L., Suematsu, T., Munoz-Tello, P., Long, M., Demir, O., Cheng, K.J., Stagno, J.R., Luecke, H., Amaro, R.E., Aphasizheva, I., Aphasizhev, R., Thore, S., “RNA Editing TUTase 1: Structural foundation of substrate recognition, complex interactions and drug targeting”, Nucleic Acids Res. 44(22):10862-78, doi: 10.1093/nar/gkw917 (2016).

78. Ottilie, S., Goldgof, G.M., Calvet, C.M., Jennings, G.K., LaMonte, G., Schenken, J., Vigil, E., Kumar, P., McCall, L.I., Lopes, E.S., Gunawan, F., Yang, J., Suzuki, Y., Siqueira-Neto, J.L., McKerrow, J.H., Amaro, R.E., Podust, L.M., Durrant, J.D., Winzeler, E.A., “Rapid Chagas Disease Drug Target Discovery Using Directed Evolution in Drug-Sensitive Yeast”, ACS Chem Biol., doi: 10.1021/acschembio.6b01037 (2016).

77. Offutt, T.L., Swift, R.V., Amaro, R.E., “Enhancing Virtual Screening Performance of Protein Kinases with Molecular Dynamics Simulations”, J Chem Inf Model, doi: 10.1021/acs.jcim.6b00261 (2016).

76. Gathiaka, S., Liu, S., Chiu, M., Yang, H., Stuckey, J.A., Kang, Y.N., Delproposto, J., Kubish, G., Dunbar, J.B., Jr., Carlson, H.A., Burley, S.K., Walters, W.P., Amaro, R.E., Feher, V.A., Gilson, M.K., “D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions”, J Comput Aided Mol Des., 30(9):651-68, doi: 10.1007/s10822-016-9946-8 (2016).

75. Buffalo, C.Z., Bahn-Suh, A.J., Hirakis, S.P., Biswas, T., Amaro, R.E., Nizet, V., Ghosh, P., “Conserved patterns hidden within group A Streptococcus M protein hypervariability recognize human C4b-binding protein”, Nat Microbiol.,1(11):16155, doi: 10.1038/nmicrobiol.2016.155 (2016).

74. Akbar, R., Jusoh, S.A., Amaro, R.E., Helms, V., “ENRI: A tool for selecting structure-based virtual screening target conformations”, Chem Biol Drug Des., doi: 10.1111/cbdd.12900 (2016).

73. Demir, O., Ieong, P.U., Amaro, R.E., “Full-length p53 tetramer bound to DNA and its quaternary dynamics”, Oncogene, doi: 10.1038/onc.2016.321 (2016).

72. Schiffer, J.M, Malmstrom, R.D., Parnell, J., Ramirez-Sarmiento, C., Reyes, J., Amaro, R.E., Komives, E.A., “Model of the Ankyrin and SOCS Box Protein, ASB9, E3 Ligase Reveals a Mechanism for Dynamic Ubiquitin Transfer”, Structure ISSN 0969-2126, doi:10.1016/j.str.2016.05.016 (2016).

71. Goldgof, G.M., Durrant, J.D., Ottilie, S., Vigil, E., Allen, K.E., Gunawan, F. Kostylev, M., Henderson, K.A., Yang, J., Schenken, J., LaMonte, G.M., Manary, M.J., Murao, A., Nachon, M., Stanhope, R., Prescott, M., McNamara, C.W., Slayman, C.W., Amaro, R.E., Suzuki, Y., Winzeler, E.A., “Comparative chemical genomics reveal that the spiroindolone antimalarial KAE609 (Cipargamin) is a P-type ATPase inhibitor”, Scientific Reports 6:27806, doi:10.1038/srep27806 (2016).

70. Purawat, S., Cowart, C., Amaro, R.E., Altintas, I., “Biomedical Big Data Training Collaborative (BBDTC): An Effort to Bridge the Talent Gap in Biomedical Science and Research”, Procedia Computer Science. 80:1791-1800, doi:10.1016/j.procs.2016.05.454 (2016).

69. Votapka, L.W., Lee, C.T., Amaro, R.E., “Two Relations to Estimate Membrane Permeability Using Milestoning”, J. Phys. Chem. B. Article ASAP, doi:10.1021/acs.jpcb.6b02814 (2016).

68. Durrant, J.D., Bush, R.M., Amaro, R.E., “Microsecond Molecular Dynamics Simulations of Influenza Neuraminidase Suggest a Mechanism for the Increased Virulence of Stalk-Deletion Mutants”, J. Phys. Chem. B. Article ASAP, doi:10.1021/acs.jpcb.6b02655 (2016).

67. Swift, R.V., Jusoh, S.A., Offutt, T.L., Li, E.S., Amaro, R.E., “Knowledge-Based Methods To Train and Optimize Virtual Screening Ensembles”, Journal of Chemical Information and Modeling, 56(5):830-842, doi:10.1021/acs.jcim.5b00684 (2016).

66. Wagner, J.R., Lee, C.T., Durrant, J.D., Malmstrom, R.D., Feher, V.A., Amaro, R.E., “Emerging Computational Methods for the Rational Discovery of Allosteric Drugs”, ACS Chemical Reviews 116 (11), 6370-6390, doi:10.1021/acs.chemrev.5b00631 (2016).

65. Lee, C.T., Comer, J., Herndon, C., Leung, N., Pavlova, A., Swift, R.V., Tung, C., Rowley, C.N., Amaro, R.E., Chipot, C., Wang, Y., and Gumbart, J.C., “Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds”, Journal of Chemical Information and Modeling 56 (4), 721-733, doi:10.1021/acs.jcim.6b00022 (2016).

64. Richards, C., Albin, J.S., Demir, O., Shaban, N.M., Luengas, E.M., Land, A.M., Anderson, B.D., Holton, J.R., Anderson, J.S., Harki, D.A., Amaro, R.E., and Harris, R.S., “The binding interface between human APOBEC3F and HIV-1 Vif elucidated by genetic and computational approaches,” Cell Reports 13(9):1781-1788, doi:10.1016/j.celrep.2015.10.067 (2015).

63. Zimmermann, S., Hall, L., Riley, S., Sorensen, J., Amaro, RE, and Schnaufer, A., “A novel high-throughput activity assay for the Trypanosoma brucei editosome enzyme REL1 and other RNA ligases,” Nucleic Acids Research, doi:10.1093/nar/gkv/938 (2015).

62. Durrant, J.D., Carlson, K. Martin, T., Offutt, T., Mayne, C. Katzenellenbogen, J.A., and Amaro, R.E., “Neural-Network Scoring Functions Identify Structurally Novel Estrogen-Receptor Ligands”, J Chem Inf Model, doi:10.1021/acs.jcim.5b00241 (2015).

