1. Clustering protein fragments to extract a shape library data clustered data library [JMB (2002) 323, 297-307]

2. Example of 2D library 4 fragments 6 residues each sample structures constructed from this library a b c d cabcab bbc

3. Longer fragments give better fit at same complexity Fits Park&Levitt protein set better than previous results complexity (states/residue) average cRMS distance 4 residue fragments 5 residue fragments 6 residue fragments 7 residue fragments

4. 1tim Approximations better Complexity 10 (100 fragments of length 5) 0.9146A cRMS Complexity 2.26 (50 fragments of length 7) 2.7805A cRMS real protein

5. Structural representation via strings of fragments For short strings exhaustive enumeration Loops Sampling string space to investigate properties of structural space [Biopolymers 02] Some techniques used for analysis of string objects can migrate Entropy of protein structure

6. Investigating folding in 2D Energy as in the HP model Use Monte-Carlo to simulate folding Pseudo triangulation mechanisms define possible expansive/contractive motions ©Ileana Streinu PHHPPPPHHHHPHHP threshold