PRISM: a web server and repository for prediction of protein-protein interactions and modeling their 3D complexes

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W285-9. doi: 10.1093/nar/gku397. Epub 2014 May 14.

Authors

Alper Baspinar¹, Engin Cukuroglu¹, Ruth Nussinov², Ozlem Keskin³, Attila Gursoy³

Affiliations

¹ Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey.
² National Cancer Institute, Cancer and Inflammation Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., National Cancer Institute, Frederick, MD 21702, USA Sackler Institute of Molecular Medicine, Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
³ Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, 34450 Istanbul, Turkey agursoy@ku.edu.tr okeskin@ku.edu.tr.

Abstract

The PRISM web server enables fast and accurate prediction of protein-protein interactions (PPIs). The prediction algorithm is knowledge-based. It combines structural similarity and accounts for evolutionary conservation in the template interfaces. The predicted models are stored in its repository. Given two protein structures, PRISM will provide a structural model of their complex if a matching template interface is available. Users can download the complex structure, retrieve the interface residues and visualize the complex model. The PRISM web server is user friendly, free and open to all users at http://cosbi.ku.edu.tr/prism.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Internet
Models, Molecular*
Multiprotein Complexes / chemistry*
Protein Conformation
Protein Interaction Mapping / methods*
Software*

Substances

Multiprotein Complexes

Associated data

PDB/1CEW
PDB/1STFEI
PDB/2GHU
PDB/2GHUA

Grants and funding

HHSN261200800001E/PHS HHS/United States