-
1
-
-
0035838976
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|