Nucleic Acids Research Advance Access originally published online on May 8, 2008
Nucleic Acids Research 2008 36(Web Server issue):W260-W264; doi:10.1093/nar/gkn185
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Nucleic Acids Research, 2008, Vol. 36, No. suppl_2 W260-W264
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions
1School of Computer Science, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 69978, Israel, 2Physical Biosciences Division, Berkeley National Lab, California, CA, USA, 3Sackler Inst. of Molecular Medicine, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel and 4Basic Research Program, SAIC-Frederick, Inc., Laboratory of Experimental and Computational Biology, NCI-Frederick, Bldg 469, Rm 151, Frederick, MD 21702, USA
*To whom correspondence should be addressed. Tel: +972 3 640 8268 or 640 5375; Fax: +972 3 640 5728 or 640 6476; Email: shulmana{at}post.ac.il Correspondence may also be addressed to Haim J. Wolfson. Email: wolfson{at}post.tau.ac.il
Received January 29, 2008. Revised March 27, 2008. Accepted March 31, 2008.
Analysis of protein–ligand complexes and recognition of spatially conserved physico-chemical properties is important for the prediction of binding and function. Here, we present two webservers for multiple alignment and recognition of binding patterns shared by a set of protein structures. The first webserver, MultiBind (http://bioinfo3d.cs.tau.ac.il/MultiBind), performs multiple alignment of protein binding sites. It recognizes the common spatial chemical binding patterns even in the absence of similarity of the sequences or the folds of the compared proteins. The input to the MultiBind server is a set of protein-binding sites defined by interactions with small molecules. The output is a detailed list of the shared physico-chemical binding site properties. The second webserver, MAPPIS (http://bioinfo3d.cs.tau.ac.il/MAPPIS), aims to analyze protein–protein interactions. It performs multiple alignment of protein–protein interfaces (PPIs), which are regions of interaction between two protein molecules. MAPPIS recognizes the spatially conserved physico-chemical interactions, which often involve energetically important hot-spot residues that are crucial for protein–protein associations. The input to the MAPPIS server is a set of protein-protein complexes. The output is a detailed list of the shared interaction properties of the interfaces.
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