메뉴 건너뛰기




Volumn 33, Issue DATABASE ISS., 2005, Pages

PDBSite: A database of the 3D structure of protein functional sites

Author keywords

[No Author keywords available]

Indexed keywords

ACCESS TO INFORMATION; ARTICLE; AUTOMATION; CATALYSIS; CONTROLLED STUDY; INFORMATION PROCESSING; INTERNET; LIGAND BINDING; PDBSITE; PRIORITY JOURNAL; PROTEIN DATA BANK; PROTEIN DATABASE; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN LOCALIZATION; PROTEIN MODIFICATION; PROTEIN PROCESSING; PROTEIN PROTEIN INTERACTION; PROTEIN RNA BINDING; PROTEIN STRUCTURE; PROTEIN TERTIARY STRUCTURE; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; COMPLEX FORMATION; COMPUTER PROGRAM; HUMAN; MATHEMATICAL COMPUTING; MUTATIONAL ANALYSIS; ONLINE SYSTEM; PROTEIN DATA BANK SITE DATABASE; STRUCTURE ACTIVITY RELATION;

EID: 13444280425     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gki105     Document Type: Article
Times cited : (80)

References (31)
  • 1
    • 0029973830 scopus 로고    scopus 로고
    • Derivation of 3D coordinate templates for searching structural databases: Application to the Ser-His-Asp catalytic triads of the serine proteinases and lipases
    • Wallace,A.C., Laskowski,R.A. and Thornton,J.M. (1996) Derivation of 3D coordinate templates for searching structural databases: application to the Ser-His-Asp catalytic triads of the serine proteinases and lipases. Protein Sci., 5, 1001-1013.
    • (1996) Protein Sci. , vol.5 , pp. 1001-1013
    • Wallace, A.C.1    Laskowski, R.A.2    Thornton, J.M.3
  • 2
    • 0141850386 scopus 로고    scopus 로고
    • An algorithm for constraint-based structural template matching: Application to 3D templates with statistical analysis
    • Barker,J.A. and Thornton,J.M. (2003) An algorithm for constraint-based structural template matching: application to 3D templates with statistical analysis. Bioinformatics, 13, 1644-1649.
    • (2003) Bioinformatics , vol.13 , pp. 1644-1649
    • Barker, J.A.1    Thornton, J.M.2
  • 3
    • 0030724039 scopus 로고    scopus 로고
    • TESS: A geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: Application to enzyme active sites
    • Wallace,A.C., Borkakoti,N. and Thornton,J.M. (1997) TESS: a geometric hashing algorithm for deriving 3D coordinate templates for searching structural databases: application to enzyme active sites. Protein Sci., 6, 2308-2323.
    • (1997) Protein Sci. , vol.6 , pp. 2308-2323
    • Wallace, A.C.1    Borkakoti, N.2    Thornton, J.M.3
  • 4
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • Stark,A. and Russell,R.B. (2003) Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res., 31, 3341-3344.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 5
  • 6
    • 0036108480 scopus 로고    scopus 로고
    • Interactive motif and fold recognition in protein structures
    • Madsen,D. and Kleywegt,G.J. (2002) Interactive motif and fold recognition in protein structures. J. Appl. Cryst., 35, 137-139.
    • (2002) J. Appl. Cryst. , vol.35 , pp. 137-139
    • Madsen, D.1    Kleywegt, G.J.2
  • 7
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt,S., Kuhn,D. and Klebe,G. (2002) A new method to detect related function among proteins independent of sequence and fold homology. J. Mol. Biol., 323, 387-406.
    • (2002) J. Mol. Biol. , vol.323 , pp. 387-406
    • Schmitt, S.1    Kuhn, D.2    Klebe, G.3
  • 8
    • 0037436339 scopus 로고    scopus 로고
    • Relibase: Design and development of a database for comprehensive analysis of protein-ligand interactions
