Outline

• GB1 chameleon

• 8-mer Peptide MD

• GB1 folding pathway

• Hierarchic folding

• Conservation scores

• Context-dependent secondary structure formation of a designed protein sequence

• Daniel L. Minor Jr, MIT

• Nature 1996

• Denaturation

• Folding Very Short Peptides Using Molecular Dynamics

• Ken Dill, UCSF

• Plos Computational Biology, 2006

• GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate

• Valerie Daggett, University of Washington

• Biophysics Journal, 2011

Folding pathway and contact maps for two unfolding simulations of GB1

• Is protein folding hierarchic? I. Local structure and peptide folding

• Robert L. Baldwin, Stanford University

• Feature, 1999

• A comparative study of conservation and variation scores

• Fredrik Johansson, Kyushu University

• BMC Bioinformatics, 2010

• A new statistical framework to assess structural alignment quality using information compression

• James H. Collier, PSU

• Bioinformatics, 2014

Methods

• Computation of the null model message length

• Computation of the alignment model message length

• Measure of alignment quality

• The time complexity of computing I-value

Null Model

Alignment Model

Alignment Quality

Time complexity

Results