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Volumn 21, Issue 9, 2005, Pages 1908-1916

Q-SiteFinder: An energy-based method for the prediction of protein-ligand binding sites

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

EID: 18744394070     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti315     Document Type: Article
Times cited : (884)

References (47)
  • 1
    • 0035838976 scopus 로고    scopus 로고
    • Automated structure-based prediction of functional sites in proteins: Applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking
    • Aloy,P. et al. (2001) Automated structure-based prediction of functional sites in proteins: applications to assessing the validity of inheriting protein function from homology in genome annotation and to protein docking. J. Mol. Biol., 311, 395-408.
    • (2001) J. Mol. Biol. , vol.311 , pp. 395-408
    • Aloy, P.1
  • 2
    • 0035896024 scopus 로고    scopus 로고
    • ConSurf: An algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information
    • Armon,A. et al. (2001) ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J. Mol. Biol., 307, 447-463.
    • (2001) J. Mol. Biol. , vol.307 , pp. 447-463
    • Armon, A.1
  • 3
    • 0027967593 scopus 로고
    • A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures
    • Artymiuk,P.J. et al. (1994) A graph-theoretic approach to the identification of three-dimensional patterns of amino acid side-chains in protein structures. J. Mol. Biol., 243, 327-344.
    • (1994) J. Mol. Biol. , vol.243 , pp. 327-344
    • Artymiuk, P.J.1
  • 4
    • 2942517681 scopus 로고    scopus 로고
    • Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods
    • Bate,P. and Warwicker,J. (2004) Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods. J. Mol. Biol., 340, 263-276.
    • (2004) J. Mol. Biol. , vol.340 , pp. 263-276
    • Bate, P.1    Warwicker, J.2
  • 5
    • 0033954256 scopus 로고    scopus 로고
    • The Protein Data Bank
    • Berman,H.M. et al. (2000) The Protein Data Bank. Nucleic Acids Res., 28, 235-242.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 235-242
    • Berman, H.M.1
  • 6
    • 0031197206 scopus 로고    scopus 로고
    • Modern computational chemistry and drug discovery: Structure generating programs
    • Bohacek,R.S. and McMartin,C. (1997) Modern computational chemistry and drug discovery: structure generating programs. Curr. Opin. Chem. Biol., 1, 157-161.
    • (1997) Curr. Opin. Chem. Biol. , vol.1 , pp. 157-161
    • Bohacek, R.S.1    McMartin, C.2
  • 7
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • 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.
    • (2000) J. Comput. Aided Mol. Des. , vol.14 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.2
  • 8
    • 0038169950 scopus 로고    scopus 로고
    • Ligand binding: Functional site location, similarity and docking
    • Campbell,S.J. et al. (2003) Ligand binding: functional site location, similarity and docking. Curr. Opin. Struct. Biol., 13, 389-395.
    • (2003) Curr. Opin. Struct. Biol. , vol.13 , pp. 389-395
    • Campbell, S.J.1
  • 9
    • 0027943157 scopus 로고
    • Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases
    • Chen,Z. et al. (1994) Crystal structure at 1.9-Å resolution of human immunodeficiency virus (HIV) II protease complexed with L-735,524, an orally bioavailable inhibitor of the HIV proteases. J. Biol. Chem., 269, 26344-26348.
    • (1994) J. Biol. Chem. , vol.269 , pp. 26344-26348
    • Chen, Z.1
  • 10
    • 0027509724 scopus 로고
    • A new approach to the automatic identification of candidates for ligand receptor sites in proteins: (I). Search for pocket regions
    • Del Carpio,C.A. et al. (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.
    • (1993) J. Mol. Graph , vol.11 , pp. 23-29
    • Del Carpio, C.A.1
  • 11
    • 0026787207 scopus 로고
    • Finding and filling protein cavities using cellular logic operations
    • Delaney,J.S. (1992) Finding and filling protein cavities using cellular logic operations. J. Mol. Graph, 10, 174-177.
    • (1992) J. Mol. Graph , vol.10 , pp. 174-177
    • Delaney, J.S.1
  • 12
    • 9144231249 scopus 로고    scopus 로고
    • E-MSD: An integrated data resource for bioinformatics
    • Database issue
    • Golovin,A. et al. (2004) E-MSD: an integrated data resource for bioinformatics. Nucleic Acids Res., 32 (Database issue), D211-D216.
    • (2004) Nucleic Acids Res. , vol.32
    • Golovin, A.1
  • 13
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • Goodford,P.J. (1985) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 28, 849-857.
    • (1985) J. Med. Chem. , vol.28 , pp. 849-857
    • Goodford, P.J.1
  • 14
    • 0027476367 scopus 로고
    • The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30->Met variant to 1.7-Å resolution
    • Hamilton,J.A. et al. (1993) The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30->Met variant to 1.7-Å resolution. J. Biol. Chem., 268, 2416-2424.
    • (1993) J. Biol. Chem. , vol.268 , pp. 2416-2424
