2024-03-29T11:12:47Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1587812021-12-27T16:21:14Zcom_10261_34com_10261_5col_10261_287
RCD+: Fast loop modeling server
López-Blanco, José R.
Canosa-Valls, Alejandro J.
Ministerio de Economía y Competitividad (España)
Modeling 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.
2018-01-03T12:53:18Z
2018-01-03T12:53:18Z
2016
2018-01-03T12:53:18Z
artículo
Nucleic Acids Research 44: W395- W400 (2016)
http://hdl.handle.net/10261/158781
10.1093/nar/gkw395
http://dx.doi.org/10.13039/501100003329
27151199
eng
Publisher's version
Sí
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BFU201-44306
http://creativecommons.org/licenses/by-nc/4.0/
openAccess
Oxford University Press