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MultiBind and MAPPIS: webservers for multiple alignment of protein 3D-binding sites and their interactions

  1. Author:
    Shulman-Peleg, A.
    Shatsky, M.
    Nussinov, R.
    Wolfson, H. J.

  2. Author Address

    Shulman-Peleg, Alexandra, Wolfson, Haim J.] Tel Aviv Univ, Raymond & Beverly Sackler Fac Exact Sci, Sch Comp Sci, IL-69978 Tel Aviv, Israel. [Nussinov, Ruth] Tel Aviv Univ, Sackler Fac Med, Sackler Inst Mol Med, IL-69978 Tel Aviv, Israel. [Shatsky, Maxim] Berkeley Natl Lab, Phys Biosci Div, Berkeley, CA USA. [Nussinov, Ruth] SAIC Frederick Inc, NCI, Lab Expt & Computat Biol, Basic Res Program, Frederick, MD 21702 USA.
    1. Year: 2008
  2. Journal: Nucleic Acids Research
    1. 36
    2. Pages: W260-W264
  4. Type of Article: Article
  1. Abstract:

    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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External Sources

  1. PMID: 18467424

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