-
1
-
-
0346022974
-
Understanding protein-ligand interactions: The price of protein flexibility
-
Rauh, D.; Klebe, G.; Stubbs, M. T. Understanding protein-ligand interactions: the price of protein flexibility. J. Mol. Biol. 2004, 335 (5), 1325-1341.
-
(2004)
J. Mol. Biol
, vol.335
, Issue.5
, pp. 1325-1341
-
-
Rauh, D.1
Klebe, G.2
Stubbs, M.T.3
-
2
-
-
33745199815
-
Virtual ligand screening: Strategies, perspectives and limitations
-
Klebe, G. Virtual ligand screening: strategies, perspectives and limitations. Drug Discovery Today 2006, 11 (13), 580-594.
-
(2006)
Drug Discovery Today
, vol.11
, Issue.13
, pp. 580-594
-
-
Klebe, G.1
-
3
-
-
34250839499
-
How reliable are current docking approaches for structure-based drug design? Lessons from aldose reductase
-
Zentgraf, M.; Steuber, H.; Koch, C.; La Motta, C.; Sartini, S.; Sotriffer, C. A.; Klebe, G. How reliable are current docking approaches for structure-based drug design? Lessons from aldose reductase. Angew. Chem., Int. Ed. 2007, 46 (19), 3575-3578.
-
(2007)
Angew. Chem., Int. Ed
, vol.46
, Issue.19
, pp. 3575-3578
-
-
Zentgraf, M.1
Steuber, H.2
Koch, C.3
La Motta, C.4
Sartini, S.5
Sotriffer, C.A.6
Klebe, G.7
-
4
-
-
0035312864
-
Statistical potentials and scoring functions applied to protein-ligand binding
-
Gohlke, H.; Klebe, G. Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol. 2001, 11 (2), 231-235.
-
(2001)
Curr. Opin. Struct. Biol
, vol.11
, Issue.2
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
5
-
-
0025008445
-
Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force
-
Hendlich, M.; Lackner, P.; Weitckus, S.; Floeckner, H.; Froschauer, R.; Gottsbacher, K.; Casari, G.; Sippl, M. J. Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 1990, 216 (1), 167-180.
-
(1990)
J. Mol. Biol
, vol.216
, Issue.1
, pp. 167-180
-
-
Hendlich, M.1
Lackner, P.2
Weitckus, S.3
Floeckner, H.4
Froschauer, R.5
Gottsbacher, K.6
Casari, G.7
Sippl, M.J.8
-
6
-
-
0016885150
-
Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins
-
Tanaka, S.; Scheraga, H. A. Statistical mechanical treatment of protein conformation. I. Conformational properties of amino acids in proteins. Macromolecules 1976, 9 (1), 142-159.
-
(1976)
Macromolecules
, vol.9
, Issue.1
, pp. 142-159
-
-
Tanaka, S.1
Scheraga, H.A.2
-
7
-
-
0029119320
-
A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design
-
Wallqvist, A.; Jernigan, R. L.; Covell, D. G. A preference-based free-energy parameterization of enzyme-inhibitor binding. Applications to HIV-1-protease inhibitor design. Protein Sci. 1995, 4 (9), 1881-1903.
-
(1995)
Protein Sci
, vol.4
, Issue.9
, pp. 1881-1903
-
-
Wallqvist, A.1
Jernigan, R.L.2
Covell, D.G.3
-
8
-
-
0028881193
-
Empirical free energy calculations of ligand-protein cristallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity
-
Verkhivker, G.; Appelt, K.; Freer, S. T.; Villafranca, J. E. Empirical free energy calculations of ligand-protein cristallographic complexes. I. Knowledge-based ligand-protein interaction potentials applied to the prediction of human immunodeficiency virus 1 protease binding affinity. Protein Eng. 1995, 8 (7), 677-691.
-
(1995)
Protein Eng
, vol.8
, Issue.7
, pp. 677-691
-
-
Verkhivker, G.1
Appelt, K.2
Freer, S.T.3
Villafranca, J.E.4
-
9
-
-
0027166270
-
Empirical scale of side-chain conformational entropy in protein folding
-
Pickett, S. D.; Sternberg, M. J. Empirical scale of side-chain conformational entropy in protein folding. J. Mol. Biol. 1993, 231 (3), 825-839.
-
(1993)
J. Mol. Biol
, vol.231
, Issue.3
, pp. 825-839
-
-
Pickett, S.D.1
Sternberg, M.J.2
-
10
-
-
0026416668
-
Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects
-
Sharp, K. A.; Nicholls, A.; Fine, R. F.; Honig, B. Reconciling the magnitude of the microscopic and macroscopic hydrophobic effects. Science 1991, 252 (5002), 106-109.
