NDLI: Docking by structural similarity at protein-protein interfaces.

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Sinha, Rohita Kundrotas, Petras J. Vakser, Ilya A.
Description	Country affiliation: United States Author Affiliation: Sinha R ( Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047-1620, USA.)
Abstract	Rapid accumulation of experimental data on protein-protein complexes drives the paradigm shift in protein docking from 'traditional,' template free approaches to template based techniques. Homology docking algorithms based on sequence similarity between target and template complexes can account for up to 20% of known protein-protein interactions. When highly homologous templates for the target complex are not available, but the structure of the target monomers is known, docking by local structural alignment may provide an adequate solution. Such an algorithm was developed based on the structural comparison of monomers to cocrystallized interfaces. A library of the interfaces was generated from cocrystallized protein-protein complexes in PDB. The partial structure alignment algorithm was validated on the DOCKGROUND benchmark sets. The optimal performance of the partial (interface) structure alignment was achieved with the interface residues defined by 12 Å distance across the interface. Overall, the partial structure alignment yielded more accurate models than the full structure alignment. Most templates identified by the partial structure alignment had low sequence identity to the target, which makes them hard to detect by sequence-based methods. The results indicate that the structure alignment techniques provide a much needed addition to the docking arsenal, with the combined structure alignment and template free docking success rate significantly surpassing that of the free docking alone.
File Format	HTM / HTML
ISSN	08873585
e-ISSN	10970134
DOI	10.1002/prot.22812
Journal	Proteins: Structure, Function, and Bioinformatics
Issue Number	15
Volume Number	78
Language	English
Publisher	Wiley-Liss
Publisher Date	2010-11-15
Publisher Place	United States
Access Restriction	Open
Subject Keyword	Research Support, N.i.h., Extramural Models, Chemical Computational Biology Discipline Biochemistry Models, Molecular Models, Statistical Protein Interaction Domains And Motifs Protein Interaction Mapping Proteins Reproducibility Of Results Chemistry Algorithms Databases, Protein Classification Structural Homology, Protein
Content Type	Text
Resource Type	Article
Subject	Structural Biology Biochemistry Molecular Biology

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