-
1
-
-
0029623184
-
Computational methods to predict binding free energy in ligand-receptor complexes
-
Ajay M.M.A. Computational methods to predict binding free energy in ligand-receptor complexes. J Med Chem. 38:1995;4953-4967.
-
(1995)
J Med Chem
, vol.38
, pp. 4953-4967
-
-
Ajay, M.M.A.1
-
2
-
-
0344558911
-
An experimental approach to mapping the binding surfaces of crystalline proteins
-
Allen K.N., Bellamacina C.R., Ding X.C., Jeffery C.J., Mattos C., Petsko G.A., Ringe D. An experimental approach to mapping the binding surfaces of crystalline proteins. J Phys Chem. 100:1996;2605-2611.
-
(1996)
J Phys Chem
, vol.100
, pp. 2605-2611
-
-
Allen, K.N.1
Bellamacina, C.R.2
Ding, X.C.3
Jeffery, C.J.4
Mattos, C.5
Petsko, G.A.6
Ringe, D.7
-
3
-
-
0030707764
-
Bioinformatics: From genome data to biological knowledge
-
Andrade M.A., Sander C. Bioinformatics. from genome data to biological knowledge Curr Opin Biotechnol. 8:1997;675-683.
-
(1997)
Curr Opin Biotechnol
, vol.8
, pp. 675-683
-
-
Andrade, M.A.1
Sander, C.2
-
4
-
-
0028155689
-
New method for predicting binding-affinity in computer-aided drug design
-
Aqvist J., Medina C., Samuelsson J.E. New method for predicting binding-affinity in computer-aided drug design. Protein Eng. 7:1994;385-391.
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
5
-
-
0029894013
-
The properties of known drugs. 1. Molecular frameworks
-
Bemis G.W., Murcko M.A. The properties of known drugs. 1. Molecular frameworks. J Med Chem. 39:1996;2887-2893.
-
(1996)
J Med Chem
, vol.39
, pp. 2887-2893
-
-
Bemis, G.W.1
Murcko, M.A.2
-
6
-
-
0024578173
-
Free energy via molecular simulation: Applications to chemical and biomolecular systems
-
Beveridge D.L., DiCapua F.M. Free energy via molecular simulation. applications to chemical and biomolecular systems Annu Rev Biophys Biophys Chem. 18:1989;431-492.
-
(1989)
Annu Rev Biophys Biophys Chem
, vol.18
, pp. 431-492
-
-
Beveridge, D.L.1
Dicapua, F.M.2
-
7
-
-
0028036120
-
Multiple highly diverse structures complementary to enzyme binding-sites - results of extensive application of a de-novo design method incorporating combinatorial growth
-
Bohacek R.S., McMartin C. Multiple highly diverse structures complementary to enzyme binding-sites - results of extensive application of a de-novo design method incorporating combinatorial growth. J Am Chem Soc. 116:1994;5560-5571.
-
(1994)
J Am Chem Soc
, vol.116
, pp. 5560-5571
-
-
Bohacek, R.S.1
McMartin, C.2
-
8
-
-
0001826929
-
De-novo design of highly diverse structures complementary to enzyme binding-sites - application to thermolysin
-
Bohacek R.S., McMartin C. De-novo design of highly diverse structures complementary to enzyme binding-sites - application to thermolysin. Comput Aided Mol Des. 589:1995;82-97.
-
(1995)
Comput Aided Mol des
, vol.589
, pp. 82-97
-
-
Bohacek, R.S.1
McMartin, C.2
-
9
-
-
0027027467
-
Ludi - rule-based automatic design of new substituents for enzyme-inhibitor leads
-
Bohm H.J. Ludi - rule-based automatic design of new substituents for enzyme-inhibitor leads. J Comput Aided Mol Des. 6:1992;593-606.
-
(1992)
J Comput Aided Mol des
, vol.6
, pp. 593-606
-
-
Bohm, H.J.1
-
10
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3-dimensional structure
-
a
-
Bohm H.J. The development of a simple empirical scoring function to estimate the binding constant for a protein ligand complex of known 3-dimensional structure. J Comput Aided Mol Des. 8:1994;243-256. a.
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 243-256
-
-
Bohm, H.J.1
-
11
-
-
0028522983
-
On the use of Ludi to search the Fine Chemicals Directory for ligands of proteins of known 3-dimensional structure
-
b
-
Bohm H.J. On the use of Ludi to search the Fine Chemicals Directory for ligands of proteins of known 3-dimensional structure. J Comput Aided Mol Des. 8:1994;623-632. b.
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 623-632
-
-
Bohm, H.J.1
-
12
-
-
0030474049
-
What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs
-
Bohm H.J., Klebe G. What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs. Angew Chem Int Ed Engl. 35:1996;2588-2614.
-
(1996)
Angew Chem Int Ed Engl
, vol.35
, pp. 2588-2614
-
-
Bohm, H.J.1
Klebe, G.2
-
13
-
-
0024566942
-
New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure
-
Boobbyer D., Goodford P., McWhinnie P., Wade R. New hydrogen-bond potentials for use in determining energetically favorable binding sites on molecules of known structure. J Med Chem. 32:1989;1083-1094.
-
(1989)
J Med Chem
, vol.32
, pp. 1083-1094
-
-
Boobbyer, D.1
Goodford, P.2
McWhinnie, P.3
Wade, R.4
-
14
-
-
0029584358
-
The meaning of component analysis - decomposition of the free-energy in terms of specific interactions
-
Boresch S., Karplus M. The meaning of component analysis - decomposition of the free-energy in terms of specific interactions. J Mol Biol. 254:1995;801-807.
-
(1995)
J Mol Biol
, vol.254
, pp. 801-807
-
-
Boresch, S.1
Karplus, M.2
-
15
-
-
0027968902
-
Free-energy simulations - The meaning of the individual contributions from a component analysis
-
Boresch S., Archontis G., Karplus M. Free-energy simulations - the meaning of the individual contributions from a component analysis. Proteins. 20:1994;25-33.
-
(1994)
Proteins
, vol.20
, pp. 25-33
-
-
Boresch, S.1
Archontis, G.2
Karplus, M.3
-
16
-
-
0002201599
-
Combinatorial chemistry
-
Borman S. Combinatorial chemistry. Chem Eng News. 75:1997;43-53.
