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      3dLOGO: a web server for the identification, analysis and use of conserved protein substructures

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          Abstract

          3dLOGO is a web server for the identification and analysis of conserved protein 3D substructures. Given a set of residues in a PDB (Protein Data Bank) chain, the server detects the matching substructure(s) in a set of user-provided protein structures, generates a multiple structure alignment centered on the input substructures and highlights other residues whose structural conservation becomes evident after the defined superposition. Conserved residues are proposed to the user for highlighting functional areas, deriving refined structural motifs or building sequence patterns. Residue structural conservation can be visualized through an expressly designed Java application, 3dProLogo, which is a 3D implementation of a sequence logo. The 3dLOGO server, with related documentation, is available at http://3dlogo.uniroma2.it/

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          Most cited references19

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          SuperPose: a simple server for sophisticated structural superposition.

          R. Maiti, G H Van Domselaar, H. Zhang … (2004)
          The SuperPose web server rapidly and robustly calculates both pairwise and multiple protein structure superpositions using a modified quaternion eigenvalue approach. SuperPose generates sequence alignments, structure alignments, PDB (Protein Data Bank) coordinates and RMSD statistics, as well as difference distance plots and images (both static and interactive) of the superimposed molecules. SuperPose employs a simple interface that requires only PDB files or accession numbers as input. All other superposition decisions are made by the program. SuperPose is uniquely able to superimpose structures that differ substantially in sequence, size or shape. It is also capable of handling a much larger range of superposition queries and situations than many standalone programs and yields results that are intuitively more in agreement with known biological or structural data. The SuperPose web server is freely accessible at http://wishart.biology.ualberta.ca/SuperPose/.
          Article 0 comments Cited 157 times – based on 0 reviews     Review now
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            The P-loop--a common motif in ATP- and GTP-binding proteins.

            M Saraste, P Sibbald, A Wittinghofer (1990)
            Many ATP- and GTP-binding proteins have a phosphate-binding loop (P-loop), the primary structure of which typically consists of a glycine-rich sequence followed by a conserved lysine and a serine or threonine. The three-dimensional structures of several ATP- and GTP-binding proteins containing P-loops have now been solved. In this review current knowledge of P-loops is discussed with the additional aim of illustrating the fascinating relationship between protein sequence, structure and function.
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              A method for simultaneous alignment of multiple protein structures.

              Ruth Nussinov, Aaron H. Wolfson, Maxim Shatsky (2004)
              Here, we present MultiProt, a fully automated highly efficient technique to detect multiple structural alignments of protein structures. MultiProt finds the common geometrical cores between input molecules. To date, most methods for multiple alignment start from the pairwise alignment solutions. This may lead to a small overall alignment. In contrast, our method derives multiple alignments from simultaneous superpositions of input molecules. Further, our method does not require that all input molecules participate in the alignment. Actually, it efficiently detects high scoring partial multiple alignments for all possible number of molecules in the input. To demonstrate the power of MultiProt, we provide a number of case studies. First, we demonstrate known multiple alignments of protein structures to illustrate the performance of MultiProt. Next, we present various biological applications. These include: (1) a partial alignment of hinge-bent domains; (2) identification of functional groups of G-proteins; (3) analysis of binding sites; and (4) protein-protein interface alignment. Some applications preserve the sequence order of the residues in the alignment, whereas others are order-independent. It is their residue sequence order-independence that allows application of MultiProt to derive multiple alignments of binding sites and of protein-protein interfaces, making MultiProt an extremely useful structural tool. Copyright 2004 Wiley-Liss, Inc.
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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): July 2007
                Publication date (Electronic): 8 May 2007
                Publication date PMC-release: 8 May 2007
                Volume: 35
                Issue: Web Server issue
                Pages: W416-W419
                Affiliations
                1Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata, 00133 Rome, Italy, 2Bioinformatics Group, I.R.B.M. P. Angeletti, MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy, 3Center for Comparative Functional Genomics, Department of Biology, New York University, NY 10003, USA and 4Systems Biology Group - Max-Delbrück-Centrum für Molekulare Medizin, Berlin
                Author notes
                *To whom correspondence should be addressed. +39 067259 4324+39 067259 4314 allegra.via@ 123456uniroma2.it Correspondence may also be addressed to Manuela Helmer-Citterich. Email: citterich@ 123456uniroma2.it
                Article
                DOI: 10.1093/nar/gkm228
                PMC ID: 1933223
                PubMed ID: 17488847
                SO-VID: 1941b020-bf89-4fca-9425-382319834f39
                Copyright © © 2007 The Author(s)
                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/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                Date received : 21 December 2006
                Date revision received : 15 March 2007
                Date accepted : 28 March 2007
                Categories
                Subject: Articles

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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