메뉴 건너뛰기




Volumn 39, Issue SUPPL. 2, 2011, Pages

DEPTH: A web server to compute depth and predict small-molecule binding cavities in proteins

Author keywords

[No Author keywords available]

Indexed keywords

ACCURACY; ANALYTIC METHOD; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPUTER PREDICTION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DATA ANALYSIS SOFTWARE; INTERNET; LIGAND BINDING; PERFORMANCE MEASUREMENT SYSTEM; PREDICTIVE VALUE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; RESIDUE ANALYSIS; SOLVENT EFFECT; STRUCTURE ANALYSIS; WEB BROWSER; X RAY CRYSTALLOGRAPHY;

EID: 79959937283     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkr356     Document Type: Article
Times cited : (82)

References (34)
  • 1
    • 0033565815 scopus 로고    scopus 로고
    • Residue depth: A novel parameter for the analysis of protein structure and stability
    • DOI 10.1016/S0969-2126(99)80097-5
    • Chakravarty, S. and Varadarajan, R. (1999) Residue depth: a novel parameter for the analysis of protein structure and stability. Structure, 7, 723-732. (Pubitemid 29329844)
    • (1999) Structure , vol.7 , Issue.7 , pp. 723-732
    • Chakravarty, S.1    Varadarajan, R.2
  • 2
    • 0015222647 scopus 로고
    • The interpretation of protein structures: Estimation of static accessibility
    • Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
    • (1971) J. Mol. Biol. , vol.55 , pp. 379-400
    • Lee, B.1    Richards, F.M.2
  • 4
    • 0037382258 scopus 로고    scopus 로고
    • Atom depth as a descriptor of the protein interior
    • Pintar, A., Carugo, O. and Pongor, S. (2003) Atom depth as a descriptor of the protein interior. Biophys. J., 84, 2553-2561. (Pubitemid 36373575)
    • (2003) Biophysical Journal , vol.84 , Issue.4 , pp. 2553-2561
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 5
    • 1542606700 scopus 로고    scopus 로고
    • Atom depth in protein structure and function
    • DOI 10.1016/j.tibs.2003.09.004, PII S0968000403002287
    • Pintar, A., Carugo, O. and Pongor, S. (2003) Atom depth in protein structure and function. Trends Biochem. Sci., 28, 593-597. (Pubitemid 38352805)
    • (2003) Trends in Biochemical Sciences , vol.28 , Issue.11 , pp. 593-597
    • Pintar, A.1    Carugo, O.2    Pongor, S.3
  • 6
    • 24644448786 scopus 로고    scopus 로고
    • The "first in-last out" hypothesis on protein folding revisited
    • DOI 10.1002/prot.20529
    • Pintar, A. and Pongor, S. (2005) The 'first in-last out' hypothesis on protein folding revisited. Proteins, 60, 584-590. (Pubitemid 41266416)
    • (2005) Proteins: Structure, Function and Genetics , vol.60 , Issue.4 , pp. 584-590
    • Pintar, A.1    Pongor, S.2
  • 7
    • 21044444449 scopus 로고    scopus 로고
    • Pocketome via comprehensive identification and classification of ligand binding envelopes
    • DOI 10.1074/mcp.M400159-MCP200
    • An, J., Totrov, M. and Abagyan, R. (2005) Pocketome via comprehensive identification and classification of ligand binding envelopes. Mol. Cell. Proteomics, 4, 752-761. (Pubitemid 40873004)
    • (2005) Molecular and Cellular Proteomics , vol.4 , Issue.6 , pp. 752-761
    • An, J.1    Totrov, M.2    Abagyan, R.3
  • 8
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • DOI 10.1023/A:1008124202956
    • Brady, G.P. Jr. and Stouten, P.F. (2000) Fast prediction and visualization of protein binding pockets with PASS. J. Comput. Aided Mol. Des., 14, 383-401. (Pubitemid 30219399)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.W.2
  • 9
    • 74549149999 scopus 로고    scopus 로고
    • Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure
    • Capra, J.A., Laskowski, R.A., Thornton, J.M., Singh, M. and Funkhouser, T.A. (2009) Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure. PLoS Comput. Biol., 5, e1000585.
    • (2009) PLoS Comput. Biol. , vol.5