-
(1997)
Chem Eng News
, vol.75
, pp. 43-53
-
-
Borman, S.1
-
17
-
-
84986512474
-
Charmm: A program for macromolecular energy, minimization, and dynamics calculations
-
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. Charmm. a program for macromolecular energy, minimization, and dynamics calculations J Comput Chem. 4:1983;187-217.
-
(1983)
J Comput Chem
, vol.4
, pp. 187-217
-
-
Brooks, B.R.1
Bruccoleri, R.E.2
Olafson, B.D.3
States, D.J.4
Swaminathan, S.5
Karplus, M.6
-
18
-
-
0003525155
-
-
New York: John Wiley & Sons
-
Brooks C.L., Karplus M., Pettitt B.N. Proteins. A Theoretical Perspective of Dynamics, Structure, and Thermodynamics:1988;John Wiley & Sons, New York.
-
(1988)
Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.N.3
-
19
-
-
0027646168
-
Workstation clusters rise and shine (Computing in Science: Perspective)
-
Buzbee B. Workstation clusters rise and shine (Computing in Science: Perspective). Science. 261:1993;852-853.
-
(1993)
Science
, vol.261
, pp. 852-853
-
-
Buzbee, B.1
-
20
-
-
0030256270
-
Computational combinatorial ligand design: Application to human alpha-thrombin
-
Caflisch A. Computational combinatorial ligand design. application to human alpha-thrombin J Comput Aided Mol Des. 10:1996;372-396.
-
(1996)
J Comput Aided Mol des
, vol.10
, pp. 372-396
-
-
Caflisch, A.1
-
21
-
-
34249753351
-
Computational combinatorial chemistry for de novo ligand design: Review and assessment
-
Caflisch A., Karplus M. Computational combinatorial chemistry for de novo ligand design. review and assessment Perspect Drug Discov Des. 3:1995;51-84.
-
(1995)
Perspect Drug Discov des
, vol.3
, pp. 51-84
-
-
Caflisch, A.1
Karplus, M.2
-
22
-
-
0027219536
-
Multiple copy simultaneous search and construction of ligands in binding sites
-
Caflisch A., Miranker A., Karplus M. Multiple copy simultaneous search and construction of ligands in binding sites. J Med Chem. 36:1993;2142-2167.
-
(1993)
J Med Chem
, vol.36
, pp. 2142-2167
-
-
Caflisch, A.1
Miranker, A.2
Karplus, M.3
-
23
-
-
0030954877
-
Structure-based discovery of ligands targeted to the RNA double helix
-
Chen Q., Shafer R.H., Kuntz I.D. Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry. 36:1997;11402-11407.
-
(1997)
Biochemistry
, vol.36
, pp. 11402-11407
-
-
Chen, Q.1
Shafer, R.H.2
Kuntz, I.D.3
-
24
-
-
0030110888
-
A technique to study molecular recognition in drug design: Preliminary application of free energy derivatives to inhibition of a malarial cysteine protease
-
Cieplak P., Kollman P.A. A technique to study molecular recognition in drug design. preliminary application of free energy derivatives to inhibition of a malarial cysteine protease J Mol Recognit. 9:1996;103-112.
-
(1996)
J Mol Recognit
, vol.9
, pp. 103-112
-
-
Cieplak, P.1
Kollman, P.A.2
-
25
-
-
0032561249
-
New goals for the US Human Genome Project: 1998-2000
-
Collins F.S., Patrinos A., Jordan E., Chakravarti A., Gesteland R., Walters L., Fearon E., Hartwelt L., Langley C.H., Mathies R.A., Olson M., Pawson A.J., Pollard T., Williamson A., Wold B., Buetow K., Branscomb E., Capecchi M., Church G., Garner H., Gibbs R.A., Hawkins T., Hodgson K., Knotek M., Meisler M., Rubin G.M., Smith L.M., Smith R.F., Westerfield M., Clayton E.W., Fisher N.L., Lerman C.E., McInerney J.D., Nebo W., Press N., Valle D. New goals for the US Human Genome Project. 1998-2000 Science. 282:1998;682-689.
-
(1998)
Science
, vol.282
, pp. 682-689
-
-
Collins, F.S.1
Patrinos, A.2
Jordan, E.3
Chakravarti, A.4
Gesteland, R.5
Walters, L.6
Fearon, E.7
Hartwelt, L.8
Langley, C.H.9
Mathies, R.A.10
Olson, M.11
Pawson, A.J.12
Pollard, T.13
Williamson, A.14
Wold, B.15
Buetow, K.16
Branscomb, E.17
Capecchi, M.18
Church, G.19
Garner, H.20
Gibbs, R.A.21
Hawkins, T.22
Hodgson, K.23
Knotek, M.24
Meisler, M.25
Rubin, G.M.26
Smith, L.M.27
Smith, R.F.28
Westerfield, M.29
Clayton, E.W.30
Fisher, N.L.31
Lerman, C.E.32
McInerney, J.D.33
Nebo, W.34
Press, N.35
Valle, D.36
more..
-
27
-
-
0029011701
-
A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules
-
Cornell W.D., Cieplak P., Bayly C.I., Gould I.R., Merz K.M., Ferguson D.M., Spellmeyer D.C., Fox T., Caldwell J.W., Kollman P.A. A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc. 117:1995;5179-5197.
-
(1995)
J Am Chem Soc
, vol.117
, pp. 5179-5197
-
-
Cornell, W.D.1
Cieplak, P.2
Bayly, 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
-
28
-
-
0032493911
-
Supercomputing - computer experts urge new federal initiative
-
Couzin J. Supercomputing - computer experts urge new federal initiative. Science. 281:1998;762.
-
(1998)
Science
, vol.281
, pp. 762
-
-
Couzin, J.1
-
29
-
-
0026124585
-
Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program
-
Davis M.E., Madura J.D., Luty B.A., McCammon J.A. Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics program. Comput Phys Commun. 62:1991;187-197.
-
(1991)
Comput Phys Commun
, vol.62
, pp. 187-197
-
-
Davis, M.E.1
Madura, J.D.2
Luty, B.A.3
McCammon, J.A.4
-
30
-
-
0000934205
-
Smog: De novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence
-
DeWitte R., Shakhnovich E. Smog. de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence J Am Chem Soc. 118:1996;11733-11744.
