Protein Flexibility
CREATED: 200701011018 Author: Anshul
** Motivation
- binding, active site determination
- structure determination
- folding
** Given two conformations, determine rigid/flexible residues
- PDB (protein database) provides ** temperature factor graph ** dihedral angles ** RMSD of sliding window ** data is noisy
- Binary matrix
compute all fragment RMSD
apply statistical test
*** assume noise is gaussian *** noise level of theta *** rigid or flexible
binary matrix, 0 -> rigid, 1 -> flexible
- Minimally flexible fragments (MFF) ** flexible fragment which does not contain flexible sub fragments
- Flexibility of a residue = size of smallest MFF that contains the residue ** MMDB (molecular motion)
** Unknown flexibility
sample loop structures
** 6 non redundant dof -inverse kinematics-> dihedral angles ** motion in null space (local sampling)
find low engergy conformations
** use proxy energy functions *** approximation to actual energy function *** indicator to quickly reject bad samples