Outline GB1 chameleon 8-mer Peptide MD GB1 folding pathway Hierarchic folding Conservation scores.

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Presentation transcript:

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