61. Boras, B.W., Hirakis, S.P., Votapka, L.W., Malmstrom, R.D., Amaro, R.E., and McCulloch, A.D., “Bridging Scales through multiscale modeling: A case study on Protein Kinase A”, Frontiers of Physiology, 6: 250, doi:10.3389/fphys.2015.00250 (2015).

60. Votapka, L.W. and Amaro, R.E., “Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics, and Milestoning,” PLOS Computational Biology, doi:10.1371/journal.pcbi.1004381 (2015).

59. Malmstrom, R., Kornev, A., Taylor, S. and Amaro, R.E., “Allostery through the computational microscope: cAMP activation of a canonical signaling domain,” Nature Communications, 6: 7588 (2015).

58. Ieong, P., Amaro, R.E., and Li, W.W., “Molecular Dynamics Analysis Of Antibody Recognition And Escape By Human H1N1 Influenza Hemagglutinin”, Biophysical Journal, 108 (11): 2704-2712 (2015). *Featured as Cover Image.

57. Balasubramaniam, D., Schiffer, J., Parnell, J., Mir, S.P., Amaro, R.E., and Komives, E.A., “How the Ankyrin and SOCS Box Protein, ASB9, Binds to Creatine Kinase”, Biochemistry, 54 (8):1673–1680. Featured as Cover Image (2015).

56. Durrant, J.D., Amaro, R.E., “Machine-Learning Techniques Applied to Antibacterial Drug Discovery”, Chemical Biology & Drug Design, 85(1), 14-21 (2015).

55. Ikram, N.K, Durrant, J.D., Muchtaridi, M., Zalaludin, A.S., Purwitasari, N., Mohamed, N., Rahim, A., Lam, C.K., Normi, Y.M., Rahman, N.A., Amaro, R.E., and Wahab, H.A., “Discovery of Plants with Confirmed Anti-H5N1 Neuraminidase Activity through Virtual Screening”, Journal of Chemical Information & Modeling, 55(2): 308-316 (2015).

54. Durrant, J.D., Votapka, L., Sørensen, J., and Amaro, R.E., “POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics”, Journal of Chemical Theory and Computation, doi: 10.1021/ct500381c (2014).

53. Cheng, Y., Lindert, S., Kekenes-Huskey, P.M., Rao, V.S., Solaro, R.J., Rosevear, P.R., Amaro, R., McCulloch, A.D., McCammon, J.A., Regnier, M., “Computational Studies of S23D/S24D Troponin I Mutation on Cardiac Troponin Structural Dynamics”, Biophysical Journal 107 (7), 1675-1685 (2014).

52. Malmstrom, R.D., Lee, C.T., Van Wart, A.T., and Amaro, R.E., “On the Application of Molecular-Dynamics Based Markov State Models to Functional Proteins”, Journal of Chemical Theory and Computation, doi: 10.1021/ct5002363 (2014).

51. Durrant J.D., Amaro R.E., “LipidWrapper: An Algorithm for Generating Large-Scale Membrane Models of Arbitrary Geometry”, PLOS Computational Biology, 10(7): e1003720 (2014).

50. Durrant, J.D., Amaro, R.E., “WebChem Viewer: A tool for the easy dissemination of chemical and structural data sets”, BMC Bioinformatics, doi:10.1186/1471-2015-15-159 (2014).

49. Amaro, R.E. and Bansal, M.,“POVME 2.0: An Enhanced Tool for Determining Pocket Shape and Volume Characteristics", Current Opinion in Structural Biology, 25: iv-v (2014).

48. Demir, O., Labaied, M., Merritt, C., Stuart, K., and Amaro, R.E., “Computer-aided Discovery of Trypanosoma brucei RNA-editing Terminal Uridylyl Transferase 2 Inhibitors”, Chemical Biology & Drug Design, doi:10.1111/cbdd.12302 (2014). *Featured as Cover Image.

47. Ieong, P.U., Sørensen, J., Vemu, P.L., Wong, C.W., Demir, Ö., Williams, N.P., Wang, J., Crawl, D., Swift, R.V., Malmstrom, R.D., Altintas, I., Amaro,R.E., “Progress towards Automated Kepler Scientific Workflows for Computer-aided Drug Discovery and Molecular Simulations”, Procedia Computer Science, 29: 1745-1755 (2014).

46. Feher, V.A., Durrant, J.D., Van Wart, A.T., and Amaro, R.E., “Computational Approaches to Mapping Allosteric Pathways”, Current Opinion in Structural Biology, 25: 98-103 (2014). *Featured as Cover Image.

45. VanWart, A., Durrant, J.D., Votapka, L., and Amaro, R.E., “Weighted Implementation of Suboptimal Paths (WISP): An optimized algorithm and tool for dynamical network analysis,” Journal of Chemical Theory and Computation, doi:10.1021/ct4008603 (2014).

44. Chen, E., Swift, R.E., Alderson, N., Feng, G-S., Amaro, R.E., “Computation-guided discovery of novel influenza endonuclease inhibitors,” ACS Medicinal Chemistry Letters, 5 (1): 61–64 (2014).

43. Rathore, A., Carpenter, M., Demir, Ö., Ikeda, T., Li, M., Shaban, N., Anokhin, D., Law, E., Brown, W., Amaro, R.E., Harris, R., “The local dinucleotide preference of APOBEC3G can be altered from 5’-CC to 5’-TC by a single amino acid substitution,” Journal of Molecular Biology, 425 (22): 4442-4454. PubMed PMID: 23938202; PMCID: PMC3812309; doi: 10.1016/j.jmb.2013.07.040 (2013).

42. Feher, V.A., Randall, A., Baldi, P.F., Bush, R.M., de la Maza, L.M., and Amaro, R.E., “A 3-dimensional trimeric beta-barrel model for Chlamydia MOMP contains conserved and novel elements of gram-negative bacterial porins”, One, 8(7): e68934. doi:10.1371/journal.pone.0068934 (2013).

41. Park, J., Czapla, L., Amaro, R.E., “Molecular Simulations of Aromatase Reveal New Insights Into the Mechanism of Ligand Binding,” Journal of Chemical Information and Modeling, 53 (8): 2047-2056 (2013).

40. Wassman, C.D., Baronio, R., Demir, Ö., Wallentine, B.D., Chen, C-K., Hall, L.V., Salehi, F., Lin, D-W., Chung, B.P., Hatfield, G.W., Chamberlin, A.R., Luecke, H., Lathrop, R.H., Kaiser, P., Amaro, R.E. “Computational Identification of a Transiently Open L1/S3 Pocket for p53 Cancer Mutant Reactivation”, Nature Communications, 4: 1407, doi:10.1038/ncomms2361, PMCID: PMC3562459 (2013).

