Mostrar el registro sencillo del ítem
dc.contributor.author
Arnautova, Yelena A.
dc.contributor.author
Vorobjev, Yury N.
dc.contributor.author
Vila, Jorge Alberto
dc.contributor.author
Scheraga, Haroldo A.
dc.date.available
2024-05-21T12:46:11Z
dc.date.issued
2009-12
dc.identifier.citation
Arnautova, Yelena A.; Vorobjev, Yury N.; Vila, Jorge Alberto; Scheraga, Haroldo A.; Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation; Wiley-liss, div John Wiley & Sons Inc.; Proteins: Structure, Function And Genetics; 77; 1; 12-2009; 38-51
dc.identifier.issn
0887-3585
dc.identifier.uri
http://hdl.handle.net/11336/235749
dc.description.abstract
Availability of energy functions which can discriminate native-like from non-native protein conformations is crucial for theoretical protein structure prediction and refinement of low-resolution protein models. This article reports the results of benchmark tests for scoring functions based on two all-atom ECEPP force fields, that is, ECEPP/3 and ECEPP05, and two implicit solvent models for a large set of protein decoys. The following three scoring functions are considered: (i) ECEPP05 plus a solvent-accessible surface area model with the parameters optimized with a set of protein decoys (ECEPP05/SA); (ii) ECEPP/3 plus the solvent-accessible surface area model of Ooi et al. (Proc Natl Acad Sci USA 1987;84:3086–3090) (ECEPP3/OONS); and (iii) ECEPP05 plus an implicit solvent model based on a solution of the Poisson equation with an optimized Fast Adaptive Multigrid Boundary Element (FAMBEpH) method (ECEPP05/FAMBEpH). Short Monte Carlo-with-Minimization (MCM) simulations, following local energy minimization, are used as a scoring method with ECEPP05/SA and ECEPP3/OONS potentials, whereas energy calculation is used with ECEPP05/FAMBEpH. The performance of each scoring function is evaluated by examining its ability to distinguish between native-like and non-native protein structures. The results of the tests show that the new ECEPP05/SA scoring function represents a significant improvement over the earlier ECEPP3/OONS version of the force field. Thus, it is able to rank native-like structures with Cα root-mean-square-deviations below 3.5 Å as lowest-energy conformations for 76% and within the top 10 for 87% of the proteins tested, compared with 69 and 80%, respectively, for ECEPP3/OONS. The use of the FAMBEpH solvation model, which provides a more accurate description of the protein-solvent interactions, improves the discriminative ability of the scoring function to 89%. All failed tests in which the native-like structures cannot be discriminated as those with low energy, are due to omission of protein–protein interactions. The results of this study represent a benchmark in force-field development, and may be useful for evaluation of the performance of different force fields. Proteins 2009.
dc.format
application/pdf
dc.language.iso
eng
dc.publisher
Wiley-liss, div John Wiley & Sons Inc.
dc.rights
info:eu-repo/semantics/restrictedAccess
dc.rights.uri
https://creativecommons.org/licenses/by-nc-sa/2.5/ar/
dc.subject
PHYSICS-BASED POTENTIALS
dc.subject
PROTEIN DECOYS
dc.subject
POISSON-BOLTZMANN CONTINUUM SOLVENT MODEL
dc.subject
SURFACE AREA
dc.subject
MOLECULAR MECHANICS
dc.subject
REFINEMENT
dc.subject.classification
Matemática Aplicada
dc.subject.classification
Matemáticas
dc.subject.classification
CIENCIAS NATURALES Y EXACTAS
dc.title
Identifying native-like protein structures with scoring functions based on all-atom ECEPP force fields, implicit solvent models and structure relaxation
dc.type
info:eu-repo/semantics/article
dc.type
info:ar-repo/semantics/artículo
dc.type
info:eu-repo/semantics/publishedVersion
dc.date.updated
2024-05-03T13:59:35Z
dc.identifier.eissn
1097-0134
dc.journal.volume
77
dc.journal.number
1
dc.journal.pagination
38-51
dc.journal.pais
Estados Unidos
dc.description.fil
Fil: Arnautova, Yelena A.. Cornell University; Estados Unidos
dc.description.fil
Fil: Vorobjev, Yury N.. Russian Academy of Science; Rusia
dc.description.fil
Fil: Vila, Jorge Alberto. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi". Universidad Nacional de San Luis. Facultad de Ciencias Físico, Matemáticas y Naturales. Instituto de Matemática Aplicada de San Luis "Prof. Ezio Marchi"; Argentina
dc.description.fil
Fil: Scheraga, Haroldo A.. Cornell University; Estados Unidos
dc.journal.title
Proteins: Structure, Function And Genetics
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/doi/https://doi.org/10.1002/prot.22414
dc.relation.alternativeid
info:eu-repo/semantics/altIdentifier/url/https://onlinelibrary.wiley.com/doi/10.1002/prot.22414
Archivos asociados