A decoy set for the thermostable subdomain from chicken villin headpiece, comparison of different free energy estimators.

ABSTRACT:

Background

Estimators of free energies are routinely used to judge the quality of protein structural models. As these estimators still present inaccuracies, they are frequently evaluated by discriminating native or native-like conformations from large ensembles of so-called decoy structures.

Results

A decoy set is obtained from snapshots taken from 5 long (100 ns) molecular dynamics (MD) simulations of the thermostable subdomain from chicken villin headpiece. An evaluation of the energy of the decoys is given using: i) a residue based contact potential supplemented by a term for the quality of dihedral angles; ii) a recently introduced combination of four statistical scoring functions for model quality estimation (FRST); iii) molecular mechanics with solvation energy estimat

SUBMITTER: Fogolari F 

PROVIDER: S-EPMC1351271 | biostudies-literature | 2005 Dec

REPOSITORIES: biostudies-literature