A coarse-grained protein force field for folding and structure prediction.
We have revisited the protein coarse-grained optimized potential for efficient structure prediction (OPEP). The training and validation sets consist of 13 and 16 protein targets. Because optimization depends on details of how the ensemble of decoys is sampled, trial conformations are generated by molecular dynamics, threading, greedy, and Monte Carlo simulations, or taken from publicly available databases. The OPEP parameters are varied by a genetic algorithm using a scoring function which requires that the native structure has the lowest energy, and the native-like structures have energy higher than the native structure but lower than the remote conformations. Overall, we find that OPEP correctly identifies 24 native or native-like states for 29 targets and has very similar capability to the all-atom discrete optimized protein energy model (DOPE), found recently to outperform five currently used energy models.
Maupetit
Julien
J
Equipe de Bioinformatique Génomique et Moléculaire, INSERM E0346, Université Paris 7, Tour 53-54, 2 place Jussieu, 75251 Paris, Cedex 05, France.
Tuffery
P
P
Derreumaux
Philippe
P
D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D011237:Predictive Value of Tests; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013329:Structure-Activity Relationship; D013816:Thermodynamics
D011506:Proteins