-
(1996)
J Am Chem Soc
, vol.118
, pp. 11733-11744
-
-
Dewitte, R.1
Shakhnovich, E.2
-
31
-
-
0031003647
-
Smog: De novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies on molecular design
-
DeWitte R., Ishchenko A., Shakhnovich E. Smog. de novo design method based on simple, fast, and accurate free energy estimates. 2. Case studies on molecular design J Am Chem Soc. 119:1997;4608-4617.
-
(1997)
J Am Chem Soc
, vol.119
, pp. 4608-4617
-
-
Dewitte, R.1
Ishchenko, A.2
Shakhnovich, E.3
-
32
-
-
0030274647
-
Genomic sciences and the medicine of tomorrow
-
Drews J. Genomic sciences and the medicine of tomorrow. Nat Biotechnol. 14:1996;1516-1518.
-
(1996)
Nat Biotechnol
, vol.14
, pp. 1516-1518
-
-
Drews, J.1
-
33
-
-
0030627637
-
Meeting review: The Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996
-
Dunbrack R.L., Gerloff D.L., Bower M., Chen X.W., Lichtarge O., Cohen F.E. Meeting review. The Second Meeting on the Critical Assessment of Techniques for Protein Structure Prediction (CASP2), Asilomar, California, December 13-16, 1996 Fold Des. 2:1997;R27-R42.
-
(1997)
Fold des
, vol.2
-
-
Dunbrack, R.L.1
Gerloff, D.L.2
Bower, M.3
Chen, X.W.4
Lichtarge, O.5
Cohen, F.E.6
-
34
-
-
0028282687
-
Hook: A program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding sites
-
Eisen M.B., Wiley D.C., Karplus M., Hubbard R.E. Hook. a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding sites Proteins. 19:1994;199-221.
-
(1994)
Proteins
, vol.19
, pp. 199-221
-
-
Eisen, M.B.1
Wiley, D.C.2
Karplus, M.3
Hubbard, R.E.4
-
35
-
-
0022596727
-
Solvation energy in protein folding and binding
-
Eisenberg D., McLachlan A.D. Solvation energy in protein folding and binding. Nature. 319:1986;199-203.
-
(1986)
Nature
, vol.319
, pp. 199-203
-
-
Eisenberg, D.1
McLachlan, A.D.2
-
36
-
-
0031226772
-
Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge M.D., Murray C.W., Auton T.R., Paolini G.V., Mee R.P. Empirical scoring functions. 1. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des. 11:1997;425-445.
-
(1997)
J Comput Aided Mol des
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
38
-
-
0030481340
-
Ionic interactions in crystalline bovine pancreatic ribonuclease A
-
Fedorov A.A., JosephMcCarthy D., Fedorov E., Sirakova D., Graf I., Almo S.C. Ionic interactions in crystalline bovine pancreatic ribonuclease A. Biochemistry. 35:1996;15962-15979.
-
(1996)
Biochemistry
, vol.35
, pp. 15962-15979
-
-
Fedorov, A.A.1
JosephMccarthy, D.2
Fedorov, E.3
Sirakova, D.4
Graf, I.5
Almo, S.C.6
-
39
-
-
0345445675
-
Computer-assisted design of syntheses for heterocyclic-compounds
-
Fick R., Ihlenfeldt W.D., Gasteiger J. Computer-assisted design of syntheses for heterocyclic-compounds. Heterocycles. 40:1995;993-1007.
-
(1995)
Heterocycles
, vol.40
, pp. 993-1007
-
-
Fick, R.1
Ihlenfeldt, W.D.2
Gasteiger, J.3
-
40
-
-
0032543623
-
Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation
-
Friedman S.H., Ganapathi P.S., Rubin Y., Kenyon G.L. Optimizing the binding of fullerene inhibitors of the HIV-1 protease through predicted increases in hydrophobic desolvation. J Med Chem. 41:1998;2424-2429.
-
(1998)
J Med Chem
, vol.41
, pp. 2424-2429
-
-
Friedman, S.H.1
Ganapathi, P.S.2
Rubin, Y.3
Kenyon, G.L.4
-
41
-
-
0031008575
-
On the calculation of binding free energies using continuum methods: Application to MHC class I protein-peptide interactions
-
Froloff N., Windemuth A., Honig B. On the calculation of binding free energies using continuum methods. application to MHC class I protein-peptide interactions Protein Sci. 6:1997;1293-1301.
-
(1997)
Protein Sci
, vol.6
, pp. 1293-1301
-
-
Froloff, N.1
Windemuth, A.2
Honig, B.3
-
42
-
-
0024365336
-
Hidden thermodynamics of mutant proteins - A molecular-dynamics analysis
-
Gao J., Kuczera K., Tidor B., Karplus M. Hidden thermodynamics of mutant proteins - a molecular-dynamics analysis. Science. 244:1989;1069-1072.
-
(1989)
Science
, vol.244
, pp. 1069-1072
-
-
Gao, J.1
Kuczera, K.2
Tidor, B.3
Karplus, M.4
-
43
-
-
0027613969
-
An approximate but efficient method to calculate free-energy trends by computer-simulation - application to dihydrofolate-reductase inhibitor complexes
-
Gerber P.R., Mark A.E., Vangunsteren W.F. An approximate but efficient method to calculate free-energy trends by computer-simulation - application to dihydrofolate-reductase inhibitor complexes. J Comput Aided Mol Des. 7:1993;305-323.
-
(1993)
J Comput Aided Mol des
, vol.7
, pp. 305-323
-
-
Gerber, P.R.1
Mark, A.E.2
Vangunsteren, W.F.3
-
44
-
-
0002820943
-
Sprout, hippo and caesa: Tools for de novo structure generation and estimation of synthetic accessibility
-
Gillet V.J., Myatt G., Zsoldos Z., Johnson A.P. Sprout, hippo and caesa. tools for de novo structure generation and estimation of synthetic accessibility Perspect Drug Discov Des. 3:1995;34-50.
-
(1995)
Perspect Drug Discov des
, vol.3
, pp. 34-50
-
-
Gillet, V.J.1
Myatt, G.2
Zsoldos, Z.3
Johnson, A.P.4
-
45
-
-
84988087911
-
Calculating the electrostatic potential of molecules in solution: Method and error assessment
-
Gilson M.K., Sharp K.A., Honig B.H. Calculating the electrostatic potential of molecules in solution. method and error assessment J Comput Chem. 9:1988;327-335.
