English   español  
Por favor, use este identificador para citar o enlazar a este item: http://hdl.handle.net/10261/158781
COMPARTIR / IMPACTO:
Estadísticas
logo share SHARE logo core CORE   Add this article to your Mendeley library MendeleyBASE

Visualizar otros formatos: MARC | Dublin Core | RDF | ORE | MODS | METS | DIDL
Exportar a otros formatos:
Título

RCD+: Fast loop modeling server

AutorLópez-Blanco, José R.; Canosa-Valls, Alejandro J.
Fecha de publicación2016
EditorOxford University Press
CitaciónNucleic Acids Research 44: W395- W400 (2016)
ResumenModeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards nearnative conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbordependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10- fold faster.
URIhttp://hdl.handle.net/10261/158781
Identificadoresdoi: 10.1093/nar/gkw395
issn: 1362-4962
Aparece en las colecciones: (IQFR) Artículos
Ficheros en este ítem:
Fichero Descripción Tamaño Formato  
NucAcRes_2016_44.pdf1,62 MBAdobe PDFVista previa
Visualizar/Abrir
Mostrar el registro completo
 

Artículos relacionados:


NOTA: Los ítems de Digital.CSIC están protegidos por copyright, con todos los derechos reservados, a menos que se indique lo contrario.