-
1
-
-
85135598766
-
-
Mancera, R. L. De novo Ligand Design with Explicit Water Molecules: An Application to Bacterial Neuraminidase. J. Comput.-Aided Mol. Des. 2002, 16, 479-499.
-
Mancera, R. L. De novo Ligand Design with Explicit Water Molecules: An Application to Bacterial Neuraminidase. J. Comput.-Aided Mol. Des. 2002, 16, 479-499.
-
-
-
-
2
-
-
0027587199
-
Structural Analysis of MHC Class I Molecules with Bound Peptide Antigens
-
Wilson, I. A.; Fremont, D. H. Structural Analysis of MHC Class I Molecules with Bound Peptide Antigens. Semin. Immunol. 1993, 5, 75-80.
-
(1993)
Semin. Immunol
, vol.5
, pp. 75-80
-
-
Wilson, I.A.1
Fremont, D.H.2
-
3
-
-
0031008974
-
Mean Field Analysis of FKBP12 Complexes with FK506 and Rapamycin: Implications for a Role of Crystallographic Water Molecules in Molecular Recognition and Specificity
-
Rejto, P. A.; Verkhivker, G. M. Mean Field Analysis of FKBP12 Complexes with FK506 and Rapamycin: Implications for a Role of Crystallographic Water Molecules in Molecular Recognition and Specificity. Proteins 1997, 28, 313-324.
-
(1997)
Proteins
, vol.28
, pp. 313-324
-
-
Rejto, P.A.1
Verkhivker, G.M.2
-
4
-
-
0033550314
-
Novel Aromatic Inhibitors of Influenza Virus Neuraminidase Make Selective Interactions with Conserved Residues and Water Molecules in the Active Site
-
Finley, J. B.; Atigadda, V. R.; Duarte, F.; Zhao, J. J.; Brouillette, M. J.; Air, G. M.; Luo, M. Novel Aromatic Inhibitors of Influenza Virus Neuraminidase Make Selective Interactions with Conserved Residues and Water Molecules in the Active Site. J. Mol. Biol. 1999, 293, 1107-1119.
-
(1999)
J. Mol. Biol
, vol.293
, pp. 1107-1119
-
-
Finley, J.B.1
Atigadda, V.R.2
Duarte, F.3
Zhao, J.J.4
Brouillette, M.J.5
Air, G.M.6
Luo, M.7
-
5
-
-
0342803187
-
Modeling Cyclooxygenase Inhibition. Implication of Active Site Hydration on the Selectivity of Ketoprofen Analogues
-
Palomer, A.; Perez, J. J.; Navea, S.; Llorens, O.; Pascual, J.; Garcia, L.; Mauleon, D. Modeling Cyclooxygenase Inhibition. Implication of Active Site Hydration on the Selectivity of Ketoprofen Analogues. J. Med. Chem. 2000, 43, 2280-2284.
-
(2000)
J. Med. Chem
, vol.43
, pp. 2280-2284
-
-
Palomer, A.1
Perez, J.J.2
Navea, S.3
Llorens, O.4
Pascual, J.5
Garcia, L.6
Mauleon, D.7
-
6
-
-
0028856716
-
Water Molecules Participate in Proteinase-Inhibitor Interactions: Crystal Structure of Leu18, Ala18, and Gly18 Variants of Turkey Ovomucoid Inhibitor Third Domain Complexed with Streptomyces griseus Proteinase B
-
Huang, K.; Lu, W.; Anderson, S.; Laskowski, M.; James, M. N. G. Water Molecules Participate in Proteinase-Inhibitor Interactions: Crystal Structure of Leu18, Ala18, and Gly18 Variants of Turkey Ovomucoid Inhibitor Third Domain Complexed with Streptomyces griseus Proteinase B. Protein Sci. 1995, 4, 1985-1997.
-
(1995)
Protein Sci
, vol.4
, pp. 1985-1997
-
-
Huang, K.1
Lu, W.2
Anderson, S.3
Laskowski, M.4
James, M.N.G.5
-
7
-
-
0032811591
-
Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein
-
Sleigh, S. H.; Seavers, P. R.; Wilkinson, A. J.; Ladbury, J. E.; Tame, J. R. H. Crystallographic and Calorimetric Analysis of Peptide Binding to OppA Protein. J. Mol. Biol. 1999, 291, 393-415.
-
(1999)
J. Mol. Biol
, vol.291
, pp. 393-415
-
-
Sleigh, S.H.1
Seavers, P.R.2
Wilkinson, A.J.3
Ladbury, J.E.4
Tame, J.R.H.5
-
8
-
-
0028452862
-
-
Tame, J. R.; Murshudov, G. N.; Dodson, E. J.; Neil, T. K.; Dodson, G. G.; Higgins, C. F.; Wilkinson, A. J. The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein. Science 1994, 264, 1578-1581.