-
(1988)
J Comput Chem
, vol.9
, pp. 327-335
-
-
Gilson, M.K.1
Sharp, K.A.2
Honig, B.H.3
-
46
-
-
0031058541
-
The statistical-thermodynamic basis for computation of binding affinities: A critical review
-
a
-
Gilson M.K., Given J.A., Bush B.L., McCammon J.A. The statistical-thermodynamic basis for computation of binding affinities. a critical review Biophys J. 72:1997;1047-1069. a.
-
(1997)
Biophys J
, vol.72
, pp. 1047-1069
-
-
Gilson, M.K.1
Given, J.A.2
Bush, B.L.3
McCammon, J.A.4
-
47
-
-
0031080551
-
A new class of models for computing receptor-ligand binding affinities
-
b
-
Gilson M.K., Given J.A., Head M.S. A new class of models for computing receptor-ligand binding affinities. Chem Biol. 4:1997;87-92. b.
-
(1997)
Chem Biol
, vol.4
, pp. 87-92
-
-
Gilson, M.K.1
Given, J.A.2
Head, M.S.3
-
48
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford P. A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J Med Chem. 28:1985;849-857.
-
(1985)
J Med Chem
, vol.28
, pp. 849-857
-
-
Goodford, P.1
-
49
-
-
0029705324
-
Automated docking of flexible ligands: Applications of AutoDock
-
Goodsell D.S., Morris G.M., Olson A.J. Automated docking of flexible ligands. applications of AutoDock J Mol Recognit. 9:1996;1-5.
-
(1996)
J Mol Recognit
, vol.9
, pp. 1-5
-
-
Goodsell, D.S.1
Morris, G.M.2
Olson, A.J.3
-
50
-
-
0030076313
-
Functionality map analysis of the active site cleft of human thrombin
-
Grootenhuis P.D.J., Karplus M. Functionality map analysis of the active site cleft of human thrombin. J Comput Aided Mol Des. 10:1996;1-10.
-
(1996)
J Comput Aided Mol des
, vol.10
, pp. 1-10
-
-
Grootenhuis, P.D.J.1
Karplus, M.2
-
51
-
-
0001452822
-
Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes
-
Grootenhuis P.D.J., van Galen P.J.M. Correlation of binding affinities with nonbonded interaction energies of thrombin-inhibitor complexes. Acta Crystallogr D. 51:1995;560-566.
-
(1995)
Acta Crystallogr D
, vol.51
, pp. 560-566
-
-
Grootenhuis, P.D.J.1
Van Galen, P.J.M.2
-
52
-
-
0003576242
-
Rational approaches towards protease inhibition: Predicting the binding of thrombin inhibitors
-
G. Wipff. Dordrecht: Kluwer Academic Press
-
Grootenhuis P.D.J., Van Helden S.P. Rational approaches towards protease inhibition. predicting the binding of thrombin inhibitors Wipff G. Computational Approaches in Supramolecular Chemistry. 1994;137-149 Kluwer Academic Press, Dordrecht.
-
(1994)
Computational Approaches in Supramolecular Chemistry
, pp. 137-149
-
-
Grootenhuis, P.D.J.1
Van Helden, S.P.2
-
54
-
-
0030964552
-
Specificity in structure-based drug design: Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase
-
Gschwend D.A., Sirawaraporn W., Santi D.V., Kuntz I.D. Specificity in structure-based drug design. Identification of a novel, selective inhibitor of Pneumocystis carinii dihydrofolate reductase Proteins. 29:1997;59-67.
-
(1997)
Proteins
, vol.29
, pp. 59-67
-
-
Gschwend, D.A.1
Sirawaraporn, W.2
Santi, D.V.3
Kuntz, I.D.4
-
55
-
-
0000381173
-
Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach
-
Guo Z., Brooks C.L., Kong X. Efficient and flexible algorithm for free energy calculations using the lambda-dynamics approach. J Phys Chem B. 102:1998;2032-2036.
-
(1998)
J Phys Chem B
, vol.102
, pp. 2032-2036
-
-
Guo, Z.1
Brooks, C.L.2
Kong, X.3
-
56
-
-
0037571112
-
Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94
-
Halgren T.A. Merck Molecular Force Field. I. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem. 17:1996;490-519.
-
(1996)
J Comput Chem
, vol.17
, pp. 490-519
-
-
Halgren, T.A.1
-
57
-
-
0031637651
-
Ligand binding affinity prediction by linear interaction energy methods
-
Hansson T., Marelius J., Aqvist J. Ligand binding affinity prediction by linear interaction energy methods. J Comput Aided Mol Des. 12:1998;27-35.
-
(1998)
J Comput Aided Mol des
, vol.12
, pp. 27-35
-
-
Hansson, T.1
Marelius, J.2
Aqvist, J.3
-
58
-
-
0030753409
-
Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin: Irreversible inhibition of infectivity
-
Hoffman L.R., Kuntz I.D., White J.M. Structure-based identification of an inducer of the low-pH conformational change in the influenza virus hemagglutinin. irreversible inhibition of infectivity J Virol. 71:1997;8808-8820.
-
(1997)
J Virol
, vol.71
, pp. 8808-8820
-
-
Hoffman, L.R.1
Kuntz, I.D.2
White, J.M.3
-
59
-
-
0029063951
-
A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site
-
Holloway M.K., Wai J.M., Halgren T.A., Fitzgerald P.M.D., Vacca J.P., Dorsey B.D., Levin R.B., Thompson W.J., Chen L.J., deSolms S.J., Gaffin N., Ghosh A.K., Giuliani E.A., Graham S.L., Guare J.P., Hungate R.W., Lyle T.A., Sanders W.M., Tucker T.J., Wiggins M., Wiscount C.M., Woltersdorf O.W., Young S.D., Darke P.L., Zugay J.A. A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. J Med Chem. 38:1995;305-317.
-
(1995)
J Med Chem
, vol.38
, pp. 305-317
-
-
Holloway, M.K.1
Wai, J.M.2
Halgren, T.A.3
Fitzgerald, P.M.D.4
Vacca, J.P.5
Dorsey, B.D.6
Levin, R.B.7
Thompson, W.J.8
Chen, L.J.9
Desolms, S.J.10
Gaffin, N.11
Ghosh, A.K.12
Giuliani, E.A.13
Graham, S.L.14
Guare, J.P.15
Hungate, R.W.16
Lyle, T.A.17
Sanders, W.M.18
Tucker, T.J.19
Wiggins, M.20
Wiscount, C.M.21
Woltersdorf, O.W.22
Young, S.D.23
Darke, P.L.24
Zugay, J.A.25
more..