    • Hendlich,M., Bergner,A., Gunther,J. and Klebe,G. (2003) Relibase: design and development of a database for comprehensive analysis of protein-ligand interactions. J. Mol. Biol., 326, 607-620.
    • (2003) J. Mol. Biol. , vol.326 , pp. 607-620
    • Hendlich, M.1    Bergner, A.2    Gunther, J.3    Klebe, G.4
  • 9
    • 0036288284 scopus 로고    scopus 로고
    • Identification of protein functions from a molecular surface database, eF-site
    • Kinoshita,K., Furui,J. and Nakamura,H. (2001) Identification of protein functions from a molecular surface database, eF-site. J. Struct. Funct. Genomics., 2, 9-22.
    • (2001) J. Struct. Funct. Genomics , vol.2 , pp. 9-22
    • Kinoshita, K.1    Furui, J.2    Nakamura, H.3
  • 10
    • 0037470573 scopus 로고    scopus 로고
    • Annotating nucleic acid-binding function based on protein structure
    • Stawiski,E.W., Gregoret,L.M. and Mandel-Gutfreund,Y. (2003) Annotating nucleic acid-binding function based on protein structure. J. Mol. Biol., 326, 1065-1079.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1065-1079
    • Stawiski, E.W.1    Gregoret, L.M.2    Mandel-Gutfreund, Y.3
  • 11
    • 3242890667 scopus 로고    scopus 로고
    • PDBSiteScan: A program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins
    • Ivanisenko,V.A., Pintus,S.S., Grigorovich,D.A. and Kolchanov,N.A. (2004) PDBSiteScan: a program for searching for active, binding and posttranslational modification sites in the 3D structures of proteins. Nucleic Acids Res., 32, W549-W554.
    • (2004) Nucleic Acids Res. , vol.32
    • Ivanisenko, V.A.1    Pintus, S.S.2    Grigorovich, D.A.3    Kolchanov, N.A.4
  • 12
    • 0027385177 scopus 로고
    • Matching chemistry and shape in molecular docking
    • Shoichet,B.K. and Kuntz,I.D. (1993) Matching chemistry and shape in molecular docking. Protein Eng., 6, 723-732.
    • (1993) Protein Eng. , vol.6 , pp. 723-732
    • Shoichet, B.K.1    Kuntz, I.D.2
  • 13
    • 1842830270 scopus 로고    scopus 로고
    • Are predicted structures good enough to preserve functional sites?
    • Wei,L., Huang,E.S. and Altman,R.B. (1999) Are predicted structures good enough to preserve functional sites? Structure, 7, 643-650.
    • (1999) Structure , vol.7 , pp. 643-650
    • Wei, L.1    Huang, E.S.2    Altman, R.B.3
  • 14
    • 0031216696 scopus 로고    scopus 로고
    • Search for sites containing functionally important substitutions in series of related or mutant proteins
    • Ivanisenko,V.A. and Eroshkin,A.M. (1997) Search for sites containing functionally important substitutions in series of related or mutant proteins. Mol. Biol. (Moskow), 31, 880-887.
    • (1997) Mol. Biol. (Moskow) , vol.31 , pp. 880-887
    • Ivanisenko, V.A.1    Eroshkin, A.M.2
  • 15
    • 0035882570 scopus 로고    scopus 로고
    • Prediction of protein interaction sites from sequence profile and residue neighbor list
    • Zhou,H.X. and Shan,Y. (2001) Prediction of protein interaction sites from sequence profile and residue neighbor list. Proteins, 44, 336-343.
    • (2001) Proteins , vol.44 , pp. 336-343
    • Zhou, H.X.1    Shan, Y.2
  • 16
    • 0031560777 scopus 로고    scopus 로고
    • Contact area difference (CAD): A robust measure to evaluate accuracy of protein models
    • Abagyan,R.A. and Totrov,M.M. (1997) Contact area difference (CAD): a robust measure to evaluate accuracy of protein models. J. Mol. Biol., 268, 678-685.