-
Tame, J. R.; Murshudov, G. N.; Dodson, E. J.; Neil, T. K.; Dodson, G. G.; Higgins, C. F.; Wilkinson, A. J. The Structural Basis of Sequence-Independent Peptide Binding by OppA Protein. Science 1994, 264, 1578-1581.
-
-
-
-
9
-
-
0024375861
-
Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules
-
Quiocho, F. A.; Wilson, D. K.; Vyas, N. K. Substrate Specificity and Affinity of a Protein Modulated by Bound Water Molecules. Nature 1989, 340, 404-407.
-
(1989)
Nature
, vol.340
, pp. 404-407
-
-
Quiocho, F.A.1
Wilson, D.K.2
Vyas, N.K.3
-
10
-
-
0028057975
-
Rational Design of Potent, Bioavailable, Non-peptide Cyclic Ureas as HIV Protease Inhibitors
-
Lam, P. Y. S.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; Wong, Y. N.; Chang, C. H.; Weber, P. C.; Jackson, D. A.; Sharpe, T. R.; Erickson-Viitanen, S. Rational Design of Potent, Bioavailable, Non-peptide Cyclic Ureas as HIV Protease Inhibitors. Science 1994, 265, 380-384.
-
(1994)
Science
, vol.265
, pp. 380-384
-
-
Lam, P.Y.S.1
Jadhav, P.K.2
Eyermann, C.J.3
Hodge, C.N.4
Ru, Y.5
Bacheler, L.T.6
Meek, J.L.7
Otto, M.J.8
Rayner, M.M.9
Wong, Y.N.10
Chang, C.H.11
Weber, P.C.12
Jackson, D.A.13
Sharpe, T.R.14
Erickson-Viitanen, S.15
-
11
-
-
0029134561
-
The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A
-
Mikol, V.; Papageorgiou, C.; Borer, X. The Role of Water Molecules in the Structure-Based Design of (5-Hydroxynorvaline)-2-cyclosporin: Synthesis, Biological Activity, and Crystallographic Analysis with Cyclophilin A. J. Med. Chem. 1995, 58, 3361-3367.
-
(1995)
J. Med. Chem
, vol.58
, pp. 3361-3367
-
-
Mikol, V.1
Papageorgiou, C.2
Borer, X.3
-
12
-
-
4143081344
-
Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes
-
Fornabaio, M.; Spyrakis, F.; Mozzarelli, A.; Cozzini, P.; Abraham, D. J.; Kellogg, G. E. Simple, Intuitive Calculations of Free Energy of Binding for Protein-Ligand Complexes. 3. The Free Energy Contribution of Structural Water Molecules in HIV-1 Protease Complexes. J. Med. Chem. 2004, 47, 4507-4516.
-
(2004)
J. Med. Chem
, vol.47
, pp. 4507-4516
-
-
Fornabaio, M.1
Spyrakis, F.2
Mozzarelli, A.3
Cozzini, P.4
Abraham, D.J.5
Kellogg, G.6
Simple, E.7
-
13
-
-
0032961895
-
The Particle Concept: Placing Discrete Water Molecules during Protein-Ligand Docking Predictions
-
Rarey, M.; Kramer, B.; Lengaure, T. The Particle Concept: Placing Discrete Water Molecules during Protein-Ligand Docking Predictions. Proteins 1999, 34, 17-28.
-
(1999)
Proteins
, vol.34
, pp. 17-28
-
-
Rarey, M.1
Kramer, B.2
Lengaure, T.3
-
14
-
-
2942659093
-
Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method
-
Hamelberg, D.; McCammon, J. A. Standard Free Energy of Releasing a Localized Water Molecule from the Binding Pockets of Proteins: Double-Decoupling Method. J. Am. Chem. Soc. 2004, 126, 7683-7689.
-
(2004)
J. Am. Chem. Soc
, vol.126
, pp. 7683-7689
-
-
Hamelberg, D.1
McCammon, J.A.2
-
15
-
-
33748513468
-
-
Lu, Y.; Yang, C.-Y.; Wang, S. Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes. J. Am. Chem. Soc. 2006, 128, 11830-11839.
-
Lu, Y.; Yang, C.-Y.; Wang, S. Binding Free Energy Contributions of Interfacial Waters in HIV-1 Protease/Inhibitor Complexes. J. Am. Chem. Soc. 2006, 128, 11830-11839.