-
60
-
-
0030666868
-
The chemical-biological interface: Developments in automated and miniaturised screening technology
-
Houston J.G., Banks M. The chemical-biological interface. developments in automated and miniaturised screening technology Curr Opin Biotechnol. 8:1997;734-740.
-
(1997)
Curr Opin Biotechnol
, vol.8
, pp. 734-740
-
-
Houston, J.G.1
Banks, M.2
-
61
-
-
0030255303
-
Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
-
Jain A.N. Scoring noncovalent protein-ligand interactions. a continuous differentiable function tuned to compute binding affinities J Comput Aided Mol Des. 10:1996;427-440.
-
(1996)
J Comput Aided Mol des
, vol.10
, pp. 427-440
-
-
Jain, A.N.1
-
62
-
-
0029796290
-
Comparison of experimental and computational functional group mapping of an RNase A structure: Implications for computer-aided drug design
-
Joseph-McCarthy D., Fedorov A.A., Almo S.C. Comparison of experimental and computational functional group mapping of an RNase A structure. implications for computer-aided drug design Protein Eng. 9:1996;773-780.
-
(1996)
Protein Eng
, vol.9
, pp. 773-780
-
-
Joseph-McCarthy, D.1
Fedorov, A.A.2
Almo, S.C.3
-
63
-
-
0030963674
-
Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs
-
Joseph-McCarthy D., Hogle J.M., Karplus M. Use of the multiple copy simultaneous search (MCSS) method to design a new class of picornavirus capsid binding drugs. Proteins. 29:1997;32-58.
-
(1997)
Proteins
, vol.29
, pp. 32-58
-
-
Joseph-McCarthy, D.1
Hogle, J.M.2
Karplus, M.3
-
64
-
-
0031425563
-
Bioinformatics in drug discovery
-
Kingsbury D.T. Bioinformatics in drug discovery. Drug Dev Res. 41:1997;120-128.
-
(1997)
Drug Dev Res
, vol.41
, pp. 120-128
-
-
Kingsbury, D.T.1
-
65
-
-
7044239742
-
Free energy calculations: Applications to chemical and biochemical phenomena
-
Kollman P. Free energy calculations. applications to chemical and biochemical phenomena Chem Rev. 93:1993;2395-2417.
-
(1993)
Chem Rev
, vol.93
, pp. 2395-2417
-
-
Kollman, P.1
-
66
-
-
0032014733
-
Knowledge-based potentials - back to the roots
-
Koppensteiner W.A., Sippl M.J. Knowledge-based potentials - back to the roots. Biochemistry Moscow. 63:1998;247-252.
-
(1998)
Biochemistry Moscow
, vol.63
, pp. 247-252
-
-
Koppensteiner, W.A.1
Sippl, M.J.2
-
67
-
-
0031296686
-
CASP2 experiences with docking flexible ligands using FLEXX
-
Kramer B., Rarey M., Lengauer T. CASP2 experiences with docking flexible ligands using FLEXX. Proteins (suppl. 1):1997;221-225.
-
(1997)
Proteins (Suppl.
, vol.1
, pp. 221-225
-
-
Kramer, B.1
Rarey, M.2
Lengauer, T.3
-
68
-
-
0026730489
-
Structure-based strategies for drug design and discovery
-
Kuntz I. Structure-based strategies for drug design and discovery. Science. 257:1992;1078-1082.
-
(1992)
Science
, vol.257
, pp. 1078-1082
-
-
Kuntz, I.1
-
69
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oarley S.J., Langridge R., Ferrin T.E. A geometric approach to macromolecule-ligand interactions. J Mol Biol. 161:1982;269-288.
-
(1982)
J Mol Biol
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oarley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
70
-
-
0028519286
-
Prediction of new serine proteinase inhibitors
-
Kurinov I.V., Harrison R.W. Prediction of new serine proteinase inhibitors. Nature Struct Biol. 1:1994;735-743.
-
(1994)
Nature Struct Biol
, vol.1
, pp. 735-743
-
-
Kurinov, I.V.1
Harrison, R.W.2
-
71
-
-
0028380643
-
Caveat - A program to facilitate the design of organic-molecules
-
Lauri G., Bartlett P.A. Caveat - a program to facilitate the design of organic-molecules. J Comput Aided Mol Des. 8:1994;51-66.
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 51-66
-
-
Lauri, G.1
Bartlett, P.A.2
-
72
-
-
0033135638
-
Effective energy function for proteins in solution
-
Lazaridis T., Karplus M. Effective energy function for proteins in solution. Proteins. 35:1999;133-152.
-
(1999)
Proteins
, vol.35
, pp. 133-152
-
-
Lazaridis, T.1
Karplus, M.2
-
74
-
-
16044363907
-
Structure-based design of parasitic protease inhibitors
-
Li R.S., Chen X.W., Gong B.Q., Selzer P.M., Li Z., Davidson E., Kurzban G., Miller R.E., Nuzum E.O., McKerrow J.H., Fletterick R.J., Gillmor S.A., Craik C.S., Kuntz I.D., Cohen F.E., Kenyon G.L. Structure-based design of parasitic protease inhibitors. Bioorg Med Chem. 4:1996;1421-1427.
-
(1996)
Bioorg Med Chem
, vol.4
, pp. 1421-1427
-
-
Li, R.S.1
Chen, X.W.2
Gong, B.Q.3
Selzer, P.M.4
Li, Z.5
Davidson, E.6
Kurzban, G.7
Miller, R.E.8
Nuzum, E.O.9
McKerrow, J.H.10
Fletterick, R.J.11
Gillmor, S.A.12
Craik, C.S.13
Kuntz, I.D.14
Cohen, F.E.15
Kenyon, G.L.16
-
75
-
-
84986528070
-
The MM3 force-field for amides, polypeptides and proteins
-
Lii J.H., Allinger N.L. The MM3 force-field for amides, polypeptides and proteins. J Comput Chem. 12:1991;186-199.
-
(1991)
J Comput Chem
, vol.12
, pp. 186-199
-
-
Lii, J.H.1
Allinger, N.L.2
-
76
-
-
0030134642
-
Estimating the relative free energy of different molecular states with respect to a single reference state
-
Liu H.Y., Mark A.E., vanGunsteren W.F. Estimating the relative free energy of different molecular states with respect to a single reference state. J Phys Chem. 100:1996;9485-9494.
