-
1
-
-
0023038504
-
Binding specificity of the periplasmic Oligopeptide-binding protein from Escherichia coli
-
Guyer, C. A.; Morgan, D. G.; Staros, J. V. Binding specificity of the periplasmic Oligopeptide-binding protein from Escherichia coli. J. Bacteriol. 1986, 168, 775-779.
-
(1986)
J. Bacteriol.
, vol.168
, pp. 775-779
-
-
Guyer, C.A.1
Morgan, D.G.2
Staros, J.V.3
-
2
-
-
0023636673
-
Uptake of cell-wall peptides by Salmonella typhimurium and Escherichia coli
-
Goodell, E. W.; Higgins, C. F. Uptake of cell-wall peptides by Salmonella typhimurium and Escherichia coli. J. Bacteriol. 1987, 169, 3861-3865.
-
(1987)
J. Bacteriol.
, vol.169
, pp. 3861-3865
-
-
Goodell, E.W.1
Higgins, C.F.2
-
3
-
-
0023279472
-
A new class of synthetic antibacterials acting on lipopolysaccharide biosynthesis
-
Hammond, S. M.; Claesson, A.; Jansson, A. M.; Larsson, L. G.; Pring, B. G.; Town, C. M.; Ekstrom, B. A new class of synthetic antibacterials acting on lipopolysaccharide biosynthesis. Nature 1987, 327, 730-732.
-
(1987)
Nature
, vol.327
, pp. 730-732
-
-
Hammond, S.M.1
Claesson, A.2
Jansson, A.M.3
Larsson, L.G.4
Pring, B.G.5
Town, C.M.6
Ekstrom, B.7
-
4
-
-
0031470826
-
Genomic sequence of a Lyme disease spirochaete, Borrelia Burgdorferi
-
Fraser, C. M.; Casjens, S.; Huang, W. M.; Sutton, G. G.; et al. Genomic sequence of a Lyme disease spirochaete, Borrelia Burgdorferi. Nature 1997, 390, 580-586.
-
(1997)
Nature
, vol.390
, pp. 580-586
-
-
Fraser, C.M.1
Casjens, S.2
Huang, W.M.3
Sutton, G.G.4
-
5
-
-
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
-
6
-
-
0032806924
-
Relating structure to thermodynamics: The crystal structures and binding affinity of eight OppA-peptide complexes
-
Davies, T. G.; Hubbard, R. E.; Tame, J. R. H. Relating structure to thermodynamics: the crystal structures and binding affinity of eight OppA-peptide complexes. Protein Sci. 1999, 8, 1432-1444.
-
(1999)
Protein Sci.
, vol.8
, pp. 1432-1444
-
-
Davies, T.G.1
Hubbard, R.E.2
Tame, J.R.H.3
-
7
-
-
0030855775
-
Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine
-
Sleigh, S. H.; Tame, J. R. H.; Dodson, E. J.; Wilkinson, A. J. Peptide binding in OppA, the crystal structures of the periplasmic oligopeptide binding protein in the unliganded form and in complex with lysyllysine. Biochemistry 1997, 36, 9747-9758.
-
(1997)
Biochemistry
, vol.36
, pp. 9747-9758
-
-
Sleigh, S.H.1
Tame, J.R.H.2
Dodson, E.J.3
Wilkinson, A.J.4
-
8
-
-
0029646113
-
The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands
-
Tame, J. R. H.; Dodson, E. J.; Murshudov, G.; Higgins, C. F.; Wilkinson, A. J. The crystal structures of the oligopeptide-binding protein OppA complexed with tripeptide and tetrapeptide ligands. Structure 1995, 3, 1395-1406.