39. Swift, R.V. and Amaro, R.E., “Back to the Future: Can Physical Models of Passive Membrane Permeability Help Reduce Drug Candidate Attrition and Move Us Beyond QSPR?”, Chemical Biology and Drug Discovery (Special Issue: Beyond the 100 Dollar Genome), 81: 61-71 (2013).

38. Swift, R.V., Ong, C., Amaro, R.E. “Magnesium-Induced Nucleophile Activation in the Guanylyltransferase mRNA Capping Enzyme”, Biochemistry, 51(51): 10236–10243 (2012).

37. Nichols, S.E., Swift. R.V., and Amaro, R.E., “Rational prediction with molecular dynamics for hit identification”, 12(18): 2002-2012. PMID: 23110535; PMCID: PMC3636520 (2012).

36. Votapka, L., Amaro, R.E., “Multistructural Hot Spot Characterization with FTProd”, BMC Bioinformatics, doi: 10.1093/bioinformatics/bts689 (2012).

35. Jansen, J.M., Amaro, R.E., Cornell, W., Tseng, Y.J., Walters, W.P., “Computational Chemistry and Drug Discovery: A call to action”, Future Medicinal Chemistry, 4: 1893-1896. (2012).

34. Jansen, J.M., Cornell, W., Tseng, Y.J., Amaro, R.E., “Teach-Discover-Treat (TDT): Collaborative Drug Discovery for Neglected Diseases”, Journal of Molecular Graphics and Modelling, 38: 360-362. (2012).

33. Van Wart, A., Eargle, J.A., Schulten, Z., Amaro, R.E., “Exploring Residue Component Contributions to Dynamical Network Models of Allostery”, Journal of Computational and Theoretical Chemistry, 8 (8): 2949–2961 (2012).

32. Votapka, L.W., Demir, O., Swift, R.V., Walker, R.C., and Amaro, R.E., “Variable ligand- and receptor-binding hot spots in key strains of influenza neuraminidase”, Journal of Molecular Genetics and Medicine, 6: 293-300 (2012).

31. Demir, O., Amaro, R.E., “Elements of Nucleotide Specificity in the Trypanosoma brucei Mitochondrial RNA Editing Enzyme RET2”, J. Chem. Inf. Model. April. doi:10.1021/ci3001327; PMCID: PMC3362124 (2012).

30. Gabrielsen, M., Beckham, K.S.H., Feher, V.A. , Zetterström, C.E. , Wang, D. , Muller, S., Elofsson, M., Amaro, R.E., Byron, O., Roe, A., “Structural Characterisation of Tpx from Yersinia pseudotuberculosis Reveals Insights into the Binding of Salicylidene Acylhydrazide Compounds”, PLOS ONE 7(2): e32217. doi:10.1371/journal.pone.0032217; PMCID: PMC3288085 (2012).

29. Votapka, L.W., Czapla, L., Zhenirovskyy, M. and Amaro, R.E., “DelEnsembleElec: Computing ensemble-averaged electrostatics using DelPhi”, Communications in Chemical Physics, 13: 256-268 (2012).

28. Swift, R.V., and Amaro, R.E., “Modeling the Pharmacodynamics of Passive Membrane Permeability”, Journal of Computer Aided Molecular Design, 25(11):1007-17. PMCID: PMC3223344 (2011).

27. Torres, R., Swift, R. V., Chim, N., Wheatley, N., Lan, B., Atwood, B. R., Pujol, C., Sankaran, B., Bliska, J. B., Amaro, R. E., Goulding, C., “Biochemical, Structural and Molecular Dynamics Analyses of the Potential Virulence Factor RipA from Yersinia pestis”, PLOS One, 6(9): e25084. doi:10.1371/journal.pone.0025084 (2011).

26. Demir, O., Baronio, R., Salehi, F., Wassman, C., Hall, L., Hatfield, G. Wesley, Chamberlin, A.R., Kaiser, P., Lathrop, R.H., Amaro, R.E., “Ensemble-based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants”, PLOS Computational Biology, PLOS Comput Biol 7(10): e1002238; doi:10.1371/journal.pcbi.1002238; PMCID: PMC3197647 (2011).

25. Amaro, R.E., Swift, R.V., Votapka, L., Li, W.W., Walker, R.C., Bush, R.M., “Mechanism of 150-Cavity Formation in Influenza Neuraminidase”, Nature Communications, 2, 388. PMCID: PMC3144582 (2011).

24. Durrant, J., Hall, L., Swift, R.V., Landon, M., Schnaufer, A., Amaro, R.E., “Novel Naphthalene-Based Inhibitors of Trypanosoma brucei RNA Editing Ligase 1”, PLOS Neglected Tropical Diseases, 4(8), e803, doi:10.1371/journal.pntd.0000803; PMCID: PMC2927429 (2010).

23. Lawrenz, M., Wereszczynski, J., Amaro, R.E., Walker, R., Roitberg, A., McCammon, J.A., “Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy”, Proteins, 78, 2523–2532. PMCID: PMC2902668 (2010).

22. Sung, J.C., Van Wynsberghe, A.W., Amaro, R.E., Li, W.W., McCammon, J.A., “The role of secondary sialic acid binding sites in influenza N1 neuraminidase”, Journal of the American Chemical Society Communication, 132(9), 2883-2885. PMCID: PMC2835425 (2010).

21. Durrant, J., Amaro, R.E., Xie, L., Urbaniak, M.D., Ferguson, M.A.J, Haapalainen, A., Chen, Z., Di Guilmi, A.M., Wunder, F., Bourne, P.E., McCammon, J.A., “A Multidimensional Strategy to Detect Polypharmacological Targets in the Absence of Structural and Sequence Homology”, PLOS Computational Biology, 6(1), e1000648. PMCID: PMC2799658 (2010).

20. Amaro, R.E., Li, W.W., “Emerging Ensemble-based Methods in Virtual Screening”, Current Topics in Medicinal Chemistry, 10(1), 3-13. PMCID: PMC3086266 (2010).

19. Swift, R.V., Amaro, R.E., “Discovery and design of DNA and RNA ligase inhibitors in infectious microorganisms”, Expert Opinion in Drug Discovery, 4(12), 1281-1294. PMCID: PMC2846787 (2009).

18. Newhouse, E.I., Xu, D., Markwick, P.R., Amaro, R.E., Pao, H.C., Wu, K.J., Alam, M., McCammon, J.A., Arzberger, P.W., Li, W.W., “Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine, and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective”, Journal of the American Chemical Society, 131(47), 17430-42. PMCID: PMC2782351 (2009).

