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