Loading...
Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed?
Sinha, Rohita Kundrotas, Petras J. Vakser, Ilya A.
Sinha, Rohita
Kundrotas, Petras J.
Vakser, Ilya A.
Citations
Altmetric:
Abstract
The increasing availability of co-crystallized protein-protein complexes provides an opportunity to use template-based modeling for protein-protein docking. Structure alignment techniques are useful in detection of remote target-template similarities. The size of the structure involved in the alignment is important for the success in modeling. This paper describes a systematic large-scale study to find the optimal definition/size of the interfaces for the structure alignment-based docking applications. The results showed that structural areas corresponding to the cutoff values <12 Å across the interface inadequately represent structural details of the interfaces. With the increase of the cutoff beyond 12 Å, the success rate for the benchmark set of 99 protein complexes, did not increase significantly for higher accuracy models, and decreased for lower-accuracy models. The 12 Å cutoff was optimal in our interface alignment-based docking, and a likely best choice for the large-scale (e.g., on the scale of the entire genome) applications to protein interaction networks. The results provide guidelines for the docking approaches, including high-throughput applications to modeled structures.
Description
Date
2012-02-13
Journal Title
Journal ISSN
Volume Title
Publisher
Public Library of Science
Collections
Research Projects
Organizational Units
Journal Issue
Keywords
Cytokine receptors, Cytokine, Enzyme structure, Hormones, Protein structure, Protein structure comparison, Sequence alignment
Citation
Sinha, R., Kundrotas, P. J., & Vakser, I. A. (2012). Protein Docking by the Interface Structure Similarity: How Much Structure Is Needed? PLoS ONE, 7(2). http://dx.doi.org/10.1371/journal.pone.0031349