17. Amaro, R.E., Cheng, X., Ivanov, I., Xu, D., McCammon, J.A., “Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-point Free Energy Calculations”, Journal of the American Chemical Society, 131(13), 4702-4709 (2009).

16. Xu, D., Newhouse, I., Amaro, R.E., Pao, H., Cheng, L., McCammon, J.A., Li, W., Arzberger, P., “Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon

Binding Different Hemagglutinins: A Molecular Dynamics Perspective”, Journal of Molecular Biology, 387, 465-491 (2009).

15. Wong, S., Amaro, R.E., McCammon, J.A., “MM-PBSA captures key role of intercalating water molecules at a protein-protein interface”, Journal of Chemical Theory and Computation, 5(2), 422-429 (2009). (Wong and Amaro contributed equally).

14. Swift, R., Durrant, J., Amaro, R.E., McCammon, J.A., “Towards Understanding the Conformational Dynamics of RNA Ligation”, Biochemistry, 48(4), 709-719 (2009).

13. Durrant, J., Amaro, R. E., McCammon, J. A., “AutoGrow: A Novel Algorithm for Protein Inhibitor Design”, Chemical Biology and Drug Design, 73, 168-178 (2009).

12. Amaro, R.E., Schnaufer, Interthal, H.A., Hol, W., Stuart, K., McCammon, J.A., “Discovery of the First Inhibitors of an Essential RNA Editing Ligase in Tyrpanosoma brucei”, Proceedings of the National Academies of Science, 105(45), 17278 – 17283 (2008). (Amaro and Schnaufer contributed equally).

11. Cheng, L.S., Amaro, R.E., Xu, D., Li, W.W., Arzberger, P.A., McCammon, J.A., “Ensemble-based Virtual Screening Reveals Novel Antiviral Compounds for Avian Influenza Neuraminidase”, Journal of Medicinal Chemistry, 51(13), 3878 – 3894 (2008). (Cheng and Amaro contributed equally).

10. Landon, M., Amaro, R.E., Baron, R., Ngan, C.H., Ozonoff, D., McCammon, J.A., Vadja, S., “Novel Druggable Hot Spots in Avian Influenza Neuraminidase H5N1 Revealed by Computational Solvent Mapping of a Reduced and Representative Receptor Ensemble”, Chemical Biology & Drug Design, 71(2), 106-116 (2008). (Article was featured on journal cover. Landon and Amaro contributed equally).

9. Amaro, R.E., Baron, R., McCammon, J.A., “An Improved Relaxed Complex Scheme for Receptor Flexibility in Rational Drug Design”, Journal of Computer-Aided Molecular Design, doi: 10.1007/s10822-007-9159-2 (2008). (Amaro and Baron contributed equally).

8. Amaro, R.E., Swift, R.V., McCammon, J.A., “Functional and Structural Insights Revealed by Molecular Dynamics Simulations of an Essential RNA Editing Ligase in Trypanosoma brucei”, PLOS Neglected Tropical Diseases, 1(2), e68. doi:10.1371/journal.pntd.0000068 (2007).

7. Amaro, R.E., Minh, D.D.L, Cheng, L.S., Lindstrom, W., Jr, Olson, A.J., Lin, J.H., Li, W.W., McCammon, J.A., “Remarkable Loop Flexibility in Avian Influenza N1 and its Implications for Antiviral Drug Design”, Journal of the American Chemical Society, 129, 7764-7765 (2007).

6. Amaro, R.E., Sethi, A., Myers, R., Davisson, V.J., Luthey-Schulten, Z., “A Network of Conserved Interactions Regulates the Allosteric Signal in a Glutamine Amidotransferase”, Biochemistry, 46, 2156-2173 (2007).

5. Amaro, R.E., Myers, R., Davisson, V.J., Luthey-Schulten, Z., “Structural Elements in IGP Synthase Exclude Water to Optimize Ammonia Transfer”, Biophysical Journal, 89, 475-487 (2005). (Article featured on journal cover. Amaro and Myers contributed equally).

4. Myers, R.S., Amaro, R.E., Luthey-Schulten, Z., Davisson, V.J., “Reaction Coupling through Interdomain Contacts in Imidazole Glycerol Phosphate Synthase”, Biochemistry, 44, 11974-11985 (2005). (Myers and Amaro contributed equally).

3. Amaro, R.E., Luthey-Schulten, Z., “Molecular dynamics simulations of substrate channeling through an α-β barrel protein”, Chem. Phys., 307, 147-155 (2004).

2. Amaro, R.E., Tajkhorshid, E., Luthey-Schulten, Z., “Developing the Energy Landscape for the Novel Function of a (β/α)8 Barrel: Ammonia Conduction through HisF”, PNAS, 100, 7599-7604 (2003).

1. O’Donoghue, P., Amaro, R.E., Luthey-Schulten, Z., “On the Structure of HisH: Structure Prediction in the Context of Functional Genomics”, J. Struct. Bio., 154, 257-268 (2001). BOOKS AND BOOK CHAPTERS

6. Sorenson, J., Fenley, M.O., and Amaro, R.E., “A Comprehensive Exploration of Physical and Numerical Parameters in the Poisson–Boltzmann Equation for Applications to Receptor–Ligand Binding”, Computational Electrostatics for Biological Applications, Springer International Publishing (2015).

5. Sorenson, J., Demir, O., Swift, R.V., Feher, V.A. and Amaro, R.E. “Molecular Docking to Flexible Targets,” Molecular Modeling of Proteins, 2nd Edition, Edited by Andreas Kukol (2014).

4. Durrant, J.D. and Amaro, R.E., “De Novo Design by Fragment Growing and Docking”, De Novo Molecular Design, First Edition, Edited by Gisbert Schneider, Wiley-VCH Verlag GmbH & Co. (2013).

3. Demir, Ö. and Amaro, R.E., “Designing Novel Inhibitors of Trypanosoma Brucei,” In S. Kortagere, Methods in Molecular Biology series Vol 993): “In Silico Models forDrug Discovery” New York, NY: Humana Press (2013).

2. Amaro, R.E., Li, W.W., Molecular-Level Simulation of Pandemic Influenza Glycoproteins. In: Baron R. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology (Methods and Protocols), Vol 819. Springer, New York, NY; doi: 10.1007/978-1-61779-465-0_34 (2012).