-
(1991)
Science
, vol.252
, Issue.5002
, pp. 106-109
-
-
Sharp, K.A.1
Nicholls, A.2
Fine, R.F.3
Honig, B.4
-
11
-
-
0000934205
-
SMoG: De Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence
-
DeWitte, R. S.; Shakhnovich, E. I. SMoG: de Novo Design Method Based on Simple, Fast, and Accurate Free Energy Estimates. 1. Methodology and Supporting Evidence. J. Am. Chem. Soc. 1996, 118 (47), 11733-11744.
-
(1996)
J. Am. Chem. Soc
, vol.118
, Issue.47
, pp. 11733-11744
-
-
DeWitte, R.S.1
Shakhnovich, E.I.2
-
12
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42 (5), 791-804.
-
(1999)
J. Med. Chem
, vol.42
, Issue.5
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
13
-
-
0028304962
-
Satisfying hydrogen bonding potential in proteins
-
McDonald, I. K.; Thornton, J. M. Satisfying hydrogen bonding potential in proteins. J. Mol. Biol. 1994, 238 (5), 777-793.
-
(1994)
J. Mol. Biol
, vol.238
, Issue.5
, pp. 777-793
-
-
McDonald, I.K.1
Thornton, J.M.2
-
14
-
-
0000882405
-
BLEEP - potential of mean force describing protein-ligand interactions II: Calculation of binding energies and comparison with experimental data
-
Mitchell, J. B. O.; Laskowski, R. A.; Alexander, A.; Forster, M. J.; Thornton, J. M. BLEEP - potential of mean force describing protein-ligand interactions II: Calculation of binding energies and comparison with experimental data. J. Comput. Chem. 1999, 20(11), 1177-1185.
-
(1999)
J. Comput. Chem
, vol.20
, Issue.11
, pp. 1177-1185
-
-
Mitchell, J.B.O.1
Laskowski, R.A.2
Alexander, A.3
Forster, M.J.4
Thornton, J.M.5
-
15
-
-
0025770179
-
Modelling of solvent positions around polar groups in proteins
-
Pitt, W. R.; Goodfellow, J. M. Modelling of solvent positions around polar groups in proteins. Protein Eng. 1991, 4 (5), 531-537.
-
(1991)
Protein Eng
, vol.4
, Issue.5
, pp. 531-537
-
-
Pitt, W.R.1
Goodfellow, J.M.2
-
16
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol. 2000, 295 (2), 337-356.
-
(2000)
J. Mol. Biol
, vol.295
, Issue.2
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
17
-
-
0036780779
-
Information-theoretic dissection of pairwise contact potentials
-
Cline, S. M.; Karplus. K.; Lathrop. R.; Smith, T. F., Jr.; Haussler, D. Information-theoretic dissection of pairwise contact potentials. Proteins 2002, 49 (1), 7-14.
-
(2002)
Proteins
, vol.49
, Issue.1
, pp. 7-14
-
-
Cline, S.M.1
Karplus, K.2
Lathrop, R.3
Smith Jr., T.F.4
Haussler, D.5
-
18
-
-
0028857906
-
Perfect temperature for protein structure prediction and folding
-
Finkelstein, A. V.; Gutin, A. M.; Badretdinov, A. Y. Perfect temperature for protein structure prediction and folding. Proteins 1995, 23 (2), 151-162.
-
(1995)
Proteins
, vol.23
, Issue.2
, pp. 151-162
-
-
Finkelstein, A.V.1
Gutin, A.M.2
Badretdinov, A.Y.3
-
19
-
-
0033150685
-
Progress in protein structure prediction: Assessment of CASP3
-
Sternberg, M. J.; Bates, P. A.; Kelley, L. A.; MacCallum, R. M. Progress in protein structure prediction: assessment of CASP3. Curr. Opin. Struct. Biol. 1999, 9 (3), 368-373.
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, Issue.3
, pp. 368-373
-
-
Sternberg, M.J.1
Bates, P.A.2
Kelley, L.A.3
MacCallum, R.M.4
-
20
-
-
10044294023
-
An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes
-
Wang, R.; Lu, Y.; Fang, X.; Wang, S. An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. J. Chem. Inf. Comput. Sci. 2004, 44 (6), 2114-2125.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, Issue.6
, pp. 2114-2125
-
-
Wang, R.1
Lu, Y.2
Fang, X.3
Wang, S.4
-
21
-
-
0035175679
-
PDBsum: Summaries and analyses of PDB structures
-
Laskowski, R. A. PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res. 2001, 29 (1), 221-222.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 221-222
-
-
Laskowski, R.A.1
-
22
-
-
0030659457
-
PDBsum: A Web-based database of summaries and analyses of all PDB structures
-
Laskowski, R. A.; Hutchinson, E. G.; Michie, A. D.; Wallace, A. C.; Jones, M. L.; Thornton, J. M. PDBsum: a Web-based database of summaries and analyses of all PDB structures. Trends Biochem. Sci. 1997, 22 (12), 488-490.