    • (1997) J. Mol. Biol. , vol.268 , pp. 678-685
    • Abagyan, R.A.1    Totrov, M.M.2
  • 17
    • 0011830097 scopus 로고
    • Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals
    • Yoshida,A., Huang,I.Y. and Ikawa,M. (1984) Molecular abnormality of an inactive aldehyde dehydrogenase variant commonly found in Orientals. Proc. Natl Acad. Sci. USA, 81, 258-261.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 258-261
    • Yoshida, A.1    Huang, I.Y.2    Ikawa, M.3
  • 19
    • 0026535237 scopus 로고
    • p53: A transdominant regulator of transcription whose function is ablated by mutations occurring in human cancer
    • Unger,T., Nau,M.M., Segal,S. and Minna,J.D. (1992) p53: a transdominant regulator of transcription whose function is ablated by mutations occurring in human cancer. EMBO J., 11, 1383-1390.
    • (1992) EMBO J. , vol.11 , pp. 1383-1390
    • Unger, T.1    Nau, M.M.2    Segal, S.3    Minna, J.D.4
  • 20
    • 0027983669 scopus 로고
    • Crystal structure of a p53 tumor suppressor-DNA complex: Understanding tumorigenic mutations
    • Cho,Y., Gorina,S., Jeffrey,P.D. and Pavletich,N.P. (1994) Crystal structure of a p53 tumor suppressor-DNA complex: understanding tumorigenic mutations. Science, 265, 346-355.
    • (1994) Science , vol.265 , pp. 346-355
    • Cho, Y.1    Gorina, S.2    Jeffrey, P.D.3    Pavletich, N.P.4
  • 23
    • 0034594995 scopus 로고    scopus 로고
    • Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: Definition of mutant states for rescue in cancer therapy
    • Bullock,A.N., Henckel,J. and Fersht,A.R. (2000) Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: definition of mutant states for rescue in cancer therapy. Oncogene, 19, 1245-1256.
    • (2000) Oncogene , vol.19 , pp. 1245-1256
    • Bullock, A.N.1    Henckel, J.2    Fersht, A.R.3
  • 24
    • 0344210364 scopus 로고    scopus 로고
    • Redox signaling and transition metals in the control of the p53 pathway
    • Meplan,C., Richard,M.-J. and Hainaut,P. (2000) Redox signaling and transition metals in the control of the p53 pathway. Biochem. Pharmacol., 59, 25-33.
    • (2000) Biochem. Pharmacol. , vol.59 , pp. 25-33
    • Meplan, C.1    Richard, M.-J.2    Hainaut, P.3
  • 25
    • 0037418548 scopus 로고    scopus 로고
    • Structure, function, and aggregation of the zinc-free form of the p53 DNA binding domain
    • Butler,J.S. and Loh,S.N. (2003) Structure, function, and aggregation of the zinc-free form of the p53 DNA binding domain. Biochemistry, 42, 2396-2403.
    • (2003) Biochemistry , vol.42 , pp. 2396-2403
    • Butler, J.S.1    Loh, S.N.2
  • 27
    • 0042622380 scopus 로고    scopus 로고
    • SWISS-MODEL: An automated protein homology-modeling server
    • Schwede,T., Kopp,J., Guex,N. and Peitsch,M.C. (2003) SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res., 31, 3381-3385.
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3381-3385
    • Schwede, T.1    Kopp, J.2    Guex, N.3    Peitsch, M.C.4
  • 30
    • 0035940421 scopus 로고    scopus 로고
    • THEMATICS: A simple computational predictor of enzyme function from structure
    • Ondrechen,M.J., Clifton,J.G. and Ringe,D. (2001) THEMATICS: a simple computational predictor of enzyme function from structure. Proc. Natl Acad. Sci. USA, 98, 12473-12478.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 12473-12478
    • Ondrechen, M.J.1    Clifton, J.G.2    Ringe, D.3
  • 31


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.