1. Swift, R.V., Amaro, R.E., Chapter 12: Molecular simulation in computer-aided drug design: Algorithms and applications. RSC Biomolecular Sciences. 281-315 (2012). POSTDOCTORAL RESEARCH SUPERVISION July 2009 – June 2014 Robert Swift, Advisor September 2009 – June 2014 Ozlem Demir, Advisor November 2010 – November 2012 Luke Czapla, Advisor September 2011 – 2017 Robert Malmstrom, Advisor October 2011 – 2015 Jesper Sorensen, Advisor March 2012 – 2016 Jacob Durrant, Advisor September 2013 – August 2015 Pekka Postila, Advisor 2015 – 2016 Symon Gathiaka, Advisor (joint with M. Gilson) 2015 – 2017 Shuai Liu, Advisor (joint with M. Gilson) 2016 – 2017 Jamie Schiffer, Advisor (joint with K. Prather) 2017 – present Zied Gaieb, Advisor (joint with M. Gilson) 2017 – present Conor Parks, Advisor (joint with M. Gilson) 2017 – present Martina Audagnotto, Advisor (joint with E. Villa) 2018 – present Lorenzo Casalino, Advisor 2018 – present Surl-Hee (Shirley) Ahn, Advisor (joint with J. A. McCammon) 2018 – present Wen Ma, Advisor (joint with J. A. McCammon) DOCTORAL CANDIDACY ADVISORSHIP (AS ADVISOR) July 2010 – 2015 Adam Van Wart September 2011 –2016 Lane Votapka

Award Winner: NSF Graduate Research Fellowship May 2013 – February 2019 Sophia Hirakis

Award Winner: NIH/HHMI Interfaces Fellow; Dissertation Award May 2013 – 2017 Tavina Claiborne

Award Winner: Bouchet Honor Society, GAANN Fellow, San Diego Fellowship Awardee

May 2013 – 2016 Jamie Schiffer Award Winner: NIH Molecular Biophysics Training Grant Fellow, Chancellor’s Dissertation Awardee, ACS COMP / NVIDIA GPU Awardee

May 2014 – 2018 Jeffrey Wagner Award Winner: NIH Molecular Biophysics Training Grant Fellow

May 2014 – March 2019 Christopher Lee (co-advised with J. Andrew McCammon) Award Winner: NIH Molecular Biophysics Training Grant Fellow, Lattimer Award Winner, Distinguished Graduate Dissertation Awardee

May 2015 – 2017 Alexandra Heyneman Award Winner: NIH/HHMI Interfaces Fellow, San Diego Fellowship Awardee

June 2015 – April 2020 Bryn Taylor, Biomedical Sciences Graduate Student January 2015 – April 2020 Emília Pécora de Barros, Chemistry Graduate Student

Award Winner: Graduate Student Association (GSA) Training Grant

January 2015 – April 2020 Benjamin Jagger, Chemistry Graduate Student (co-advised with J. Andrew McCammon) Award Winner: NIH Molecular Biophysics Training Grant Fellow

January 2015 – November 2019

Sarah Kochanek, Chemistry Graduate Student (co-advised with J. Andrew McCammon). Award Winner: NIH Molecular Biophysics Training Grant Fellow

May 2016 – present Christian Seitz, Chemistry Graduate Student (Co-advised with J. Andrew McCammon) Award Winner: NIH/HHMI Interface Training Fellow; NSF GRFP Fellow

August 2017 – present Abigail Dommer, Chemistry Graduate Student January 2019 – present Philip Belzeski, Chemistry Graduate Student (Co-advised with E.

Komives) January 2019 – present Mia Rosenfeld, Chemistry Graduate Student

Award Winner: UCSD Interdisciplinary Ph.D. Specialization in Multi-Scale Biology (formerly: Interfaces Graduate Training Program)

January 2019 – present Nicholas Wauer, Chemistry Graduate Student November 2019 – present Simon J. Park, Biochemistry Graduate Student DOCTORAL CANDIDACY ADVISORSHIP (AS MEMBER) Graduated 2013 Nicholas Brunn, Dept. of Chemistry and Biochemistry, UC San

Diego Graduated 2013 Michael White, Dept. of Mathematics, UC San Diego Graduated 2013 Paul Gasper, Dept. of Chemistry and Biochemistry, UC San Diego Graduated 2014 Yoonsoon Kang, Dept. of Chemistry, UC San Diego/San Diego

State University joint Doctoral Program Graduated 2014 Sulyman Barkho, Dept. of Chemistry and Biochemistry, UC San

Diego Graduated 2015 Britton Boras, Dept. of Bioengineering, UC San Diego Spencer Swarts, Dept. of Chemistry, UC San Diego/San Diego

State University joint Doctoral Program Graduated 2015 Tapaswini Das, Dept. of Bioengineering, UC San Diego Interfaces

Training Program Graduated 2015 Joseph Kaus, Dept. of Chemistry and Biochemistry, UC San Diego Graduated 2015 Meekyum Olivia Kim, Dept. of Chemistry and Biochemistry, UC

San Diego Graduated 2016 Kara Finzel, Dept. of Chemistry and Biochemistry, UC San Diego Graduated 2016 Don Nguyen, Dept. of Chemistry and Biochemistry, UC San Diego Graduated 2017 Kevin Sibucao, Dept. of Chemistry and Biochemistry, UC San

Diego Graduated 2017 Dylan Gilbert, Dept. of Physics, UC San Diego Graduated 2017 Francesca Grogan, Dept. of Mathematics, UC San Diego

Graduated 2017 Christopher Lee, Dept. of Chemistry and Biochemistry, UC San Diego

Graduated 2017 Alisha Caliman, Dept. of Biomedical Sciences, UC San Diego Graduated 2015; 2018 Brenton Maisel, Dept. of Chemistry and Biochemistry, UC San

Diego Daniel Klein, Dept. of Physics, UC San Diego Graduated 2018 Charles Lin, Dept. of Chemistry and Biochemistry, UC San Diego Graduated 2020 Ryan Lumpkin, Dept. of Chemistry and Biochemistry, UC San

Diego Graduated 2019 Kimberly McCabe, Dept. of Biomedical Engineering, UC San

Diego Ittipat Meewan, Dept. of Chemistry and Biochemistry, UC San

Diego Matthew Pendergraft, Scripps Institution of Oceanography, UC San

Diego Graduated 2019 Jasmina Radoicic, Dept. of Chemistry and Biochemistry, UC San

Diego Da Shi, Dept. of Chemistry and Biochemistry, UC San Diego Woojoo Eunice Kim, Dept. of Chemistry and Biochemistry, UC

San Diego Colin Deniston, Dept. of Chemistry and Biochemistry, UC San

Diego Graduated 2019 Greg Trieger, Dept. of Chemistry and Biochemistry, UC San Diego PROJECT SCIENTIST RESEARCH SUPERVISION January 2011 – 2016 Victoria Feher, Advisor July 2014 – 2015 Robert Swift, Advisor July 2014 – present Ozlem Demir, Advisor January 2019 – present Daniel Roston, Advisor MASTER’S CANDIDANCY COMMITTEE (AS ADVISOR) September 2014 – March 2016 Pek Ieong, Advisor