-
(1995)
Structure
, vol.3
, pp. 1395-1406
-
-
Tame, J.R.H.1
Dodson, E.J.2
Murshudov, G.3
Higgins, C.F.4
Wilkinson, A.J.5
-
9
-
-
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
-
10
-
-
0030466444
-
Just 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.E.1
-
11
-
-
0034635345
-
Specificity and interactions of the protein OppA: Partitioning solvent binding effects using mass spectrometry
-
Rostom, A. A.; Tame, J. R. H.; Ladbury, J. E.; Robinson, C. V. Specificity and interactions of the protein OppA: partitioning solvent binding effects using mass spectrometry. J. Mol. Biol. 2000, 296, 269-279.
-
(2000)
J. Mol. Biol.
, vol.296
, pp. 269-279
-
-
Rostom, A.A.1
Tame, J.R.H.2
Ladbury, J.E.3
Robinson, C.V.4
-
12
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Bohm, H. J. The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure. J. Comput.-Aided Mol. Des. 1994, 12, 243-256.
-
(1994)
J. Comput.-Aided Mol. Des.
, vol.12
, pp. 243-256
-
-
Bohm, H.J.1
-
13
-
-
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, 791-804.
-
(1999)
J. Med. Chem.
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
14
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman, P. Free energy calculations: Applications to chemical and biochemical phenomena. Chem. Rev. 1993, 93, 2395-2417.
-
(1993)
Chem. Rev.
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
15
-
-
0031012579
-
Enzyme-inhibitor association thermodynamics: Explicit and continuum solvent studies
-
Resat, H.; Marrone, T. J.; McCammon, J. A. Enzyme-inhibitor association thermodynamics: explicit and continuum solvent studies. Biophys. J. 1997, 72, 522-532.
-
(1997)
Biophys. J.
, vol.72
, pp. 522-532
-
-
Resat, H.1
Marrone, T.J.2
McCammon, J.A.3
-
16
-
-
0035846166
-
Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
-
Pearlman, D. A.; Charifson, P. S. Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system. J. Med. Chem. 2001, 44, 3417-3423.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
17
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz, A. R.; Pisabarro, M. T.; Gago, F.; Wade, R. C. Prediction of Drug Binding Affinities by Comparative Binding Energy Analysis. J. Med. Chem. 1995, 38, 2681-2691.
-
(1995)
J. Med. Chem.
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
18
-
-
0011063965
-
Derivation of QSARs using 3D structural models of protein-ligand complexes by COMBINE analysis
-
Holtje, H.-D., Sippl, W., Eds.; Prous Science S. A.: Barcelona
-
Wade, R. C. Derivation of QSARs using 3D structural models of protein-ligand complexes by COMBINE analysis. In Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships; Holtje, H.-D., Sippl, W., Eds.; Prous Science S. A.: Barcelona, 2001; pp 23-28.
-
(2001)
Rational Approaches to Drug Design: 13th European Symposium on Quantitative Structure-Activity Relationships
, pp. 23-28
-
-
Wade, R.C.1
-
19
-
-
0030892498
-
Reliability of comparative molecular field analysis models: Effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors
-
Ortiz, A. R.; Pastor, M.; Palomer, A.; Cruciani, G.; Gago, F.; Wade, R. C. Reliability of comparative molecular field analysis models: effects of data scaling and variable selection using a set of human synovial fluid phospholipase A2 inhibitors. J. Med. Chem. 1997, 40, 1136-1148.
-
(1997)
J. Med. Chem.
, vol.40
, pp. 1136-1148
-
-
Ortiz, A.R.1
Pastor, M.2
Palomer, A.3
Cruciani, G.4
Gago, F.5
Wade, R.C.6
-
20
-
-
0032510317
-
Comparative binding energy analysis of HIV-1 protease inhibitors: Incorporation of solvent effects and validation as a powerful tool in receptor-based drug design
-
Perez, C.; Pastor, M.; Ortiz, A. R.; Gago, F. Comparative binding energy analysis of HIV-1 protease inhibitors: incorporation of solvent effects and validation as a powerful tool in receptor-based drug design. J. Med. Chem. 1998, 41, 836-852.