    • Hamilton, J.A.1
  • 15
    • 0032214649 scopus 로고    scopus 로고
    • Databases for protein-ligand complexes
    • Hendlich,M. (1998) Databases for protein-ligand complexes. Acta Crystallogr. D, 54, 1178-1182.
    • (1998) Acta Crystallogr. D , vol.54 , pp. 1178-1182
    • Hendlich, M.1
  • 16
    • 0031370977 scopus 로고    scopus 로고
    • LIGSITE: Automatic and efficient detection of potential small molecule-binding sites in proteins
    • Hendlich,M. et al. (1997) LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins. J. Mol. Graph Model, 15, 359-363.
    • (1997) J. Mol. Graph Model , vol.15 , pp. 359-363
    • Hendlich, M.1
  • 17
    • 0032169688 scopus 로고    scopus 로고
    • PQS: A protein quaternary structure file server
    • Henrick,K. and Thornton,J.M. (1998) PQS: a protein quaternary structure file server. Trends Biochem. Sci., 23, 358-361.
    • (1998) Trends Biochem. Sci. , vol.23 , pp. 358-361
    • Henrick, K.1    Thornton, J.M.2
  • 18
    • 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
  • 19
    • 0041418274 scopus 로고    scopus 로고
    • Recent advances in de novo design strategy for practical lead identification
    • Honma,T. (2003) Recent advances in de novo design strategy for practical lead identification. Med. Res. Rev., 23, 606-632.
    • (2003) Med. Res. Rev. , vol.23 , pp. 606-632
    • Honma, T.1
  • 20
    • 0036022961 scopus 로고    scopus 로고
    • Q-fit: A probabilistic method for docking molecular fragments by sampling low energy conformational space
    • Jackson,R.M. (2002) Q-fit: a probabilistic method for docking molecular fragments by sampling low energy conformational space. J. Comput. Aided Mol. Des., 16, 43-57.
    • (2002) J. Comput. Aided Mol. Des. , vol.16 , pp. 43-57
    • Jackson, R.M.1
  • 21
    • 0032512619 scopus 로고    scopus 로고
    • Rapid refinement of protein interfaces incorporating solvation: Application to the docking problem
    • Jackson,R.M. et al. (1998) Rapid refinement of protein interfaces incorporating solvation: application to the docking problem. J. Mol. Biol., 276, 265-285.
    • (1998) J. Mol. Biol. , vol.276 , pp. 265-285
    • Jackson, R.M.1
  • 22
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • Jain,A.N. (1996) Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. J. Comput. Aided Mol. Des., 10, 427-440.
    • (1996) J. Comput. Aided Mol. Des. , vol.10 , pp. 427-440
    • Jain, A.N.1
  • 23
    • 0027995683 scopus 로고
    • Detection, delineation, measurement and display of cavities in macromolecular structures
    • Kleywegt,G.J. (1994) Detection, delineation, measurement and display of cavities in macromolecular structures. Acta Crystallogr. D, 50, 178-185.
    • (1994) Acta Crystallogr. D , vol.50 , pp. 178-185
    • Kleywegt, G.J.1
  • 24
    • 0035853280 scopus 로고    scopus 로고
    • Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins
    • Landgraf,R. et al. (2001) Three-dimensional cluster analysis identifies interfaces and functional residue clusters in proteins. J. Mol. Biol., 307, 1487-1502.
    • (2001) J. Mol. Biol. , vol.307 , pp. 1487-1502
    • Landgraf, R.1
  • 25
    • 0028881975 scopus 로고
    • SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions
    • Laskowski,R.A. (1995) SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. J. Mol. Graph, 13, 323-330.
    • (1995) J. Mol. Graph , vol.13 , pp. 323-330
    • Laskowski, R.A.1
  • 26
    • 0030447531 scopus 로고    scopus 로고
    • Protein clefts in molecular recognition and function
    • Laskowski,R.A. et al. (1996) Protein clefts in molecular recognition and function. Protein Sci., 5, 2438-2452.
    • (1996) Protein Sci. , vol.5 , pp. 2438-2452
    • Laskowski, R.A.1
  • 27
    • 0027053611 scopus 로고
    • POCKET: A computer graphics method for identifying and displaying protein cavities and their surrounding amino acids
    • 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.
    • (1992) J. Mol. Graph , vol.10 , pp. 229-234
    • Levitt, D.G.1    Banaszak, L.J.2
  • 28
    • 0031687653 scopus 로고    scopus 로고
    • Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design
    • Liang,J. et al. (1998) Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci., 7, 1884-1897.
    • (1998) Protein Sci. , vol.7 , pp. 1884-1897
    • Liang, J.1
  • 29
    • 0029913807 scopus 로고    scopus 로고
    • An evolutionary trace method defines binding surfaces common to protein families
    • Lichtarge,O. et al. (1996) An evolutionary trace method defines binding surfaces common to protein families. J. Mol. Biol., 257, 342-358.
    • (1996) J. Mol. Biol. , vol.257 , pp. 342-358
    • Lichtarge, O.1
  • 30
    • 0029550088 scopus 로고
    • Detection and geometric modeling of molecular surfaces and cavities using digital mathematical morphological operations
    • 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.
    • (1995) J. Mol. Graph , vol.13 , pp. 331-336
    • Masuya, M.1    Doi, J.2
  • 31
    • 0028181134 scopus 로고