Award Winner: NSF Graduate Research Fellowship Honorable Mention

September 2015 – July 2016 Garrett Chan, Advisor MASTER’S CANDIDANCY COMMITTEE (AS MEMBER) 2014 George Murano 2015 Joshua Chan 2016 Daniel Kim 2016 Meixin Wu 2017 Derrick Buntin, BENG 2017 Goqing Gu 2017 Justine Liang MD/PHD RESEARCH SUPERVISION (ROTATION) July 2019 — August 2019 Althea Hansel July 2019 — August 2019 Victoria Smith

UNDERGRADUATE RESEARCH SUPERVISION November 2009 – April 2010 Stephanie Melton November 2009 – September 2010 Brian Atwood September 2009 – December 2010 BaoTran Le

Award Winner: Undergraduate Summer Research Fellowship, Summer 2011

September 2009 – June 2011 Chau Ong June 2010 – September 2011 Tiffany Sun June 2010 – August 2011 Adam Gonzales June 2012 – September 2011 Alexandra DeLaney (co-advised with Wilfred Li) June 2012 – June 2014 Pek Ieong (co-advised with Wilfred Li)

Award Winner: Dean’s Award for Excellence In Undergraduate Research, Spring 2013

February 2013 – May 2014 Sharon Grubner, PRIME Student, Summer 2013 Award Winner: Julia Brown Research Scholarship, Summer 2013

September 2013 – December 2014 Prasantha Vemu, Bioengineering Undergraduate September 2013 – June 2015 Garrett Chan, Chemistry Undergraduate September 2013 – June 2015 Celia Wong, Chemistry and Computer Science Undergraduate June 2014 – June 2016 Nathan Hensley, Bioengineering Undergraduate October 2014 – July 2016 Kevin Cheng, Chemistry Undergraduate January 2017 – June 2018 Egbert Castro, Pharmacological Chemistry Undergraduate August 2016 – September 2018 Thuy Tien Nguyen, Pharmacological Chemistry Undergraduate May 2018 – present Alexandre Duclos, Chemistry/Biochemistry Undergraduate June 2018 — present Andrew Mitchell, Chemistry/Applied Mathematics Undergraduate

Award Winner: Undergraduate Research Award (2019) October 2018 – June 2019 Teresa Jackson, Chemistry/Biochemistry Undergraduate April 2019 — present Ying Huang, Pharmacological Chemistry Undergraduate April 2019 — present Andrew Tao, Biochemistry Undergraduate (Business minor) January 2020 — present Michaela Lucas, Molecular Biology Undergraduate DIRECTED INDIVIDUAL/INDEPENDENT STUDY September 2019 – November 2019 Kate Kenney, Advisor. High school student August 2019 – present Oscar Arnold, Advisor. High school student June 2019 – present Krishay Mukhija, Advisor. High school student October 2018 – March 2019 Gray Thoron, Advisor. High school student June 2018 – June 2019 Cynthia Chen, Advisor. BioChemCoRe student June 2018 – present Jessie Gan, Advisor. BioChemCoRe student June 2018 – June 2019 Gaurie Gunasekaran, Advisor. BioChemCoRe student June 2018 – November 2019 Mason Holst, Advisor. BioChemCoRe student June 2018 – November 2019 Dhruv Kumar, Advisor. BioChemCoRe student June 2018 – August 2018 Kien Malarney, Advisor. BioChemCoRe student June 2018 – August 2018 Michael Tu, Advisor. BioChemCoRe student June 2018 – August 2018 Vainvavi Viswanath, Advisor. BioChemCoRe student June 2018 – August 2018 Neel Mittal, Advisor. BioChemCoRe student June 2018 – August 2018 Emmanuel Ledesma, Advisor. BioChemCoRe student / Pinhead

Institute June 2018 – August 2018 Tyler Kraft, Advisor. BioChemCoRe student / Pinhead Institute June 2017 – August 2017 Vainavi Viswanath, Advisor. BioChemCoRe student

June 2017 – August 2017 Roxana Sida, Advisor. BioChemCoRe student June 2017 – August 2017 Sankalp Nigam, Advisor. BioChemCoRe student June 2017 – August 2017 Yuhsuan Lee, Advisor. BioChemCoRe student June 2017 – August 2017 Ben Konecny, Advisor. BioChemCoRe student June 2017 – August 2017 Devashi Ghosal, Advisor. BioChemCoRe student June 2017 – August 2017 Enrique, Advisor. BioChemCoRe student June 2017 – August 2017 Mariana Cazares Morales, Advisor. BioChemCoRe student June 2016 – August 2016 Andrew Wilbur, Advisor. BioChemCoRe student June 2016 – August 2016 Sona Trika, Advisor. BioChemCoRe student June 2016 – August 2016 Shreya Shriram, Advisor. BioChemCoRe student June 2016 – August 2016 Olivia Shiah, Advisor. BioChemCoRe student June 2016 – August 2016 Hillary Pratt, Advisor. BioChemCoRe student June 2016 – August 2016 Thuy Tien Nguyen, Advisor. BioChemCoRe student June 2016 – August 2016 Amy Liu, Advisor. BioChemCoRe student June 2016 – August 2016 Ethan Lan, Advisor. BioChemCoRe student June 2016 – August 2016 Michelle Hoy, Advisor. BioChemCoRe student / Pinhead Institute June 2016 – August 2016 Divya Ghoshal, Advisor. BioChemCoRe student June 2016 – August 2016 Roxana Sida Elguea, Advisor. BioChemCoRe student June 2016 – August 2016 Lynnlee Duck Reynolds, Advisor. BioChemCoRe student June 2015 – August 2015 Shelby Friends, Advisor. BioChemCoRe student, UC San Diego

NSF REU Program June 2015 – August 2015 Nathalie Del Rosario, Advisor. BioChemCoRe student, UC San

Diego STARS Program June 2015 – August 2015 Sona Trika, Advisor. BioChemCoRe student June 2015 – August 2015 Roxana Sida Elguea, Advisor. BioChemCoRe student, REACH

Program June 2015 – August 2015 Aditya Ravipati, Advisor. BioChemCoRe student June 2015 – August 2015 Eric Li, Advisor. BioChemCoRe student June 2015 – August 2015 Elora Lawyer, Advisor. BioChemCoRe student, REACH Program June 2015 – August 2015 Arathi Kumar, Advisor. BioChemCoRe student June 2015 – August 2015 Rose Goueth, Advisor. BioChemCoRe student June 2015 – August 2015 Lynnlee Duck-Reynolds, Advisor. BioChemCoRe student June 2015 – August 2015 Herta Calvo-Faugier, Advisor. BioChemCoRe student, REACH