-
-
-
-
16
-
-
0029450365
-
Hydration in Drug Design. 1. Multiple Hydrogen-Bonding Features of Water Molecules in Mediating Protein-Ligand Interactions
-
Poornima, C. S.; Dean, P. M. Hydration in Drug Design. 1. Multiple Hydrogen-Bonding Features of Water Molecules in Mediating Protein-Ligand Interactions. J. Comput.-Aided Mol. Des. 1995, 9, 500-512.
-
(1995)
J. Comput.-Aided Mol. Des
, vol.9
, pp. 500-512
-
-
Poornima, C.S.1
Dean, P.M.2
-
17
-
-
0029444719
-
Hydration in Drug Design. 2. Influence of Local Site Surface Shape on Water Binding
-
Poornima, C. S.; Dean, P. M. Hydration in Drug Design. 2. Influence of Local Site Surface Shape on Water Binding. J. Comput. -Aided Mol. Des. 1995, 9, 513-520.
-
(1995)
J. Comput. -Aided Mol. Des
, vol.9
, pp. 513-520
-
-
Poornima, C.S.1
Dean, P.M.2
-
18
-
-
19544372768
-
Hydration of Protein-Protein Interfaces
-
Rodier, F.; Bahadur, R. P.; Chakrabarti, P.; Janin, J. Hydration of Protein-Protein Interfaces. Proteins: Struct., Funct., Bioinf. 2005, 60, 36-45.
-
(2005)
Proteins: Struct., Funct., Bioinf
, vol.60
, pp. 36-45
-
-
Rodier, F.1
Bahadur, R.P.2
Chakrabarti, P.3
Janin, J.4
-
19
-
-
0033081137
-
How Many Water Molecules Can Be Detected by Protein Crystallography?
-
Carugo, O.; Bordo, D. How Many Water Molecules Can Be Detected by Protein Crystallography? Acta Crystallogr., Sect. D 1999, 55, 479-483.
-
(1999)
Acta Crystallogr., Sect. D
, vol.55
, pp. 479-483
-
-
Carugo, O.1
Bordo, D.2
-
20
-
-
2542530042
-
The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures
-
Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind Database: Collection of Binding Affinities for Protein-Ligand Complexes with Known Three-Dimensional Structures. J. Med. Chem. 2004, 47, 2977-2980.
-
(2004)
J. Med. Chem
, vol.47
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
21
-
-
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, 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, 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
-
22
-
-
0024442361
-
Is γ-chymoTrypsin a Tetrapeptide Acyl-enzyme Adduct of a Chymotrypsin?
-
Dixon, M. M.; Matthews, B. W. Is γ-chymoTrypsin a Tetrapeptide Acyl-enzyme Adduct of a Chymotrypsin? Biochemistry 1989, 28, 7033-7038.
-
(1989)
Biochemistry
, vol.28
, pp. 7033-7038
-
-
Dixon, M.M.1
Matthews, B.W.2
-
23
-
-
0020483485
-
Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Å Resolution
-
Ghosh, D.; O'Donnell, S.; Furey, W., Jr.; Robbins, A. H.; Stout, C. D. Iron-Sulfur Clusters and Protein Structure of Azotobacter Ferredoxin at 2.0 Å Resolution. J. Mol. Biol. 1982, 158, 73-109.
-
(1982)
J. Mol. Biol
, vol.158
, pp. 73-109
-
-
Ghosh, D.1
O'Donnell, S.2
Furey Jr., W.3
Robbins, A.H.4
Stout, C.D.5
-
24
-
-
0002518563
-
Knowledge-Based B-Factor Restraints for the Refinement of Proteins
-
Tronrude, D. E. Knowledge-Based B-Factor Restraints for the Refinement of Proteins. J. Appl. Crystallogr. 1996, 29, 100-104.
-
(1996)
J. Appl. Crystallogr
, vol.29
, pp. 100-104
-
-
Tronrude, D.E.1
-
25
-
-
0019075327
-
Structural Dynamics of Liganded Myoglobin
-
Frauenfelder, H.; Petsko, G. A. Structural Dynamics of Liganded Myoglobin. Biophys. J. 1980, 32, 465-478.
-
(1980)
Biophys. J
, vol.32
, pp. 465-478
-
-
Frauenfelder, H.1
Petsko, G.A.2
-
26
-
-
0015222647
-
The Interpretation of Protein Structures: Estimation of Static Accessibility
-
Lee, B.; Richards, F. M. The Interpretation of Protein Structures: Estimation of Static Accessibility. J. Mol. Biol. 1971, 55, 379-400.
