Clustering protein fragments to extract a shape library

1
Clustering protein fragments to extract a shape
library
JMB (2002) 323, 297-307
2
Example of 2D library

• 4 fragments 6 residues each
• sample structures constructed from this library

3
Longer fragments give better fit at same
complexity

• Longer fragments give better fit at same
  complexity
• Fits ParkLevitt protein set better than previous
  results

average cRMS distance
complexity (states/residue)
4
1tim Approximations
real protein
better
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

threshold
PHHPPPPHHHHPHHP