Program June 2015 – August 2015 Lynn Bi, Advisor. BioChemCoRe student June 2015 – August 2015 Dariana Archiniega, Advisor. BioChemCoRe student, REACH

Program June 2014 – August 2014 Maria Jose Seaman, Advisor. BioChemCoRe student, REACH

Program June 2014 – August 2014 Lorenia Hurtado, Advisor. BioChemCoRe student, REACH

Program June 2014 – August 2014 Clare Zhu, Advisor. BioChemCoRe student June 2014 – August 2014 Mikaela Sampayan, Advisor. BioChemCoRe student June 2014 – August 2014 Taylor Perison, Advisor. BioChemCoRe student June 2014 – August 2014 Michael Murphy, Advisor. BioChemCoRe student June 2014 – August 2014 Ezra Kosviner, Advisor. BioChemCoRe student June 2014 – August 2014 Divya Ghoshal, Advisor. BioChemCoRe student June 2014 – August 2014 Chris Condon, Advisor. BioChemCoRe student June 2014 – August 2014 Kevin Cheng, Advisor. BioChemCoRe student

June 2014 – August 2014 Lynn Bi, Advisor. BioChemCoRe student June 2013 – August 2013 Anastassia Gomez, Advisor. BioChemCoRe student, UC San Diego

Competitive Edge Program June 2013 – August 2013 Prasantha Vemu, Advisor. BioChemCoRe student June 2013 – August 2013 Nathan Mih, Advisor. BioChemCoRe student June 2013 – August 2013 Garrett Chan, Advisor. BioChemCoRe student June 2013 – August 2013 Celia Wong, Advisor. BioChemCoRe student June 2013 – August 2013 Ashley Wu, Advisor. BioChemCoRe student June 2013 – August 2013 Lucy Ladefoged, Advisor. BioChemCoRe student June 2013 – August 2013 Leah Krause, Advisor. BioChemCoRe student June 2013 – August 2013 Brianna Fernandez, Advisor. BioChemCoRe student, ENLACE

Program June 2013 – August 2013 Alexandra Heyneman, Advisor. BioChemCoRe student July 2012 – September 2013 Saira Ikram, Advisor. CompChemBioCamp student July 2012 – May 2013 Sophia Hirakis, Advisor. CompChemBioCamp student July 2012 – December 2012 Francesca Bardinelli, Advisor. CompChemBioCamp student June 2012 – August 2014 Rachel Li, Advisor. Rachel first started as a Torrey Pines High

School High School student, then later as a summer intern from UC Berkeley

June 2012 – August 2014 Eric Chen**, Advisor. Eric was a San Dieguito Academy High School student **Award-winner: 3rd Place, International BioGENEius Challenge, Summer 2013, Top Ten – National BioGENEius Challenge, Spring 2013; INTEL Science Finalist, Summer 2013; Google Science Fair Global Finalist, Summer 2013. Subsequently he attended Harvard University

June 2012 – August 2012 Emilia Pecora de Barros, Advisor. CompChemBioCamp student November 2010 – September 2011 Lane Votapka, Advisor August 2010 – August 2014 Jiho (Jason) Park*, Advisor. Jason was an intern from University

High in Irvine, CA. Subsequently he attended Harvard University. *Award winner: 2nd Place, International BioGENEius Challenge, Summer 2013, Top Ten – National BioGENEius Challenge, Spring 2013

June 2010 – August 2010 Meghan Cain, Advisor. Meghan was a summer intern visiting from Rensselaer Polytechnic Institute

June 2010 – July 2010 Jessica Rutherford, Advisor. Pinhead Institute

TEACHING UC San Diego CHEM 118: Pharmacology and Toxicology (Winter 2019) CHEM 167: Medicinal Chemistry (Winter 2019) CHEM 118: Pharmacology and Toxicology (Spring 2018) CHEM 167: Medicinal Chemistry (Spring 2018) CHEM 167: Medicinal Chemistry (Spring 2017) CHEM 118: Pharmacology and Toxicology (Winter 2017) CHEM 185/285: Computational Chemistry (Spring 2016) CHEM 118: Pharmacology and Toxicology (Winter 2016)

CHEM 167: Medicinal Chemistry (Spring 2014) CHEM 167: Medicinal Chemistry (Spring 2013) CHEM 185: Computational Chemistry (Fall 2013) CHEM 185/285: Computational Chemistry (Fall 2012) UC Irvine CHEM/ PHRMSCI 177: Medicinal Chemistry (Winter 2011) PHRMSCI 170A: Molecular Pharmacology I (Winter 2010) CS 295: Computational Biophysics and Drug Discovery (Fall 2009) EXTERNAL REVIEWS OF PRIMARY CREATIVE WORK “Rescuing the Guardian of the Genome”, Robert Service, Science, Vol. 354, Issue 6308, pp. 26-28, 07 Oct 2016; doi: 10.1126/science.354.6308.26 “Computing Transforms Chemistry, Biotech”, San Diego Union Tribune, 19 March 2016 http://www.sandiegouniontribune.com/business/biotech/sdut-computers-chemistry-amaro-chen-2016mar19-htmlstory.html “C&EN Talks with Rommie Amaro, Computational Chemist”, Vol. 95, Issue 2, pp. 20-21; 09 January 2017 https://cen.acs.org/articles/95/i2/CEN-talks-Rommie-Amaro-computational.html

“Supercomputer Models Critical Protein that Suppresses Cancer”, Top 500, 29 October 2016 https://www.top500.org/news/supercomputer-models-critical-protein-that-suppresses-cancer/

“Supercomputing the p53 protein as a promising anticancer therapy”, Texas Advanced Computing Center, 27 October 2016 https://www.tacc.utexas.edu/-/supercomputing-the-p53-protein-as-a-promising-anticancer-therapy “Stampede Unravels the p53 Protein”, ScienceNode, 02 Nov 2016 https://sciencenode.org/feature/stampede-is-down-with-p53-.php

“Blue Waters Enables Massive Flu Simulations”, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, 23 March 2016 http://www.ncsa.illinois.edu/news/story/blue_waters_enables_massive_flu_simulations

GRANTS

Amaro, Rommie E. (Principal Investigator), NIH – “APOBEC Mutagenesis in Breast Cancer”, $275,511 (May 2019 – July 2024).