-
(1996)
J Phys Chem
, vol.100
, pp. 9485-9494
-
-
Liu, H.Y.1
Mark, A.E.2
Vangunsteren, W.F.3
-
77
-
-
0001349177
-
Constructing ab initio force fields for molecular dynamics simulations
-
Liu Y.P., Kim K., Berne B.J., Friesner R.A., Rick S.W. Constructing ab initio force fields for molecular dynamics simulations. J Chem Phys. 108:1998;4739-4755.
-
(1998)
J Chem Phys
, vol.108
, pp. 4739-4755
-
-
Liu, Y.P.1
Kim, K.2
Berne, B.J.3
Friesner, R.A.4
Rick, S.W.5
-
78
-
-
0028467094
-
Computer-assisted synthetic analysis - performance of tactical combinations of transforms
-
Long A.K., Kappos J.C. Computer-assisted synthetic analysis - performance of tactical combinations of transforms. J Chem Inf Comput Sci. 34:1994;915-921.
-
(1994)
J Chem Inf Comput Sci
, vol.34
, pp. 915-921
-
-
Long, A.K.1
Kappos, J.C.2
-
79
-
-
0031965676
-
Flexible ligand docking using conformational ensembles
-
Lorber D.M., Shoichet B.K. Flexible ligand docking using conformational ensembles. Protein Sci. 7:1998;938-950.
-
(1998)
Protein Sci
, vol.7
, pp. 938-950
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
80
-
-
0041784950
-
All-atom empirical potential for molecular modeling and dynamics studies of proteins
-
MacKerell A.D., Bashford D., Bellott M., Dunbrack R.L., Evanseck J.D., Field M.J., Fischer S., Gao J., Guo H., Ha S., Joseph-McCarthy D., Kuchnir L., Kuczera K., Lau F.T.K., Mattos C., Michnick S., Ngo T., Nguyen D.T., Prodhom B., Reiher W.E., Roux B., Schlenkrich M., Smith J.C., Stote R., Straub J., Watanabe M., Wiorkiewicz-Kuczera J., Yin D., Karplus M. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 102:1998;3586-3616.
-
(1998)
J Phys Chem B
, vol.102
, pp. 3586-3616
-
-
MacKerell, A.D.1
Bashford, D.2
Bellott, M.3
Dunbrack, R.L.4
Evanseck, J.D.5
Field, M.J.6
Fischer, S.7
Gao, J.8
Guo, H.9
Ha, S.10
Joseph-McCarthy, D.11
Kuchnir, L.12
Kuczera, K.13
Lau, F.T.K.14
Mattos, C.15
Michnick, S.16
Ngo, T.17
Nguyen, D.T.18
Prodhom, B.19
Reiher, W.E.20
Roux, B.21
Schlenkrich, M.22
Smith, J.C.23
Stote, R.24
Straub, J.25
Watanabe, M.26
Wiorkiewicz-Kuczera, J.27
Yin, D.28
Karplus, M.29
more..
-
81
-
-
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. 91:1995;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
-
82
-
-
0001139413
-
Automated flexible ligand docking method and its application for database search
-
Makino S., Kuntz I.D. Automated flexible ligand docking method and its application for database search. J Comput Chem. 18:1997;1812-1825.
-
(1997)
J Comput Chem
, vol.18
, pp. 1812-1825
-
-
Makino, S.1
Kuntz, I.D.2
-
83
-
-
0002496235
-
Calculation of ligand binding free energies from molecular dynamics simulations
-
Marelius J., Hansson T., Aqvist J. Calculation of ligand binding free energies from molecular dynamics simulations. Int J Quantum Chem. 69:1998;77-88.
-
(1998)
Int J Quantum Chem
, vol.69
, pp. 77-88
-
-
Marelius, J.1
Hansson, T.2
Aqvist, J.3
-
84
-
-
84986525856
-
A comprehensive study of the rotational energy profiles of organic-systems by ab-initio MO theory, forming a basis for peptide torsional parameters
-
Maxwell D.S., Tiradorives J., Jorgensen W.L. A comprehensive study of the rotational energy profiles of organic-systems by ab-initio MO theory, forming a basis for peptide torsional parameters. J Comput Chem. 16:1995;984-1010.
-
(1995)
J Comput Chem
, vol.16
, pp. 984-1010
-
-
Maxwell, D.S.1
Tiradorives, J.2
Jorgensen, W.L.3
-
85
-
-
0031181346
-
Qxp: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C., Bohacek R.S. Qxp. Powerful, rapid computer algorithms for structure-based drug design J Comput Aided Mol Des. 11:1997;333-344.
-
(1997)
J Comput Aided Mol des
, vol.11
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
86
-
-
84986432941
-
Automated docking with grid-based energy evaluation
-
Meng E.C., Shoichet B.K., Kuntz I.D. Automated docking with grid-based energy evaluation. J Comput Chem. 13:1992;505-524.
-
(1992)
J Comput Chem
, vol.13
, pp. 505-524
-
-
Meng, E.C.1
Shoichet, B.K.2
Kuntz, I.D.3
-
87
-
-
0025916872
-
Functionality maps of binding sites: A multiple copy simultaneous search method
-
Miranker A., Karplus M. Functionality maps of binding sites. a multiple copy simultaneous search method Proteins. 11:1991;29-34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
88
-
-
0029586802
-
An automated method for dynamic ligand design
-
Miranker A., Karplus M. An automated method for dynamic ligand design. Proteins. 23:1995;472-490.
-
(1995)
Proteins
, vol.23
, pp. 472-490
-
-
Miranker, A.1
Karplus, M.2
-
89
-
-
0026345685
-
Computer design of bioactive molecules: A method for receptor-based de novo ligand design
-
Moon J., Howe W. Computer design of bioactive molecules. a method for receptor-based de novo ligand design Proteins. 11:1991;314-328.
-
(1991)
Proteins
, vol.11
, pp. 314-328
-
-
Moon, J.1
Howe, W.2
-
90
-
-
0030203710
-
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
-
Morris G.M., Goodsell D.S., Huey R., Olson A.J. Distributed automated docking of flexible ligands to proteins. parallel applications of AutoDock 2.4 J Comput Aided Mol Des. 10:1996;293-304.
