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The distance-dependent knowledge-based DrugScorePPI 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, DrugScorePPI/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 DrugScorePPI 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 DrugScorePPI/ FRODOCK will be successful. © 2014 Krüger et al.

Pertenece a

Digital.CSIC  

Autor(es)

Krüger, D.M. -  Garzón, José Ignacio -  Chacón, Pablo -  Gohlke, H. - 

Id.: 71529385

Idioma: eng  - 

Versión: 1.0

Estado: Final

Tipo de recurso: Artículo  - 

Tipo de Interactividad: Expositivo

Nivel de Interactividad: muy bajo

Audiencia: Estudiante  -  Profesor  -  Autor  - 

Estructura: Atomic

Coste: no

Copyright: sí

: openAccess

Requerimientos técnicos:  Browser: Any - 

Relación: [References] Publisher's version

Fecha de contribución: 13-jul-2018

Contacto:

Localización:
* doi: 10.1371/journal.pone.0089466
* issn: 1932-6203
* PLoS ONE 9 (2014)

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