-
(1998)
J. Med. Chem.
, vol.41
, pp. 836-852
-
-
Perez, C.1
Pastor, M.2
Ortiz, A.R.3
Gago, F.4
-
21
-
-
0002759123
-
Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: Comparison with GRID/GOLPE models
-
Gundertofte, K., Jorgensen, F. S., Eds.; Kluwer: New York
-
Pastor, M.; Gago, F.; Cruciani, G. Comparative binding energy (COMBINE) analysis on a series of glycogen phosphorylase inhibitors: comparison with GRID/GOLPE models. In Molecular Modeling and Prediction of Bioactivity; Gundertofte, K., Jorgensen, F. S., Eds.; Kluwer: New York, 2000; pp 329-330.
-
(2000)
Molecular Modeling and Prediction of Bioactivity
, pp. 329-330
-
-
Pastor, M.1
Gago, F.2
Cruciani, G.3
-
22
-
-
0035866695
-
Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
-
Wang, T.; Wade, R. C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J. Med. Chem. 2001, 44, 961-971.
-
(2001)
J. Med. Chem.
, vol.44
, pp. 961-971
-
-
Wang, T.1
Wade, R.C.2
-
23
-
-
0034050042
-
3D-QSAR methods on the basis of ligand receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 Ligands
-
Lozano, J. J.; Pastor, M.; Cruciani, G.; Gaedt, K.; Centeno, N. B.; Gago, F.; Sanz, F. 3D-QSAR methods on the basis of ligand receptor complexes. Application of COMBINE and GRID/GOLPE methodologies to a series of CYP1A2 Ligands. J. Comput.-Aided Mol. Des. 2000, 14, 341-353.
-
(2000)
J. Comput.-Aided Mol. Des.
, vol.14
, pp. 341-353
-
-
Lozano, J.J.1
Pastor, M.2
Cruciani, G.3
Gaedt, K.4
Centeno, N.B.5
Gago, F.6
Sanz, F.7
-
24
-
-
0035979364
-
Comparative Binding Energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from xanthobacter autotrophicus GJ10
-
Kmunicek, J.; Luengo, S.; Gago, F.; Ortiz, A. R.; Wade, R. C.; Damborsky, J. Comparative Binding Energy (COMBINE) analysis of the substrate specificity of haloalkane dehalogenase from xanthobacter autotrophicus GJ10. Biochemistry 2001, 40, 8905-8917.
-
(2001)
Biochemistry
, vol.40
, pp. 8905-8917
-
-
Kmunicek, J.1
Luengo, S.2
Gago, F.3
Ortiz, A.R.4
Wade, R.C.5
Damborsky, J.6
-
25
-
-
0034069171
-
Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis
-
Tomic, S.; Nilsson, L.; Wade, R. C. Nuclear receptor-DNA binding specificity: A COMBINE and Free-Wilson QSAR analysis. J. Med. Chem. 2000, 43, 1780-1792.
-
(2000)
J. Med. Chem.
, vol.43
, pp. 1780-1792
-
-
Tomic, S.1
Nilsson, L.2
Wade, R.C.3
-
26
-
-
0025398721
-
WHAT IF: A molecular modelling and drug design program
-
Vriend, G. WHAT IF: a molecular modelling and drug design program. J. Mol. Graph. 1990, 8, 52-56.
-
(1990)
J. Mol. Graph.
, vol.8
, pp. 52-56
-
-
Vriend, G.1
-
27
-
-
0030442990
-
Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures
-
Hooft, R. W. W.; Sander, C.; Vriend, G. Positioning hydrogen atoms by optimizing hydrogen bond networks in protein structures. Proteins 1996, 26, 363-376.
-
(1996)
Proteins
, vol.26
, pp. 363-376
-
-
Hooft, R.W.W.1
Sander, C.2
Vriend, G.3
-
28
-
-
0029011701
-
A second generation force field for the simulation of proteins, nucleic acids and organic molecules
-
Cornell, W. D.; Cieplak, P.; Payly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids and Organic Molecules. J. Am. Chem. Soc. 1995, 117, 5179-5197.
