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

2. Context-dependent secondary structure formation of a designed protein sequence Daniel L. Minor Jr, MIT Nature 1996

7. Denaturation

8. Folding Very Short Peptides Using Molecular Dynamics Ken Dill, UCSF Plos Computational Biology, 2006

14. GB1 is not a two-state folder: identification and characterization of an on-pathway intermediate Valerie Daggett, University of Washington Biophysics Journal, 2011

15. Folding pathway and contact maps for two unfolding simulations of GB1

16. Is protein folding hierarchic? I. Local structure and peptide folding Robert L. Baldwin, Stanford University Feature, 1999

18. A comparative study of conservation and variation scores Fredrik Johansson, Kyushu University BMC Bioinformatics, 2010

22. A new statistical framework to assess structural alignment quality using information compression James H. Collier, PSU Bioinformatics, 2014

29. 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

30. Null Model

32. Alignment Model

35. Alignment Quality

36. Time complexity

37. Results