    • Capra, J.A.1    Laskowski, R.A.2    Thornton, J.M.3    Singh, M.4    Funkhouser, T.A.5
  • 10
    • 0027509724 scopus 로고
    • A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I) Search for pocket regions
    • DOI 10.1016/0263-7855(93)85003-9
    • Del Carpio, C.A., Takahashi, Y. and Sasaki, S. (1993) A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I). Search for pocket regions. J. Mol. Graph., 11, 23-29, 42. (Pubitemid 23103812)
    • (1993) Journal of Molecular Graphics , vol.11 , Issue.1 , pp. 23-29
    • Del Carpio, C.A.1    Takahashi, Y.2    Sasaki, S.3
  • 11
    • 0026787207 scopus 로고
    • Finding and filling protein cavities using cellular logic operations
    • 163
    • Delaney, J.S. (1992) Finding and filling protein cavities using cellular logic operations. J. Mol. Graph., 10, 174-177, 163.
    • (1992) J. Mol. Graph. , vol.10 , pp. 174-177
    • Delaney, J.S.1
  • 12
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • DOI 10.1016/S1093-3263(98)00002-3, PII S1093326398000023
    • Hendlich, M., Rippmann, F. and Barnickel, G. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph. Model., 15, 359-363, 389. (Pubitemid 28409807)
    • (1997) Journal of Molecular Graphics and Modelling , vol.15 , Issue.6 , pp. 359-363
    • Hendlich, M.1    Rippmann, F.2    Barnickel, G.3
  • 13
    • 0025656474 scopus 로고
    • Cavity search: An algorithm for the isolation and display of cavity-like binding regions
    • Ho, C.M. and Marshall, G.R. (1990) Cavity search: an algorithm for the isolation and display of cavity-like binding regions. J. Comput. Aided Mol. Des., 4, 337-354.
    • (1990) J. Comput. Aided Mol. Des. , vol.4 , pp. 337-354
    • Ho, C.M.1    Marshall, G.R.2
  • 14
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • DOI 10.1107/S0907444993011333
    • Kleywegt, G.J. and Jones, T.A. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D Biol. Crystallogr., 50, 178-185. (Pubitemid 2054290)
    • (1994) Acta Crystallographica Section D: Biological Crystallography , vol.50 , Issue.2 , pp. 178-185
    • Kleywegt, G.J.1    Alwyn Jones, T.2
  • 15
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces cavities, and intermolecular interactions
    • 307-328
    • Laskowski, R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph., 13, 323-330, 307-328.
    • (1995) J. Mol. Graph. , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 16
    • 18744394070 scopus 로고    scopus 로고
    • Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites
    • DOI 10.1093/bioinformatics/bti315
    • Laurie, A.T. and Jackson, R.M. (2005) Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites. Bioinformatics, 21, 1908-1916. (Pubitemid 40668026)
    • (2005) Bioinformatics , vol.21 , Issue.9 , pp. 1908-1916
    • Laurie, A.T.R.1    Jackson, R.M.2
  • 17
    • 67649422714 scopus 로고    scopus 로고
    • Fpocket: An open source platform for ligand pocket detection
    • Le Guilloux, V., Schmidtke, P. and Tuffery, P. (2009) Fpocket: an open source platform for ligand pocket detection. BMC Bioinformatics, 10, 168.
    • (2009) BMC Bioinformatics , vol.10 , pp. 168
    • Le Guilloux, V.1    Schmidtke, P.2    Tuffery, P.3
  • 18
    • 0027053611 scopus 로고
    • POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • DOI 10.1016/0263-7855(92)80074-N
    • Levitt, D.G. and Banaszak, L.J. (1992) POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids. J. Mol. Graph., 10, 229-234. (Pubitemid 23018967)
    • (1992) Journal of Molecular Graphics , vol.10 , Issue.4 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 19
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang, J., Edelsbrunner, H. and Woodward, C. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884-1897. (Pubitemid 28432430)
    • (1998) Protein Science , vol.7 , Issue.9 , pp. 1884-1897
    • Liang, J.1    Edelsbrunner, H.2    Woodward, C.3
