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

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 estimated either according to the generalized Born surface area (GBSA) or iv) the Poisson-Boltzmann surface area (PBSA) method. Conclusion: The decoy set presented here has the following features which make it attractiv...

• Type: Journal
• Year: 2005
• Where: BMCBI
• Authors: Federico Fogolari, Silvio C. E. Tosatto, Giorgio Colombo
• Keywords: BMCBI 2005, Decoy, Molecular Dynamics, Scoring Functions