Introduction to Computational Biology: Curriculum Development
Ruijun ZhaoKai ShenShaneka Simmons Presented by:
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CREATING THE CURRICULUM FOR COMPUTATIONAL BIOLOGY 1
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QUESTIONS CONSIDERED FOR EFFECTIVE COURSE DESIGN 1.What
students will you target and what are their needs? 2.What do you
want them to learn? 3.What content matter will engage the students?
4.What will your students discover about the class that they can
relate to everyday life? a.Drug design b.Enzyme modification c.Food
Industry 5.What are your strengths put into this course? 6.Teach
students how to identify and solve problems? 7.Teach students how
to utilize modern tools and promote current topics of interest?
8.Who will be your collaborators (invited speakers, course
development)
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3 Course Objectives Brainstorm
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Shaneka Simmons, Jackson State University Introduction to Data
Visualization Kai Shen, Savannah State University Introduction to
Computational Biochemistry Ruijun Zhao, Minnesota State University
Introduction to Molecular Dynamics Course Collaboration
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Curriculum 4
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Course Objectives 1.Students will be able to set up, run a
simulation and interpret the simulation results through case
studies. 2.Students will be able to utilize mainstream
bioinformatics tools. 3.Students learn to effectively collaborate
with their peers.
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Student Preliminary Assessment Foldit game at the introduction
of the class and after the introduction to molecular dynamics
Homework assignments Concept understanding Justification of protein
selection Group projects Exploring tools and solve a real problem
What is the structure-function relationship Proteopedia
(www.proteopedia.org) Math Scoring using Protein Docking
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Future Work Design modules Video modules Powerpoint
presentations Source files for community utilization Introductory
teaching tutorials for students Design online courses
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Why should we care? Conveying: Introduction to Computational
Biology http://www.ebi.ac.uk/ luscombe/docs/ imia_review.pdf
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5 SAMPLE COURSE TOPICS
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Module 1: Protein Structures-Basic Introduction Chemical bonds,
weak forces involved in protein structures Amino acids, primary
structures, secondary, and tertiary structures Side chains of
protein residues, protein- protein/protein-ligand interaction
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Module 2. Molecular Visualization Visualization software
DescriptionURL PDBeEBI's Protein Data Bank in Europe
http://www.ebi.ac.uk/pdbe/ PDBRCSBs database of
proteinhttp://www.pdb.org/ PyMOLMolecular visulization
softwarehttp://www.pymol.org JMolOpen source Java Viewer for 3D
structures http://jmol.sourceforge.net VMDMolecular visualization
and dynamics software www.ks.uiuc.edu/Research/vmd/
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Module 3. Protein Docking Principles of Docking Review
interactions, chemical bonds, and protein structures Search
algorithm Scoring functions Working with docking software suits
with a focus on open source packages HADDOCK, AUTODOCK, ZDOCK, etc.
Application Drug discovery Tutorial
http://ringo.ams.sunysb.edu/index.php/2012_DOCK_tutoria
l_with_Streptavidin
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Docking Software Packages
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Module 4: Molecular Dynamics
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Selected Textbooks for Molecular Dynamics Statistical Physics
of Biomolecules: An Introduction by D. M. Zuckerman Understanding
Molecular Simulation: From Algorithms to Applications, Second
Edition by D. Frenkel and B. Smit Molecular Modelling: Principles
and Applications (2nd Edition) by Andrew Leach
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Selected Software for Molecular Dynamics Simulation Software
DescriptionURL AMBERAssisted Model Building and Energy Refinement
http://ambermd.org/ CHARMmChemistry at HARvard Macromolecular
Mechanics http://www.charmm.org/ GROMACSGroningen Machine for
Chemical Simulations http://www.gromacs.org/ NAMDScalable Molecular
Dynamicswww.ks.uiuc.edu/Research/na md/
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Harry Richards Stephen Everse Ethel Stanley Sandra Orchard
Garby Rustici Sam Donovan John Jungck Bert Overduin Colleagues
Acknowledgments