-
(1996)
J Comput Aided Mol des
, vol.10
, pp. 293-304
-
-
Morris, G.M.1
Goodsell, D.S.2
Huey, R.3
Olson, A.J.4
-
91
-
-
0000036869
-
Simulation of activation energies in molecular systems
-
Neria E., Fischer S., Karplus M. Simulation of activation energies in molecular systems. J Chem Phys. 105:1996;1902-1921.
-
(1996)
J Chem Phys
, vol.105
, pp. 1902-1921
-
-
Neria, E.1
Fischer, S.2
Karplus, M.3
-
92
-
-
84986486656
-
A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
-
Nicholls A., Honig B. A rapid finite-difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation. J Comput Chem. 12:1991;435-445.
-
(1991)
J Comput Chem
, vol.12
, pp. 435-445
-
-
Nicholls, A.1
Honig, B.2
-
93
-
-
0031547977
-
Empirical free energy calculations: A blind test and further improvements to the method
-
Novotny J., Bruccoleri R.E., Davis M., Sharp K.A. Empirical free energy calculations. a blind test and further improvements to the method J Mol Biol. 268:1997;401-411.
-
(1997)
J Mol Biol
, vol.268
, pp. 401-411
-
-
Novotny, J.1
Bruccoleri, R.E.2
Davis, M.3
Sharp, K.A.4
-
95
-
-
0023338543
-
Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides
-
Ooi W., Oobataki M., Nemethy G., Scheraga H.A. Accessible surface areas as a measure of the thermodynamic parameters of hydration of peptides. Proc Natl Acad Sci USA. 84:1987;3086-3090.
-
(1987)
Proc Natl Acad Sci USA
, vol.84
, pp. 3086-3090
-
-
Ooi, W.1
Oobataki, M.2
Nemethy, G.3
Scheraga, H.A.4
-
96
-
-
0009235161
-
A comparison of alternative approaches to free energy calculations
-
Pearlman D.A. A comparison of alternative approaches to free energy calculations. J Phys Chem. 98:1994;1487-1493.
-
(1994)
J Phys Chem
, vol.98
, pp. 1487-1493
-
-
Pearlman, D.A.1
-
97
-
-
0029965861
-
Concerts: Dynamic connection of fragments as an approach to de novo ligand design
-
Pearlman D.A., Murcko M. Concerts. dynamic connection of fragments as an approach to de novo ligand design J Med Chem. 39:1996;1651-1663.
-
(1996)
J Med Chem
, vol.39
, pp. 1651-1663
-
-
Pearlman, D.A.1
Murcko, M.2
-
98
-
-
0001797110
-
Rapid generation of high quality approximate 3D molecular structures
-
Pearlman R.S. Rapid generation of high quality approximate 3D molecular structures. Chem Des Aut News. 2:1987;1-6.
-
(1987)
Chem des Aut News
, vol.2
, pp. 1-6
-
-
Pearlman, R.S.1
-
99
-
-
0029911948
-
For medicinal purposes
-
Petsko G.A. For medicinal purposes. Nature. 384:1996;7-9.
-
(1996)
Nature
, vol.384
, pp. 7-9
-
-
Petsko, G.A.1
-
100
-
-
0030076041
-
Placement of medium-sized molecular fragments into active sites of proteins
-
Rarey M., Wefing S., Lengauer T. Placement of medium-sized molecular fragments into active sites of proteins. J Comput Aided Mol Des. 10:1996;41-54.
-
(1996)
J Comput Aided Mol des
, vol.10
, pp. 41-54
-
-
Rarey, M.1
Wefing, S.2
Lengauer, T.3
-
101
-
-
0027697487
-
Comparison of conformations of small-molecule structures from the protein data-bank with those generated by Concord, Cobra, Chemdbs-3d, and Converter and those extracted from the Cambridge Structural Database
-
Ricketts E.M., Bradshaw J., Hann M., Hayes F., Tanna N., Ricketts D.M. Comparison of conformations of small-molecule structures from the protein data-bank with those generated by Concord, Cobra, Chemdbs-3d, and Converter and those extracted from the Cambridge Structural Database. J Chem Inf Comput Sci. 33:1993;905-925.
-
(1993)
J Chem Inf Comput Sci
, vol.33
, pp. 905-925
-
-
Ricketts, E.M.1
Bradshaw, J.2
Hann, M.3
Hayes, F.4
Tanna, N.5
Ricketts, D.M.6
-
102
-
-
0027480452
-
Structure-based inhibitor design by using protein models for the development of antiparasitic agents
-
Ring C., Sun E., McKerrow J., Lee G., Rosenthal P., Kuntz I., Cohen F. Structure-based inhibitor design by using protein models for the development of antiparasitic agents. Proc Natl Acad Sci USA. 90:1993;3583-3587.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 3583-3587
-
-
Ring, C.1
Sun, E.2
McKerrow, J.3
Lee, G.4
Rosenthal, P.5
Kuntz, I.6
Cohen, F.7
-
103
-
-
0028077638
-
Structure-assisted design of nonpeptide human immunodeficiency virus-1 protease inhibitors
-
Rose J.R., Craik C.S. Structure-assisted design of nonpeptide human immunodeficiency virus-1 protease inhibitors. Am J Respir Crit Care Med. 150:1994;S176-S182.
-
(1994)
Am J Respir Crit Care Med
, vol.150
-
-
Rose, J.R.1
Craik, C.S.2
-
104
-
-
0032521218
-
Marrying structure and genomics
-
Rost B. Marrying structure and genomics. Structure. 6:1998;259-263.
-
(1998)
Structure
, vol.6
, pp. 259-263
-
-
Rost, B.1
-
106
-
-
0027193713
-
Groupbuild - A fragment-based method for de novo drug design
-
b
-
Rotstein S.H., Murcko M.A. Groupbuild - a fragment-based method for de novo drug design. J Med Chem. 36:1993;1700-1710. b.
-
(1993)
J Med Chem
, vol.36
, pp. 1700-1710
-
-
Rotstein, S.H.1
Murcko, M.A.2
-
107
-
-
0025283002
-
Electrostatic interactions in macromolecules - theory and applications
-
Sharp K.A., Honig B. Electrostatic interactions in macromolecules - theory and applications. Annu Rev Biophys Biophys Chem. 19:1990;301-332.
