Clustering protein fragments to extract a shape library - PowerPoint PPT Presentation
Title:
Clustering protein fragments to extract a shape library
Description:
Longer fragments give better fit at same complexity. Fits Park&Levitt protein set better than previous results. complexity (states/residue) ... – PowerPoint PPT presentation
Number of Views:27
Avg rating:3.0/5.0
Title: 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
Recommended
CrystalGraphics Presentations
