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

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Presentation transcript:

Clustering protein fragments to extract a shape library data clustered data library [JMB (2002) 323, ]

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

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

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

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

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