-
(1990)
Annu Rev Biophys Biophys Chem
, vol.19
, pp. 301-332
-
-
Sharp, K.A.1
Honig, B.2
-
108
-
-
0027522358
-
Structure-based discovery of inhibitors of thymidylate synthase
-
Shoichet B.K., Stroud R.M., Santi D.V., Kuntz I.D., Perry K.M. Structure-based discovery of inhibitors of thymidylate synthase. Science. 259:1993;1445-1450.
-
(1993)
Science
, vol.259
, pp. 1445-1450
-
-
Shoichet, B.K.1
Stroud, R.M.2
Santi, D.V.3
Kuntz, I.D.4
Perry, K.M.5
-
110
-
-
0029836953
-
Discovering high-affinity ligands for proteins: SAR by NMR
-
Shuker S.B., Hajduk P.J., Meadows R.P., Fesik S.W. Discovering high-affinity ligands for proteins. SAR by NMR Science. 274:1996;1531-1534.
-
(1996)
Science
, vol.274
, pp. 1531-1534
-
-
Shuker, S.B.1
Hajduk, P.J.2
Meadows, R.P.3
Fesik, S.W.4
-
111
-
-
0031561292
-
Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding
-
Simonson T., Archontis G., Karplus M. Continuum treatment of long-range interactions in free energy calculations. Application to protein-ligand binding. J Phys Chem B. 101:1997;8349-8362.
-
(1997)
J Phys Chem B
, vol.101
, pp. 8349-8362
-
-
Simonson, T.1
Archontis, G.2
Karplus, M.3
-
112
-
-
0033045557
-
A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors
-
So S.S., Karplus M. A comparative study of ligand-receptor complex binding affinity prediction methods based on glycogen phosphorylase inhibitors. J Comput Aided Mol Des. 13:1999;243-258.
-
(1999)
J Comput Aided Mol des
, vol.13
, pp. 243-258
-
-
So, S.S.1
Karplus, M.2
-
113
-
-
0005123846
-
Automated chemical hypothesis generation and database searching with Catalyst®
-
Sprague P.W. Automated chemical hypothesis generation and database searching with Catalyst® Perspect Drug Discov Des. 3:1995;1-20.
-
(1995)
Perspect Drug Discov des
, vol.3
, pp. 1-20
-
-
Sprague, P.W.1
-
115
-
-
0345445667
-
Pharmacophore-based molecular docking. In O. F. Guner (Ed.), Pharmacophore perception, development, and use in drug design
-
Thomas B.E. IV, Joseph-McCarthy D., Alvarez J.C. Pharmacophore-based molecular docking. In O. F. Guner (Ed.), Pharmacophore perception, development, and use in drug design. La Jolla: International University Press. in press:1999.
-
(1999)
La Jolla: International University Press
-
-
Thomas B.E. IV1
Joseph-McCarthy, D.2
Alvarez, J.C.3
-
116
-
-
33751385859
-
Simulated annealing on free-energy surfaces by a combined molecular-dynamics and Monte-Carlo approach
-
Tidor B. Simulated annealing on free-energy surfaces by a combined molecular-dynamics and Monte-Carlo approach. J Phys Chem. 97:1993;1069-1073.
-
(1993)
J Phys Chem
, vol.97
, pp. 1069-1073
-
-
Tidor, B.1
-
117
-
-
0028773887
-
Structure-based drug design: Progress, results and challenges
-
Verlinde C.L.M.J., Hol W.G.J. Structure-based drug design. progress, results and challenges Structure. 2:1994;577-587.
-
(1994)
Structure
, vol.2
, pp. 577-587
-
-
Verlinde, C.L.M.J.1
Hol, W.G.J.2
-
118
-
-
0030044141
-
A study of the active site of influenza virus sialidase: An approach to the rational design of novel anti-influenza drugs
-
von Itzstein M., Dyason J.C., Oliver S.W., White H.F., Wu W.Y., Kok G.B., Pegg M.S. A study of the active site of influenza virus sialidase. an approach to the rational design of novel anti-influenza drugs J Med Chem. 39:1996;388-391.
-
(1996)
J Med Chem
, vol.39
, pp. 388-391
-
-
Von Itzstein, M.1
Dyason, J.C.2
Oliver, S.W.3
White, H.F.4
Wu, W.Y.5
Kok, G.B.6
Pegg, M.S.7
-
119
-
-
0027510004
-
Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds
-
Wade R., Goodford P. Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 2. Ligand probe groups with the ability to form more than two hydrogen bonds. J Med Chem. 36:1993;148-156.
-
(1993)
J Med Chem
, vol.36
, pp. 148-156
-
-
Wade, R.1
Goodford, P.2
-
120
-
-
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., Clark K., Goodford P. 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. 36:1993;140-147.
-
(1993)
J Med Chem
, vol.36
, pp. 140-147
-
-
Wade, R.1
Clark, K.2
Goodford, P.3
-
121
-
-
0030154893
-
Hammerhead: Fast, fully automated docking of flexible ligands to protein binding sites
-
Welch W., Ruppert J., Jain A.N. Hammerhead. fast, fully automated docking of flexible ligands to protein binding sites Chem Biol. 3:1996;449-462.
-
(1996)
Chem Biol
, vol.3
, pp. 449-462
-
-
Welch, W.1
Ruppert, J.2
Jain, A.N.3
-
123
-
-
84888116612
-
Combinatorial chemistry
-
Wilson E.K. Combinatorial chemistry. Chem Eng News. 75:1997;24-25.
-
(1997)
Chem Eng News
, vol.75
, pp. 24-25
-
-
Wilson, E.K.1
-
124
-
-
0031804609
-
Inhibitors of HIV-1 protease: A major success of structure-assisted drug design
-
Wlodawer A., Vondrasek J. Inhibitors of HIV-1 protease. a major success of structure-assisted drug design Annu Rev Biophys Biomol Struct. 27:1998;249-284.
-
(1998)
Annu Rev Biophys Biomol Struct
, vol.27
, pp. 249-284
-
-
Wlodawer, A.1
Vondrasek, J.2
-
125
-
-
0032540860
-
Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A(2)
-
Xu G.Y., McDonagh T., Yu H.A., Nalefski E.A., Clark J.D., Cumming D.A. Solution structure and membrane interactions of the C2 domain of cytosolic phospholipase A(2). J Mol Biol. 280:1998;485-500.
-
(1998)
J Mol Biol
, vol.280
, pp. 485-500
-
-
Xu, G.Y.1
McDonagh, T.2
Yu, H.A.3
Nalefski, E.A.4
Clark, J.D.5
Cumming, D.A.6
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