    • Crystal structures of soybean beta-amylase reacted with betamaltose and maltal: Active site components and their apparent roles in catalysis
    • Mikami,B. et al. (1994) Crystal structures of soybean beta-amylase reacted with betamaltose and maltal: active site components and their apparent roles in catalysis. Biochemistry, 33, 7779-7787.
    • (1994) Biochemistry , vol.33 , pp. 7779-7787
    • Mikami, B.1
  • 32
    • 0025916872 scopus 로고
    • Functionality maps of binding sites: A multiple copy simultaneous search method
    • Miranker,A. and Karplus,M. (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins, 11, 29-34.
    • (1991) Proteins , vol.11 , pp. 29-34
    • Miranker, A.1    Karplus, M.2
  • 33
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin,A.G. et al. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1
  • 34
    • 0013133162 scopus 로고    scopus 로고
    • A new test set for validating predictions of protein-ligand interaction
    • Nissink,J.W. et al. (2002) A new test set for validating predictions of protein-ligand interaction. Proteins, 49, 457-471.
    • (2002) Proteins , vol.49 , pp. 457-471
    • Nissink, J.W.1
  • 35
    • 0029935202 scopus 로고    scopus 로고
    • The automatic search for ligand binding sites in proteins of known three-dimensional structure using only geometric criteria
    • Peters,K.P. et al. (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.
    • (1996) J. Mol. Biol. , vol.256 , pp. 201-213
    • Peters, K.P.1
  • 36
    • 0029197510 scopus 로고
    • Time-efficient docking of flexible ligands into active sites of proteins
    • Rarey,M. et al. (1995) Time-efficient docking of flexible ligands into active sites of proteins. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 300-308.
    • (1995) Proc. Int. Conf. Intell. Syst. Mol. Biol. , vol.3 , pp. 300-308
    • Rarey, M.1
  • 37
    • 0030979125 scopus 로고    scopus 로고
    • Automatic identification and representation of protein binding sites for molecular docking
    • Ruppert,J. et al. (1997) Automatic identification and representation of protein binding sites for molecular docking. Protein Sci., 6, 524-533.
    • (1997) Protein Sci. , vol.6 , pp. 524-533
    • Ruppert, J.1
  • 38
    • 0036406643 scopus 로고    scopus 로고
    • A new method to detect related function among proteins independent of sequence and fold homology
    • Schmitt,S. et al. (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
  • 39
    • 0042386537 scopus 로고    scopus 로고
    • Identification of substrate binding sites in enzymes by computational solvent mapping
    • Silberstein,M. et al. (2003) Identification of substrate binding sites in enzymes by computational solvent mapping. J. Mol. Biol., 332, 1095-1113.
    • (2003) J. Mol. Biol. , vol.332 , pp. 1095-1113
    • Silberstein, M.1
  • 40
    • 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
  • 41
    • 0029643790 scopus 로고
    • Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere
    • Tong,L. et al. (1995) Crystal structures of HIV-2 protease in complex with inhibitors containing the hydroxyethylamine dipeptide isostere. Structure, 3, 33-40.
    • (1995) Structure , vol.3 , pp. 33-40
    • Tong, L.1
  • 42
    • 0033520936 scopus 로고    scopus 로고
    • The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-Å resolution
    • Uitdehaag,J.C. et al. (1999) The cyclization mechanism of cyclodextrin glycosyltransferase (CGTase) as revealed by a gamma-cyclodextrin-CGTase complex at 1.8-Å resolution. J. Biol. Chem., 274, 34868-34876.
    • (1999) J. Biol. Chem. , vol.274 , pp. 34868-34876
    • Uitdehaag, J.C.1
  • 43
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • Venkatachalam,C.M. et al. (2003) LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph Model, 21, 289-307.
    • (2003) J. Mol. Graph Model , vol.21 , pp. 289-307
    • Venkatachalam, C.M.1
  • 44
    • 0035970295 scopus 로고    scopus 로고
    • SuperStar: Improved knowledge-based interaction fields for protein binding sites
    • Verdonk,M.L. et al. (2001) SuperStar: improved knowledge-based interaction fields for protein binding sites. J. Mol. Biol., 307, 841-859.
    • (2001) J. Mol. Biol. , vol.307 , pp. 841-859
    • Verdonk, M.L.1
  • 45
    • 0024583269 scopus 로고
    • The role of hydrogen-bonds in drug binding
    • Wade,R.C. and Goodford,P.J. (1989) The role of hydrogen-bonds in drug binding. Prog. Clin. Biol. Res., 289, 433-444.
    • (1989) Prog. Clin. Biol. Res. , vol.289 , pp. 433-444
    • Wade, R.C.1    Goodford, P.J.2
  • 46
    • 0027439587 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
    • Wade,R.C. et al. (1993) Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds. J. Med. Chem., 36, 140-147.
    • (1993) J. Med. Chem. , vol.36 , pp. 140-147
    • Wade, R.C.1
  • 47
    • 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. et al. (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


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