A coarse-grained protein force field for folding and structure prediction
| Autor: | Pierre Tufféry, Philippe Derreumaux, Julien Maupetit |
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| Rok vydání: | 2007 |
| Předmět: |
Models
Molecular Protein Folding Protein Conformation Chemistry Monte Carlo method Proteins Biochemistry Force field (chemistry) Kinetics Structure-Activity Relationship Molecular dynamics Discrete optimized protein energy Predictive Value of Tests Structural Biology Computational chemistry Thermodynamics Computer Simulation Threading (protein sequence) Biological system Molecular Biology Native structure |
| Zdroj: | Proteins: Structure, Function, and Bioinformatics. 69:394-408 |
| ISSN: | 1097-0134 0887-3585 |
| DOI: | 10.1002/prot.21505 |
| Popis: | 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. Proteins 2007. © 2007 Wiley-Liss, Inc. |
| Databáze: | OpenAIRE |
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