  • 20
    • 0029550088 scopus 로고
    • Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations
    • DOI 10.1016/0263-7855(95)00071-2
    • Masuya, M. and Doi, J. (1995) Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations. J. Mol. Graph., 13, 331-336. (Pubitemid 26089613)
    • (1995) Journal of Molecular Graphics , vol.13 , Issue.6 , pp. 331-336
    • Masuya, M.1    Doi, J.2
  • 21
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • DOI 10.1006/jmbi.1996.0077
    • Peters, K.P., Fauck, J. and Frommel, C. (1996) The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria. J. Mol. Biol., 256, 201-213. (Pubitemid 26104219)
    • (1996) Journal of Molecular Biology , vol.256 , Issue.1 , pp. 201-213
    • Peters, K.P.1    Fauck, J.2    Frommel, C.3
  • 22
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • DOI 10.1016/S1093-3263(02)00164-X, PII S109332630200164X
    • Venkatachalam, C.M., Jiang, X., Oldfield, T. and Waldman, M. (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model., 21, 289-307. (Pubitemid 35441326)
    • (2003) Journal of Molecular Graphics and Modelling , vol.21 , Issue.4 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 23
    • 34547341277 scopus 로고    scopus 로고
    • Pocket Picker: Analysis of ligand binding-sites with shape descriptors
    • Weisel, M., Proschak, E. and Schneider, G. (2007) PocketPicker: analysis of ligand binding-sites with shape descriptors. Chem. Cent. J., 1, 7.
    • (2007) Chem. Cent. J. , vol.1 , pp. 7
    • Weisel, M.1    Proschak, E.2    Schneider, G.3
  • 24
    • 77953504480 scopus 로고    scopus 로고
    • In silico prediction of binding sites on proteins
    • Leis, S., Schneider, S. and Zacharias, M. (2010) In silico prediction of binding sites on proteins. Curr. Med. Chem., 17, 1550-1562.
    • (2010) Curr. Med. Chem. , vol.17 , pp. 1550-1562
    • Leis, S.1    Schneider, S.2    Zacharias, M.3
  • 28
    • 0015866154 scopus 로고
    • Environment and exposure to solvent of protein atoms Lysozyme and insulin
    • Shrake, A. and Rupley, J.A. (1973) Environment and exposure to solvent of protein atoms. Lysozyme and insulin. J. Mol. Biol., 79, 351-371.
    • (1973) J. Mol. Biol. , vol.79 , pp. 351-371
    • Shrake, A.1    Rupley, J.A.2
  • 29
    • 0000338489 scopus 로고
    • Comparison of solvent-inaccessible cores of homologous proteins: Definitions useful for protein modelling
    • Hubbard, T.J. and Blundell, T.L. (1987) Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling. Protein Eng., 1, 159-171. (Pubitemid 18025225)
    • (1987) Protein Engineering , vol.1 , Issue.3 , pp. 159-171
    • Hubbard, T.J.P.1    Blundell, T.L.2
  • 31
    • 38549088882 scopus 로고    scopus 로고
    • LigASite - A database of biologically relevant binding sites in proteins with known apo-structures
    • DOI 10.1093/nar/gkm839
    • Dessailly, B.H., Lensink, M.F., Orengo, C.A. and Wodak, S.J. (2008) LigASite-a database of biologically relevant binding sites in proteins with known apo-structures. Nucleic Acids Res., 36, D667-D673. (Pubitemid 351149804)
    • (2008) Nucleic Acids Research , vol.36 , Issue.SUPPL. 1
    • Dessailly, B.H.1    Lensink, M.F.2    Orengo, C.A.3    Wodak, S.J.4
  • 32
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • DOI 10.1016/S0968-0004(98)01253-5, PII S0968000498012535
    • Henrick, K. and Thornton, J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361. (Pubitemid 28461869)
    • (1998) Trends in Biochemical Sciences , vol.23 , Issue.9 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 33
    • 0016772212 scopus 로고
    • Comparison of the predicted and observed secondary structure of T4 phage lysozyme
    • Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
    • (1975) Biochim. Biophys. Acta , vol.405 , pp. 442-451
    • Matthews, B.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.