DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.

The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes....

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Dennis M Krüger, José Ignacio Garzón, Pablo Chacón, Holger Gohlke
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/82ab4e5a13144034b0ab0806efa2c1b5
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:82ab4e5a13144034b0ab0806efa2c1b5
record_format	dspace
spelling	oai:doaj.org-article:82ab4e5a13144034b0ab0806efa2c1b52021-11-18T08:31:30ZDrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.1932-620310.1371/journal.pone.0089466https://doaj.org/article/82ab4e5a13144034b0ab0806efa2c1b52014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24586799/?tool=EBIhttps://doaj.org/toc/1932-6203The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking "unbound perturbation" ("unbound docking") decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScore(PPI)/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼ 2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScore(PPI) balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScore(PPI)/FRODOCK will be successful.Dennis M KrügerJosé Ignacio GarzónPablo ChacónHolger GohlkePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e89466 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Dennis M Krüger José Ignacio Garzón Pablo Chacón Holger Gohlke DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
description	The distance-dependent knowledge-based DrugScore(PPI) potentials, previously developed for in silico alanine scanning and hot spot prediction on given structures of protein-protein complexes, are evaluated as a scoring and objective function for the structure prediction of protein-protein complexes. When applied for ranking "unbound perturbation" ("unbound docking") decoys generated by Baker and coworkers a 4-fold (1.5-fold) enrichment of acceptable docking solutions in the top ranks compared to a random selection is found. When applied as an objective function in FRODOCK for bound protein-protein docking on 97 complexes of the ZDOCK benchmark 3.0, DrugScore(PPI)/FRODOCK finds up to 10% (15%) more high accuracy solutions in the top 1 (top 10) predictions than the original FRODOCK implementation. When used as an objective function for global unbound protein-protein docking, fair docking success rates are obtained, which improve by ∼ 2-fold to 18% (58%) for an at least acceptable solution in the top 10 (top 100) predictions when performing knowledge-driven unbound docking. This suggests that DrugScore(PPI) balances well several different types of interactions important for protein-protein recognition. The results are discussed in view of the influence of crystal packing and the type of protein-protein complex docked. Finally, a simple criterion is provided with which to estimate a priori if unbound docking with DrugScore(PPI)/FRODOCK will be successful.
format	article
author	Dennis M Krüger José Ignacio Garzón Pablo Chacón Holger Gohlke
author_facet	Dennis M Krüger José Ignacio Garzón Pablo Chacón Holger Gohlke
author_sort	Dennis M Krüger
title	DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
title_short	DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
title_full	DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
title_fullStr	DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
title_full_unstemmed	DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.
title_sort	drugscoreppi knowledge-based potentials used as scoring and objective function in protein-protein docking.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/82ab4e5a13144034b0ab0806efa2c1b5
work_keys_str_mv	AT dennismkruger drugscoreppiknowledgebasedpotentialsusedasscoringandobjectivefunctioninproteinproteindocking AT joseignaciogarzon drugscoreppiknowledgebasedpotentialsusedasscoringandobjectivefunctioninproteinproteindocking AT pablochacon drugscoreppiknowledgebasedpotentialsusedasscoringandobjectivefunctioninproteinproteindocking AT holgergohlke drugscoreppiknowledgebasedpotentialsusedasscoringandobjectivefunctioninproteinproteindocking
_version_	1718421693046718464

DrugScorePPI knowledge-based potentials used as scoring and objective function in protein-protein docking.

Ejemplares similares