-
(1997)
Trends Biochem. Sci
, vol.22
, Issue.12
, pp. 488-490
-
-
Laskowski, R.A.1
Hutchinson, E.G.2
Michie, A.D.3
Wallace, A.C.4
Jones, M.L.5
Thornton, J.M.6
-
23
-
-
13444254300
-
PDBsum more: New summaries and analyses of the known 3D structures of proteins and nucleic acids
-
database issue, D266-D268
-
Laskowski, R. A.; Chistyakov, V. V.; Thornton, J. M. PDBsum more: new summaries and analyses of the known 3D structures of proteins and nucleic acids. Nucleic Acids Res. 2005, 33 (database issue), D266-D268.
-
(2005)
Nucleic Acids Res
, vol.33
-
-
Laskowski, R.A.1
Chistyakov, V.V.2
Thornton, J.M.3
-
24
-
-
0033954256
-
The Protein Data Bank
-
Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. The Protein Data Bank. Nucleic Acids Res. 2000, 28 (1), 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
25
-
-
0028961335
-
SCOP: A structural classification of proteins database for the investigation of sequences and structures
-
Murzin, A. G.; Brenner, S. E.; Hubbard, T.; Chothia, C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 1995, 247 (4), 536-540.
-
(1995)
J. Mol. Biol
, vol.247
, Issue.4
, pp. 536-540
-
-
Murzin, A.G.1
Brenner, S.E.2
Hubbard, T.3
Chothia, C.4
-
26
-
-
0001094923
-
Carbonyl-Carbonyl Interactions can be Competitive with Hydrogen Bonds
-
Allen, F. H.; Baalham, C. A.; Lommerse, J. P. M.; Raithby, P. R. Carbonyl-Carbonyl Interactions can be Competitive with Hydrogen Bonds. Acta Crystallogr., Sect. B: Struct. Sci. 1998, 54 (3), 320-329.
-
(1998)
Acta Crystallogr., Sect. B: Struct. Sci
, vol.54
, Issue.3
, pp. 320-329
-
-
Allen, F.H.1
Baalham, C.A.2
Lommerse, J.P.M.3
Raithby, P.R.4
-
27
-
-
35248839997
-
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
-
Diago, L. A.; Morell, P.; Aguilera, L.; Moreno, E. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. BMC Bioinfo. 2007, 8, 310.
-
(2007)
BMC Bioinfo
, vol.8
, pp. 310
-
-
Diago, L.A.1
Morell, P.2
Aguilera, L.3
Moreno, E.4
-
28
-
-
0036533469
-
Geometric and chemical patterns of interaction in protein-ligand complexes and their application in docking
-
Moreno, E.; León, K. Geometric and chemical patterns of interaction in protein-ligand complexes and their application in docking. Proteins 2002, 47 (1), 1-13.
-
(2002)
Proteins
, vol.47
, Issue.1
, pp. 1-13
-
-
Moreno, E.1
León, K.2
-
29
-
-
0033674405
-
Virtual screening with solvation and ligand-induced complementarity
-
Schnecke, V.; Kuhn, L. A. Virtual screening with solvation and ligand-induced complementarity. Perspect. Drug Discovery Des. 2004, 20 (1), 171-190.
-
(2004)
Perspect. Drug Discovery Des
, vol.20
, Issue.1
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.A.2
-
30
-
-
0036284090
-
VEGA: A versatile program to convert, handle and visualize molecular structure on Windows-based PCs
-
Pedretti, A.; Villa, L.; Vistoli, G. VEGA: a versatile program to convert, handle and visualize molecular structure on Windows-based PCs. J. Mol. Graphics Model. 2002, 21 (1), 47-49.
-
(2002)
J. Mol. Graphics Model
, vol.21
, Issue.1
, pp. 47-49
-
-
Pedretti, A.1
Villa, L.2
Vistoli, G.3
-
31
-
-
4043162793
-
VEGA-an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming
-
Pedretti, A.; Villa, L.; Vistoli, G. VEGA-an open platform to develop chemo-bio-informatics applications, using plug-in architecture and script programming. J. Comput.-Aided. Mol. Des, 2004, 18 (3), 167-173.
