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Flexible relaxation of rigid-body docking solutions.
Król, Marcin; Tournier, Alexander L; Bates, Paul A.
Afiliación
  • Król M; Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute Lincoln's Inn Fields Laboratories, 44 Lincoln's Inn Fields, London WC2A 3PX, United Kingdom. mykrol@cyf-kr.edu.pl
Proteins ; 68(1): 159-69, 2007 Jul 01.
Article en En | MEDLINE | ID: mdl-17397060
Molecular Dynamics (MD) simulations have been performed on a set of rigid-body docking poses, carried out over 25 protein-protein complexes. The results show that fully flexible relaxation increases the fraction of native contacts (NC) by up to 70% for certain docking poses. The largest increase in the fraction of NC is observed for docking poses where anchor residues are able to sample their bound conformation. For each MD simulation, structural snap-shots were clustered and the centre of each cluster used as the MD-relaxed docking pose. A comparison between two energy-based scoring schemes, the first calculated for the MD-relaxed poses, the second for energy minimized poses, shows that the former are better in ranking complexes with large hydrophobic interfaces. Furthermore, complexes with large interfaces are generally ranked well, regardless of the type of relaxation method chosen, whereas complexes with small hydrophobic interfaces remain difficult to rank. In general, the results indicate that current force-fields are able to correctly describe direct intermolecular interactions between receptor and ligand molecules. However, these force-fields still fail in cases where protein-protein complexes are stabilized by subtle energy contributions.
Asunto(s)
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Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Unión Proteica / Proteínas / Biología Computacional / Mapeo de Interacción de Proteínas / Complejos Multiproteicos Tipo de estudio: Prognostic_studies Idioma: En Revista: Proteins Asunto de la revista: BIOQUIMICA Año: 2007 Tipo del documento: Article País de afiliación: Reino Unido Pais de publicación: Estados Unidos
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Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Unión Proteica / Proteínas / Biología Computacional / Mapeo de Interacción de Proteínas / Complejos Multiproteicos Tipo de estudio: Prognostic_studies Idioma: En Revista: Proteins Asunto de la revista: BIOQUIMICA Año: 2007 Tipo del documento: Article País de afiliación: Reino Unido Pais de publicación: Estados Unidos