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      ProBiS: a web server for detection of structurally similar protein binding sites

      research-article
      Author(s): 1 , 1 , 2 , *
      Publication date (Electronic):
      Journal: Nucleic Acids Research
      Publisher: Oxford University Press

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          Abstract

          A web server, ProBiS, freely available at http://probis.cmm.ki.si, is presented. This provides access to the program ProBiS (Protein Binding Sites), which detects protein binding sites based on local structural alignments. Detailed instructions and user guidelines for use of ProBiS are available at the server under ‘HELP’ and selected examples are provided under ‘EXAMPLES’.

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          ProBiS algorithm for detection of structurally similar protein binding sites by local structural alignment

          Janez Konc, Dušanka Janežič (2010)
          Motivation: Exploitation of locally similar 3D patterns of physicochemical properties on the surface of a protein for detection of binding sites that may lack sequence and global structural conservation. Results: An algorithm, ProBiS is described that detects structurally similar sites on protein surfaces by local surface structure alignment. It compares the query protein to members of a database of protein 3D structures and detects with sub-residue precision, structurally similar sites as patterns of physicochemical properties on the protein surface. Using an efficient maximum clique algorithm, the program identifies proteins that share local structural similarities with the query protein and generates structure-based alignments of these proteins with the query. Structural similarity scores are calculated for the query protein's surface residues, and are expressed as different colors on the query protein surface. The algorithm has been used successfully for the detection of protein–protein, protein–small ligand and protein–DNA binding sites. Availability: The software is available, as a web tool, free of charge for academic users at http://probis.cmm.ki.si Contact: dusa@cmm.ki.si Supplementary information: Supplementary data are available at Bioinformatics online.
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            The relationship between protein structure and function: a comprehensive survey with application to the yeast genome.

            H Hegyi, M. Gerstein (1999)
            For most proteins in the genome databases, function is predicted via sequence comparison. In spite of the popularity of this approach, the extent to which it can be reliably applied is unknown. We address this issue by systematically investigating the relationship between protein function and structure. We focus initially on enzymes functionally classified by the Enzyme Commission (EC) and relate these to by structurally classified domains the SCOP database. We find that the major SCOP fold classes have different propensities to carry out certain broad categories of functions. For instance, alpha/beta folds are disproportionately associated with enzymes, especially transferases and hydrolases, and all-alpha and small folds with non-enzymes, while alpha+beta folds have an equal tendency either way. These observations for the database overall are largely true for specific genomes. We focus, in particular, on yeast, analyzing it with many classifications in addition to SCOP and EC (i.e. COGs, CATH, MIPS), and find clear tendencies for fold-function association, across a broad spectrum of functions. Analysis with the COGs scheme also suggests that the functions of the most ancient proteins are more evenly distributed among different structural classes than those of more modern ones. For the database overall, we identify the most versatile functions, i.e. those that are associated with the most folds, and the most versatile folds, associated with the most functions. The two most versatile enzymatic functions (hydro-lyases and O-glycosyl glucosidases) are associated with seven folds each. The five most versatile folds (TIM-barrel, Rossmann, ferredoxin, alpha-beta hydrolase, and P-loop NTP hydrolase) are all mixed alpha-beta structures. They stand out as generic scaffolds, accommodating from six to as many as 16 functions (for the exceptional TIM-barrel). At the conclusion of our analysis we are able to construct a graph giving the chance that a functional annotation can be reliably transferred at different degrees of sequence and structural similarity. Supplemental information is available from http://bioinfo.mbb.yale.edu/genome/foldfunc++ +. Copyright 1999 Academic Press.
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              Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures.

              Robert B. Russell, Alexander Stark (2003)
              The detection of local structural patterns in proteins (e.g. active sites) can provide insights into protein function in the absence of sequence or fold similarity. Methods to detect such similarities are key during structural annotation, for example with results from Structural Genomics initiatives. PINTS (Patterns in Non-homologous Tertiary Structures, http://pints.embl.de) performs database searches for such patterns and most importantly provides a measure of statistical significance for any similarity uncovered. To aid functional annotation of proteins, we allow comparisons of pre-defined patterns against databases of complete structures and of entire structures to databases of particular residues likely to be functionally important.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Journal ID (hwp): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 1 July 2010
                Publication date (Electronic): 26 May 2010
                Publication date PMC-release: 26 May 2010
                Volume: 38
                Issue: Web Server issue
                Pages: W436-W440
                Affiliations
                1National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana and 2University of Primorska, Faculty for Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000 Koper, Slovenia
                Author notes
                *To whom correspondence should be addressed. Tel: +386 1 476 0321; Fax: +386 1 476 0300; Email: dusa@ 123456cmm.ki.si
                Article
                Publisher ID: gkq479
                DOI: 10.1093/nar/gkq479
                PMC ID: 2896105
                PubMed ID: 20504855
                SO-VID: c9e4ddda-577c-4b97-b6af-551878e94adb
                Copyright © © The Author(s) 2010. Published by Oxford University Press.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 27 February 2010
                Date revision received : 29 April 2010
                Date accepted : 13 May 2010
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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