-
1
-
-
40949163431
-
Role of the active-site solvent thermodynamics of factor Xa ligand binding
-
Abel R., Young T., Farid R., Berne B.J., and Friesner R.A. Role of the active-site solvent thermodynamics of factor Xa ligand binding. J. Am. Chem. Soc. 130 (2008) 2817-2831
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 2817-2831
-
-
Abel, R.1
Young, T.2
Farid, R.3
Berne, B.J.4
Friesner, R.A.5
-
2
-
-
36749008588
-
Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
-
Arora K., and Brooks III C.L. Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 18496-18501
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 18496-18501
-
-
Arora, K.1
Brooks III, C.L.2
-
3
-
-
43049129991
-
Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase
-
Babaoglu K., Simeonov A., Irwin J.J., Nelson M.E., Feng B., Thomas C.J., Cancian L., Costi M.P., Maltby D.A., Jadhav A., et al. Comprehensive mechanistic analysis of hits from high-throughput and docking screens against beta-lactamase. J. Med. Chem. 51 (2008) 2502-2511
-
(2008)
J. Med. Chem.
, vol.51
, pp. 2502-2511
-
-
Babaoglu, K.1
Simeonov, A.2
Irwin, J.J.3
Nelson, M.E.4
Feng, B.5
Thomas, C.J.6
Cancian, L.7
Costi, M.P.8
Maltby, D.A.9
Jadhav, A.10
-
4
-
-
0001158480
-
Structural analysis of a series of antiviral agents complexed with human rhinovirus 14
-
Badger J., Minor I., Kremer M.J., Oliveira M.A., Smith T.J., Griffith J.P., Guerin D.M.A., Krishnaswamy S., Luo M., Rossmann M.G., et al. Structural analysis of a series of antiviral agents complexed with human rhinovirus 14. Proc. Natl. Acad. Sci. U.S.A. 85 (1988) 3304-3308
-
(1988)
Proc. Natl. Acad. Sci. U.S.A.
, vol.85
, pp. 3304-3308
-
-
Badger, J.1
Minor, I.2
Kremer, M.J.3
Oliveira, M.A.4
Smith, T.J.5
Griffith, J.P.6
Guerin, D.M.A.7
Krishnaswamy, S.8
Luo, M.9
Rossmann, M.G.10
-
5
-
-
33847655150
-
Classification of water molecules in protein binding sites
-
Barillari C., Taylor J., Viner R., and Essex J.W. Classification of water molecules in protein binding sites. J. Am. Chem. Soc. 129 (2007) 2577-2587
-
(2007)
J. Am. Chem. Soc.
, vol.129
, pp. 2577-2587
-
-
Barillari, C.1
Taylor, J.2
Viner, R.3
Essex, J.W.4
-
6
-
-
0023106632
-
Calculation of the relative change in binding free energy of a protein-inhibitor complex
-
Bash P.A., Singh U.C., Brown F.K., Langridge R., and Kollman P.A. Calculation of the relative change in binding free energy of a protein-inhibitor complex. Science 235 (1987) 574-576
-
(1987)
Science
, vol.235
, pp. 574-576
-
-
Bash, P.A.1
Singh, U.C.2
Brown, F.K.3
Langridge, R.4
Kollman, P.A.5
-
7
-
-
0024498518
-
Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding
-
Birdsall B., Feeney J., Tendler S.J.B., Hammond S.J., and Roberts G.C.K. Dihydrofolate reductase: multiple conformations and alternative modes of substrate binding. Biochemistry 28 (1989) 2297-2305
-
(1989)
Biochemistry
, vol.28
, pp. 2297-2305
-
-
Birdsall, B.1
Feeney, J.2
Tendler, S.J.B.3
Hammond, S.J.4
Roberts, G.C.K.5
-
8
-
-
33748781457
-
The dynamic energy landscape of dihydrofolate reductase catalysis
-
Boehr D.D., McElheny D., Dyson H.J., and Wright P.E. The dynamic energy landscape of dihydrofolate reductase catalysis. Science 313 (2006) 1638-1642
-
(2006)
Science
, vol.313
, pp. 1638-1642