-
(1971)
J. Mol. Biol
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
27
-
-
84927514013
-
Nouveles Applications des Parameters Continues a la Theorie des Formes Quadratique
-
Voronoi, G. Nouveles Applications des Parameters Continues a la Theorie des Formes Quadratique. J. Reine Angew. Math. 1908, 134, 198-287.
-
(1908)
J. Reine Angew. Math
, vol.134
, pp. 198-287
-
-
Voronoi, G.1
-
28
-
-
0036773411
-
Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure
-
McConkey, B. J.; Sobolev, V.; Edelman, M. Quantification of Protein Surfaces, Volumes and Atom-Atom Contacts Using a Constrained Voronoi Procedure. Bioinformatics 2002, 18, 1365-1373.
-
(2002)
Bioinformatics
, vol.18
, pp. 1365-1373
-
-
McConkey, B.J.1
Sobolev, V.2
Edelman, M.3
-
30
-
-
0031592453
-
Predicting Conserved Water-Mediated and Polar Ligand Interaction in Proteins using a K-Nearest-Neighbors Genetic Algorithm
-
Raymer, M. L.; Sanschagrin, P. C.; Punch, W. F.; Venkataraman, S.; Goodman, E. D.; Kuhn, L. A. Predicting Conserved Water-Mediated and Polar Ligand Interaction in Proteins using a K-Nearest-Neighbors Genetic Algorithm. J. Mol. Biol. 1997, 265, 445-464.
-
(1997)
J. Mol. Biol
, vol.265
, pp. 445-464
-
-
Raymer, M.L.1
Sanschagrin, P.C.2
Punch, W.F.3
Venkataraman, S.4
Goodman, E.D.5
Kuhn, L.A.6
-
31
-
-
0027918556
-
-
Levitt, M.; Park, B. H. Water: Now You See It, Now You Don't. Structure 1993, 1, 223-226.
-
Levitt, M.; Park, B. H. Water: Now You See It, Now You Don't. Structure 1993, 1, 223-226.
-
-
-
-
32
-
-
0028095182
-
Buried Waters and Internal Cavities in Monomeric Proteins
-
Williams, M. A.; Goodfellow, J. M.; Thornton, J. M. Buried Waters and Internal Cavities in Monomeric Proteins. Protein Sci. 1994, 3, 1224-1235.
-
(1994)
Protein Sci
, vol.3
, pp. 1224-1235
-
-
Williams, M.A.1
Goodfellow, J.M.2
Thornton, J.M.3
-
33
-
-
0030471364
-
The Role of Water in Sequence Independent Ligand Binding by an Oligopeptide Transporter Protein
-
Tame, J. R. H.; Sleigh, S. H.; Wilkinson, A. J.; Ladbury, J. E. The Role of Water in Sequence Independent Ligand Binding by an Oligopeptide Transporter Protein. Nat. Struct. Biol. 1996, 3, 998-1001.
-
(1996)
Nat. Struct. Biol
, vol.3
, pp. 998-1001
-
-
Tame, J.R.H.1
Sleigh, S.H.2
Wilkinson, A.J.3
Ladbury, J.E.4
-
34
-
-
4544316921
-
The Polar Hydrophobicity of Fluorinated Compounds
-
Biffinger, J. C.; Kim, H. W.; DiMagno, S. G. The Polar Hydrophobicity of Fluorinated Compounds. ChemBioChem 2004, 5, 622-627.
-
(2004)
ChemBioChem
, vol.5
, pp. 622-627
-
-
Biffinger, J.C.1
Kim, H.W.2
DiMagno, S.G.3
-
35
-
-
0028228418
-
The Entropic Cost of Bound Water in Crystals and Biomolecules
-
Dunitz J. D. The Entropic Cost of Bound Water in Crystals and Biomolecules. Science 1994, 264, 670-671.
-
(1994)
Science
, vol.264
, pp. 670-671
-
-
Dunitz, J.D.1
-
36
-
-
0030466444
-
Add Water! The Effect of Water on the Specificity of Protein-Ligand Binding Sites and Its Potential Application to Drug Design
-
Ladbury, J. E. Just Add Water! The Effect of Water on the Specificity of Protein-Ligand Binding Sites and Its Potential Application to Drug Design. Chem. Biol. 1996, 3, 973-980.
-
(1996)
Chem. Biol
, vol.3
, pp. 973-980
-
-
Ladbury, J.1
Just, E.2
-
37
-
-
0037533880
-
Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease
-
Li, Z.; Lazaridis, T. Thermodynamic Contributions of the Ordered Water Molecule in HIV-1 Protease. J. Am. Chem. Soc. 2003, 125, 6636-6637.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 6636-6637
-
-
Li, Z.1
Lazaridis, T.2
|