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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W290-5. doi: 10.1093/nar/gku437. Epub 2014 May 22.

PredHS: a web server for predicting protein-protein interaction hot spots by using structural neighborhood properties.

Author information

1
School of Software, Central South University, Changsha 410075, China Department of Computer Science and Technology, Tongji University, Shanghai 201804, China.
2
Department of Biochemistry and Molecular Biophysics and Center for Computational Biology and Bioinformatics, Columbia University, New York 10032, USAShanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai 200433, China.
3
School of Software, Central South University, Changsha 410075, China.
4
Department of Computer Science and Technology, Tongji University, Shanghai 201804, China sgzhou@fudan.edu.cn.
5
Shanghai Key Lab of Intelligent Information Processing and School of Computer Science, Fudan University, Shanghai 200433, China sgzhou@fudan.edu.cn.

Abstract

Identifying specific hot spot residues that contribute significantly to the affinity and specificity of protein interactions is a problem of the utmost importance. We present an interactive web server, PredHS, which is based on an effective structure-based hot spot prediction method. The PredHS prediction method integrates many novel structural and energetic features with two types of structural neighborhoods (Euclidian and Voronoi), and combines random forest and sequential backward elimination algorithms to select an optimal subset of features. PredHS achieved the highest performance identifying hot spots compared with other state-of-the-art methods, as benchmarked by using an independent experimentally verified dataset. The input to PredHS is protein structures in the PDB format with at least two chains that form interfaces. Users can visualize their predictions in an interactive 3D viewer and download the results as text files. PredHS is available at http://www.predhs.org.

PMID:
24852252
PMCID:
PMC4086081
DOI:
10.1093/nar/gku437
[Indexed for MEDLINE]
Free PMC Article

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