SiteFiNDER|3D: a web-based tool for predicting the location of functional sites in proteins

被引:31
作者
Innis, C. Axel [1 ]
机构
[1] Yale Univ, Howard Hughes Med Inst, Dept Mol Biophys & Biochem, New Haven, CT 06520 USA
关键词
D O I
10.1093/nar/gkm422
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Although knowledge of a protein's functional site is a key requirement for understanding its mode of action at the molecular level, our ability to locate such sites experimentally is far exceeded by the rate at which sequence and structural information is being accumulated. siteFiNDER|3D is an online tool for the prediction of functionally important regions in proteins of known structure. At the core of the server lies the CFG analysis algorithm, which uses a moving 3D window to correlate patterns of functional/ chemical group conservation in the query protein with the location of functional sites. Here, we give a general overview of the functionality offered by the siteFiNDER|3D server, along with general recommendations aimed at maximizing the accuracy and predictive value of this tool in a variety of contexts. siteFiNDER|3D can be accessed at: 'http://sage.csb.yale.edu/sitefinder3d' and requires, at a minimum, the atomic coordinates of a query protein in PDB format.
引用
收藏
页码:W489 / W494
页数:6
相关论文
共 26 条
  • [1] BASIC LOCAL ALIGNMENT SEARCH TOOL
    ALTSCHUL, SF
    GISH, W
    MILLER, W
    MYERS, EW
    LIPMAN, DJ
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 1990, 215 (03) : 403 - 410
  • [2] ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    Armon, A
    Graur, D
    Ben-Tal, N
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2001, 307 (01) : 447 - 463
  • [3] The universal protein resource (UniProt)
    Bairoch, Amos
    Bougueleret, Lydie
    Altairac, Severine
    Amendolia, Valeria
    Auchincloss, Andrea
    Puy, Ghislaine Argoud
    Axelsen, Kristian
    Baratin, Delphine
    Blatter, Marie-Claude
    Boeckmann, Brigitte
    Bollondi, Laurent
    Boutet, Emmanuel
    Quintaje, Silvia Braconi
    Breuza, Lionel
    Bridge, Alan
    deCastro, Edouard
    Coral, Danielle
    Coudert, Elisabeth
    Cusin, Isabelle
    Dobrokhotov, Pavel
    Dornevil, Dolnide
    Duvaud, Severine
    Estreicher, Anne
    Famiglietti, Livia
    Feuermann, Marc
    Gehant, Sebastian
    Farriol-Mathis, Nathalie
    Ferro, Serenella
    Gasteiger, Elisabeth
    Gateau, Alain
    Gerritsen, Vivienne
    Gos, Arnaud
    Gruaz-Gumowski, Nadine
    Hinz, Ursula
    Hulo, Chantal
    Hulo, Nicolas
    Ioannidis, Vassilios
    Ivanyi, Ivan
    James, Janet
    Jain, Eric
    Jimenez, Silvia
    Jungo, Florence
    Junker, Vivien
    Keller, Guillaume
    Lachaize, Corinne
    Lane-Guermonprez, Lydie
    Langendijk-Genevaux, Petra
    Lara, Vicente
    Lemercier, Philippe
    Le Saux, Virginie
    [J]. NUCLEIC ACIDS RESEARCH, 2007, 35 : D193 - D197
  • [4] The Protein Data Bank
    Berman, HM
    Westbrook, J
    Feng, Z
    Gilliland, G
    Bhat, TN
    Weissig, H
    Shindyalov, IN
    Bourne, PE
    [J]. NUCLEIC ACIDS RESEARCH, 2000, 28 (01) : 235 - 242
  • [5] Delano WL, 2002, PYMOL USERS MANUAL
  • [6] MUSCLE: multiple sequence alignment with high accuracy and high throughput
    Edgar, RC
    [J]. NUCLEIC ACIDS RESEARCH, 2004, 32 (05) : 1792 - 1797
  • [7] AMINO-ACID SUBSTITUTION MATRICES FROM PROTEIN BLOCKS
    HENIKOFF, S
    HENIKOFF, JG
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 1992, 89 (22) : 10915 - 10919
  • [8] Prediction of functional sites in proteins using conserved functional group analysis
    Innis, CA
    Anand, AP
    Sowdhamini, R
    [J]. JOURNAL OF MOLECULAR BIOLOGY, 2004, 337 (04) : 1053 - 1068
  • [9] New structural motifs on the chymotrypsin fold and their potential roles in complement factor B
    Jing, H
    Xu, YY
    Carson, M
    Moore, D
    Macon, KJ
    Volanakis, JE
    Narayana, SVL
    [J]. EMBO JOURNAL, 2000, 19 (02) : 164 - 173
  • [10] DETECTION, DELINEATION, MEASUREMENT AND DISPLAY OF CAVITIES IN MACROMOLECULAR STRUCTURES
    KLEYWEGT, GJ
    JONES, TA
    [J]. ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 : 178 - 185