Contact Potential for Structure Prediction of Proteins and Protein Complexes from Potts Model.
Biophys J
; 115(5): 809-821, 2018 09 04.
Article
en En
| MEDLINE
| ID: mdl-30122295
ABSTRACT
The energy function is the key component of protein modeling methodology. This work presents a semianalytical approach to the development of contact potentials for protein structure modeling. Residue-residue and atom-atom contact energies were derived by maximizing the probability of observing native sequences in a nonredundant set of protein structures. The optimization task was formulated as an inverse statistical mechanics problem applied to the Potts model. Its solution by pseudolikelihood maximization provides consistent estimates of coupling constants at atomic and residue levels. The best performance was achieved when interacting atoms were grouped according to their physicochemical properties. For individual protein structures, the performance of the contact potentials in distinguishing near-native structures from the decoys is similar to the top-performing scoring functions. The potentials also yielded significant improvement in the protein docking success rates. The potentials recapitulated experimentally determined protein stability changes upon point mutations and protein-protein binding affinities. The approach offers a different perspective on knowledge-based potentials and may serve as the basis for their further development.
Texto completo:
1
Colección:
01-internacional
Banco de datos:
MEDLINE
Asunto principal:
Proteínas
/
Modelos Moleculares
Tipo de estudio:
Prognostic_studies
/
Risk_factors_studies
Idioma:
En
Revista:
Biophys J
Año:
2018
Tipo del documento:
Article