-
(2004)
J. Comput.-Aided. Mol. Des
, vol.18
, Issue.3
, pp. 167-173
-
-
Pedretti, A.1
Villa, L.2
Vistoli, G.3
-
32
-
-
56449109005
-
Memoryless Finite Schemes
-
1st ed, Dover Publications: Mineola, NY
-
Reza, F. Memoryless Finite Schemes. In An Introduction to Information Theory, 1st ed.; Dover Publications: Mineola, NY, 1994; Vol. 1, pp 104-106.
-
(1994)
An Introduction to Information Theory
, vol.1
, pp. 104-106
-
-
Reza, F.1
-
33
-
-
84856043672
-
A Mathematical Theory of Communication
-
Shannon, C. E. A Mathematical Theory of Communication. The Bell System Tech. J. 1948, 27 (4), 623-656.
-
(1948)
The Bell System Tech. J
, vol.27
, Issue.4
, pp. 623-656
-
-
Shannon, C.E.1
-
34
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk, M. L.; Cole, J. C.; Hartshorn, M. J.; Murray, C. W.; Taylor, R. D. Improved protein-ligand docking using GOLD. Proteins 2003, 52 (4), 609-623.
-
(2003)
Proteins
, vol.52
, Issue.4
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
35
-
-
56449111805
-
-
accessed July 26, 2007
-
Ladbury, J. E. Scorpio Database, http://www.biochem.ucl.ac.uk/scorpio/ scorpio.html(accessed July 26, 2007).
-
Database
-
-
Ladbury, J.1
Scorpio, E.2
-
36
-
-
0035171884
-
BIND-The Biomolecular Interaction Network Database
-
Bader, G. D.; Donaldson, I.; Wolting, C.; Ouellette, B. F.; Pawson, T.; Hogue, C. W. BIND-The Biomolecular Interaction Network Database. Nucleic Acids Res. 2001, 29 (1), 242-245.
-
(2001)
Nucleic Acids Res
, vol.29
, Issue.1
, pp. 242-245
-
-
Bader, G.D.1
Donaldson, I.2
Wolting, C.3
Ouellette, B.F.4
Pawson, T.5
Hogue, C.W.6
-
37
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking. J. Med. Chem. 2006, 49 (23), 6789-6801.
-
(2006)
J. Med. Chem
, vol.49
, Issue.23
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
38
-
-
33644862638
-
Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring
-
Zhang, Q. M. I. Scaffold Hopping through Virtual Screening Using 2D and 3D Similarity Descriptors: Ranking, Voting, and Consensus Scoring. J. Med. Chem. 2006, 49 (5), 1536-1548.
-
(2006)
J. Med. Chem
, vol.49
, Issue.5
, pp. 1536-1548
-
-
Zhang, Q.M.I.1
-
39
-
-
0037434582
-
Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine
-
Jain, A. N. Surflex: Fully Automatic Flexible Molecular Docking Using a Molecular Similarity-Based Search Engine. J. Med. Chem. 2003, 46 (4), 499-511.
-
(2003)
J. Med. Chem
, vol.46
, Issue.4
, pp. 499-511
-
-
Jain, A.N.S.1
-
40
-
-
0034332970
-
DARWIN: A program for docking flexible molecules
-
Taylor, J. S.; Burnett, R. M. DARWIN: a program for docking flexible molecules. Proteins 2000, 41 (2), 173-191.
-
(2000)
Proteins
, vol.41
, Issue.2
, pp. 173-191
-
-
Taylor, J.S.1
Burnett, R.M.2
-
41
-
-
10244252834
-
Predicting protein-ligand binding affinities: A low scoring game
-
Marsden, P. M.; Puvanendrampillai, D.; Mitchell, J. B. O.; Glen, R. C. Predicting protein-ligand binding affinities: a low scoring game. Org. Biomol. Chem. 2004, 2, 3267-3273.
-
(2004)
Org. Biomol. Chem
, vol.2
, pp. 3267-3273
-
-
Marsden, P.M.1
Puvanendrampillai, D.2
Mitchell, J.B.O.3
Glen, R.C.4
-
42
-
-
0033451033
-
Estimating binding constants - The hydrophobic effect and cooperativity
-
Williams, D. H.; Bardsley, B. Estimating binding constants - The hydrophobic effect and cooperativity. Perspect. Drug Discovery Des. 1999, 17 (1), 43-59.
-
(1999)
Perspect. Drug Discovery Des
, vol.17
, Issue.1
, pp. 43-59
-
-
Williams, D.H.1
Bardsley, B.2
|