-
(1995)
J. Am. Chem. Soc.
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Payly, C.I.3
Gould, I.R.4
Merz, K.M.5
Ferguson, D.M.6
Spellmeyer, D.C.7
Fox, T.8
Caldwell, J.W.9
Kollman, P.A.10
-
29
-
-
0004150411
-
-
Molecular Simulations Inc.: San Diego, CA
-
InsightII, version 2000; Molecular Simulations Inc.: San Diego, CA.
-
(2000)
InsightII, version 2000
-
-
-
31
-
-
0029633152
-
Electrostatics and diffusion of molecules in solution: Simulations with the university of Houston brownian dynamics program
-
Madura, J. D.; Briggs, J. M.; Wade, R. C.; Davis, M. E.; Luty, B. A.; Ilin, A.; Antosiewicz, J.; Gilson, M. K.; Bagheri, B.; Scott, L. R.; McCammon, J. A. Electrostatics and diffusion of molecules in solution: simulations with the university of Houston brownian dynamics program. Comput. Phys. Commun. 1995, 91, 57-95.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 57-95
-
-
Madura, J.D.1
Briggs, J.M.2
Wade, R.C.3
Davis, M.E.4
Luty, B.A.5
Ilin, A.6
Antosiewicz, J.7
Gilson, M.K.8
Bagheri, B.9
Scott, L.R.10
McCammon, J.A.11
-
32
-
-
0027310371
-
Generating optimal linear PLS estimations (GOLPE): An advanced chemometric tool for handling 3D-QSAR problems
-
Baroni, M.; Costantino, G.; Cruciani, G.; Riganelli, D.; Valigi, R.; Clementi, S. Generating optimal linear PLS estimations (GOLPE): an advanced chemometric tool for handling 3D-QSAR problems. Quant. Struct.-Act. Relat. 1993, 12, 9-20.
-
(1993)
Quant. Struct.-Act. Relat.
, vol.12
, pp. 9-20
-
-
Baroni, M.1
Costantino, G.2
Cruciani, G.3
Riganelli, D.4
Valigi, R.5
Clementi, S.6
-
33
-
-
0034601808
-
Thermodynamic basis of resistance to HIV-1 protease inhibition: Calorimetric analysis of the V82F/I84V active site resistant mutant
-
Todd, M. J.; Luque, I.; Valazquez-Campoy, A.; Freire, E. Thermodynamic basis of resistance to HIV-1 protease inhibition: calorimetric analysis of the V82F/I84V active site resistant mutant. Biochemistry 2000, 39, 11876-11883.
-
(2000)
Biochemistry
, vol.39
, pp. 11876-11883
-
-
Todd, M.J.1
Luque, I.2
Valazquez-Campoy, A.3
Freire, E.4
-
34
-
-
0026573247
-
In human malaria protective antibodies are directed mainly against the Lys-Glu ion pair within the Lys-Glu-Lys motif of the synthetic vaccine SPf66
-
Molano, A.; Segura, C.; Guzman, F.; Lozada, D.; Patarroyo, M. E. In human malaria protective antibodies are directed mainly against the Lys-Glu ion pair within the Lys-Glu-Lys motif of the synthetic vaccine SPf66. Parasite Immunol. 1992, 14, 111-124.
-
(1992)
Parasite Immunol.
, vol.14
, pp. 111-124
-
-
Molano, A.1
Segura, C.2
Guzman, F.3
Lozada, D.4
Patarroyo, M.E.5
-
35
-
-
0026696688
-
Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. 1. Mapping the rotamers of residue 188 of viral protein 1
-
Wade, R. C.; McCammon, J. A. Binding of an antiviral agent to a sensitive and a resistant human rhinovirus. Computer simulation studies with sampling of amino acid side-chain conformations. 1. Mapping the rotamers of residue 188 of viral protein 1. J. Mol. Biol. 1992, 225, 679-696.
-
(1992)
J. Mol. Biol.
, vol.225
, pp. 679-696
-
-
Wade, R.C.1
McCammon, J.A.2
|