Amaro, Rommie E. (Principal Investigator), NIH – “Targeting the Achilles Heel of P53”, $312,186 (April

2019 – March 2023). Amaro, Rommie E. (Co-Investigator), Prather, Kimberly (Principal Investigator), NSF – “CCI Center for

Aerosol Impacts on Climate and the Environment”, $20,000,000 ($86,000+ annual direct costs) (October 2018 –September 2023).

Amaro, Rommie E. (Co-Investigator), Yang, G. (Principal Investigator), NIH – “Development of

Promoters of Dendritic Spine Formation”, $1797,652 ($250,000 annual direct costs) (August 2016 – May 2021).

Amaro, Rommie E. (Co-Investigator), Fraser, James (Principal Investigator), UC Lab Fees Research

Program, “Macromolecular movements by simulation and diffuse scatter”, $55,000 (annual direct costs) (March 2017 – February 2020).

Amaro, Rommie E. (Principal Investigator), NSF – “Structural and Dynamical Determinants of Influenza

Transmissibility”, $10,500 (May 2018 – December 2019).

Amaro, Rommie E. (Co-Investigator), Prather, Kimberly (Principal Investigator), NSF – “CCI Center for Aerosol Impacts on Climate and the Environment”, $20,000,000 ($51,207 annual direct costs) (October 2013-September 2018, sub-award initiated November 2016).

Amaro, Rommie E. (Principal Investigator), “UC San Diego EDI Innovation Award: BioChemCoRe”,

$5,000 (May 2015 – April 2016). Amaro, Rommie E. (Co-Investigator), Harki, Daniel (Principal Investigator), NIH R01 – “Chemical

Interrogation of Human DNA Cytosine Deaminases”, $242,597 ($31,2018 annual direct costs) (July 1 2015 – April 30, 2020).

Amaro, Rommie E. and Handel, Tracy (Multi-Principal Investigators), “UC San Diego Frontiers of

Innovation Graduate Student Award: Chemokine Receptor Dynamics and Druggability”, $25,000 (January 2015 – December 2015).

Amaro, Rommie E. and McKerrow, James (Multi-Principal Investigators), “UC San Diego Frontiers of

Innovation Center Award: UCSD Center for Translational Computer-Aided Drug Discovery and Project Management”, $75,000 (January 2015 – July 2016).

Altintas-Callefon, I. and Amaro, Rommie E. (Multi-Principal Investigators), NIH R25 – “An Open Resource for Collaborative Biomedical Big Data Training”, $199,848 (annual direct costs) (September 29, 2014 – August 31, 2017).

Amaro, Rommie E., Feher, Victoria A., Gilson, Michael (Multi-Principal Investigators), NIH U01 – “An

Open Resource to Advance Computer-Aided Drug Design”, $3,639,450, (September 15, 2014 – August 31, 2020).

Amaro, Rommie E. (Principal Investigator), NIH P41 – “National Biomedical Computation Resource”, ~

$9,500,000, (August 2014 – April 2020). Amaro, Rommie E. (Principle Investigator), NSF – “Extreme Science and Engineering Discovery

Environment (XSEDE) Research Allocation”, 12,000,000 SUs (January 2015 – December 2015). Amaro, Rommie E., Figueroa, Joshua, and Lennard, Erica (Multi-Principal Investigators), “UC San Diego

PRIME Award: A Community- and Mentoring-Based Approach to Increase Retention of URM and Female Chemistry MS and PhD Students in the Department of Chemistry and Biochemistry”, $5,000 (July 2014 – December 2015).

Amaro, Rommie E. (Principal Investigator), NSF Petascale Resource Allocation Committee (PRAC)

Award for “Blue Waters Computing: Structural and Dynamical Determinants of Influenza Transmissibility and Virulence”, 6 Million Node Hours on Blue Waters Petascale Machine, $10,500 plus 6 million node hours on Blue Waters (estimated monetary value $2,500,000, August 2014 – July 2015).

Amaro, Rommie E. (Principle Investigator), NSF – “Extreme Science and Engineering Discovery

Environment (XSEDE) Research Allocation”, SUs (January 2014 – December 2014). Amaro, Rommie E. (Principal Investigator), NVIDIA Foundation – “Accelerating the Cure: GPU-driven

drug discovery for Anti-cancer targets”, $200,000 (awarded December 2013). Amaro, Rommie E. (Principal Investigator), California Cancer Research Coordinating Committee –

“Computation Guided Discovery of p53 Reactivation Compounds”, $47,500 (July 1, 2013 – June 30, 2014).

Amaro, Rommie E. (Principal Investigator), NIH P41 – “National Biomedical Computation Resource”,

$10,470,367 (August 1, 2014 – March 31, 2020). Amaro, Rommie E. (Co-Principal Investigator), Arzberger, Peter (Principal Investigator), NIH P41

Competitive Revision Supplement, $814,349 (July 2012 – July 2014).

Amaro, Rommie E. (Principle Investigator), NSF – “Extreme Science and Engineering Discovery Environment (XSEDE) Research Allocation”, 15,562,053 SUs (January 2013 – December 2013).

Amaro, Rommie E. (Principal Investigator), Hellman Foundation Award – “CompChemBioCAMP:

Explore – Discover – Excel”, $30,000. (July 1, 2012 – June 30, 2013). Amaro, Rommie E. (Principal Investigator), NIH – “A Structural Systems Biology Approach to Drug

Discovery”, $2,295,000.00. (September 30, 2010 – October 2016).

Amaro, Rommie E. (Co-Principal Investigator), Schnaufer, Achim (Principal Investigator), Greaney, Michael (Co-Principal Investigator), Wellcome-Trust – “An integrated screening strategy to develop inhibitors of Trypanosoma brucei

RNA editing ligase 1”, $569,275.00. (June 1, 2011 – May 31, 2016).

Amaro, Rommie E. (Co-Principal Investigator), Goulding, Celia (Principal Investigator), PSWRCE (Pacific Southwest Regional Center of Excellence) – “Probing a novel pathway found in distally related pathogens required for survival in macrophages”, $301,748.00. (July 2010 – June 2012).

Amaro, Rommie E. (Principal Investigator), NIH – “Towards a Structural Systems Biology Approach for

Anti-Trypanosomal Therapeutics”, $270,000.00. (July 2010 – June 2012). Amaro, Rommie E. (Principal Investigator), NSF – 5,000,000 SUs. (January 1, 2011 – December 31,

2011). Amaro, Rommie E. (Principal Investigator), NSF – “NPACI Medium Resource Allocation Award”,

482,000 SUs. (January 1, 2008 – June 30, 2009). Amaro, Rommie E. (Principal Investigator), NIH – “The SMD-Relaxed Complex Method for Drug

Design”, $180,000.00 (September 1, 2006 – June 30, 2009).