TY - JOUR
T1 - Predicting protein-protein interface residues using local surface structural similarity
AU - Jordan, Rafael A.
AU - El-Manzalawy, Yasser
AU - Dobbs, Drena
AU - Honavar, Vasant
N1 - Funding Information:
This work was funded in part by the National Institutes of Health grant GM066387 to Vasant Honavar and Drena Dobbs and in part by a research assistantship funded by the Center for Computational Intelligence, Learning, and Discovery. The authors thank Li Xue, Rasna Walia, and Fadi Towfic for useful discussions and suggestions. The work of Vasant Honavar while working at the National Science Foundation was supported by the National Science Foundation. Any opinion, finding, and conclusions contained in this article are those of the authors and do not necessarily reflect the views of the National Science Foundation.
PY - 2012/3/18
Y1 - 2012/3/18
N2 - Background: Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein tend to be conserved even among remote structural homologs, we introduce PrISE, a family of local structural similarity-based computational methods for predicting protein-protein interface residues.Results: We present a novel representation of the surface residues of a protein in the form of structural elements. Each structural element consists of a central residue and its surface neighbors. The PrISE family of interface prediction methods uses a representation of structural elements that captures the atomic composition and accessible surface area of the residues that make up each structural element. Each of the members of the PrISE methods identifies for each structural element in the query protein, a collection of similar structural elements in its repository of structural elements and weights them according to their similarity with the structural element of the query protein. PrISEL relies on the similarity between structural elements (i.e. local structural similarity). PrISEG relies on the similarity between protein surfaces (i.e. general structural similarity). PrISEC, combines local structural similarity and general structural similarity to predict interface residues. These predictors label the central residue of a structural element in a query protein as an interface residue if a weighted majority of the structural elements that are similar to it are interface residues, and as a non-interface residue otherwise. The results of our experiments using three representative benchmark datasets show that the PrISEC outperforms PrISEL and PrISEG; and that PrISEC is highly competitive with state-of-the-art structure-based methods for predicting protein-protein interface residues. Our comparison of PrISEC with PredUs, a recently developed method for predicting interface residues of a query protein based on the known interface residues of its (global) structural homologs, shows that performance superior or comparable to that of PredUs can be obtained using only local surface structural similarity. PrISEC is available as a Web server at http://prise.cs.iastate.edu/. Conclusions: Local surface structural similarity based methods offer a simple, efficient, and effective approach to predict protein-protein interface residues.
AB - Background: Identification of the residues in protein-protein interaction sites has a significant impact in problems such as drug discovery. Motivated by the observation that the set of interface residues of a protein tend to be conserved even among remote structural homologs, we introduce PrISE, a family of local structural similarity-based computational methods for predicting protein-protein interface residues.Results: We present a novel representation of the surface residues of a protein in the form of structural elements. Each structural element consists of a central residue and its surface neighbors. The PrISE family of interface prediction methods uses a representation of structural elements that captures the atomic composition and accessible surface area of the residues that make up each structural element. Each of the members of the PrISE methods identifies for each structural element in the query protein, a collection of similar structural elements in its repository of structural elements and weights them according to their similarity with the structural element of the query protein. PrISEL relies on the similarity between structural elements (i.e. local structural similarity). PrISEG relies on the similarity between protein surfaces (i.e. general structural similarity). PrISEC, combines local structural similarity and general structural similarity to predict interface residues. These predictors label the central residue of a structural element in a query protein as an interface residue if a weighted majority of the structural elements that are similar to it are interface residues, and as a non-interface residue otherwise. The results of our experiments using three representative benchmark datasets show that the PrISEC outperforms PrISEL and PrISEG; and that PrISEC is highly competitive with state-of-the-art structure-based methods for predicting protein-protein interface residues. Our comparison of PrISEC with PredUs, a recently developed method for predicting interface residues of a query protein based on the known interface residues of its (global) structural homologs, shows that performance superior or comparable to that of PredUs can be obtained using only local surface structural similarity. PrISEC is available as a Web server at http://prise.cs.iastate.edu/. Conclusions: Local surface structural similarity based methods offer a simple, efficient, and effective approach to predict protein-protein interface residues.
UR - http://www.scopus.com/inward/record.url?scp=84858175431&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=84858175431&partnerID=8YFLogxK
U2 - 10.1186/1471-2105-13-41
DO - 10.1186/1471-2105-13-41
M3 - Article
C2 - 22424103
AN - SCOPUS:84858175431
SN - 1471-2105
VL - 13
JO - BMC bioinformatics
JF - BMC bioinformatics
IS - 1
M1 - 41
ER -