-
-
Boehr, D.D.1
McElheny, D.2
Dyson, H.J.3
Wright, P.E.4
-
9
-
-
0028454828
-
The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
-
Böhm 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. 8 (1993) 243-256
-
(1993)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 243-256
-
-
Böhm, H.J.1
-
10
-
-
0030474049
-
What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
-
Böhm H.J., and 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
-
-
Böhm, H.J.1
Klebe, G.2
-
11
-
-
0141682863
-
Absolute binding free energies: a quantitative approach for their calculation
-
Boresch S., Tettinger F., Leitgeb M., and Karplus M. Absolute binding free energies: a quantitative approach for their calculation. J. Phys. Chem. A 107 (2003) 9535-9551
-
(2003)
J. Phys. Chem. A
, vol.107
, pp. 9535-9551
-
-
Boresch, S.1
Tettinger, F.2
Leitgeb, M.3
Karplus, M.4
-
12
-
-
33750981540
-
Do structurally similar ligands bind in a similar fashion?
-
Bostrom J., Hogner A., and Schmitt S. Do structurally similar ligands bind in a similar fashion?. J. Med. Chem. 49 (2006) 6716-6725
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6716-6725
-
-
Bostrom, J.1
Hogner, A.2
Schmitt, S.3
-
13
-
-
33645060728
-
Probing molecular docking at a charged model binding site
-
Brenk R., Vetter S.W., Boyce S.E., Goodin D.B., and Shoichet B.K. Probing molecular docking at a charged model binding site. J. Mol. Biol. 357 (2006) 1449-1470
-
(2006)
J. Mol. Biol.
, vol.357
, pp. 1449-1470
-
-
Brenk, R.1
Vetter, S.W.2
Boyce, S.E.3
Goodin, D.B.4
Shoichet, B.K.5
-
14
-
-
5644287368
-
Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm
-
Chang C.E., and Gilson M.K. Free energy, entropy, and induced fit in host-guest recognition: calculations with the second-generation mining minima algorithm. J. Am. Chem. Soc. 126 (2004) 13156-13164
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 13156-13164
-
-
Chang, C.E.1
Gilson, M.K.2
-
16
-
-
0008589609
-
Recent successes and continuing limitations in computer aided drug design
-
Charifson P.S. (Ed), Dekker, New York
-
Charifson P.S., and Kuntz I.D. Recent successes and continuing limitations in computer aided drug design. In: Charifson P.S. (Ed). Practical Application of Computer Aided Drug Design (1997), Dekker, New York
-
(1997)
Practical Application of Computer Aided Drug Design
-
-
Charifson, P.S.1
Kuntz, I.D.2
-
17
-
-
0031788539
-
Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution
-
Cheatham T.E., Srinivasan J., Case D.A., and Kollman P.A. Molecular dynamics and continuum solvent studies of the stability of polyG-polyC and polyA-polyT DNA duplexes in solution. J. Biomol. Struct. Dyn. 16 (1998) 265-280
-
(1998)
J. Biomol. Struct. Dyn.
, vol.16
, pp. 265-280
-
-
Cheatham, T.E.1
Srinivasan, J.2
Case, D.A.3
Kollman, P.A.4
-
18
-
-
16344395749
-
Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design
-
Chen W., Chang C.E., and Gilson M.K. Calculation of cyclodextrin binding affinities: energy, entropy, and implications for drug design. Biophys. J. 87 (2004) 3035-3049
-
(2004)
Biophys. J.
, vol.87
, pp. 3035-3049
-
-
Chen, W.1
Chang, C.E.2
Gilson, M.K.3
-
19
-
-
33644955487
-
The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution
-
Chen Y., Minasov G., Roth T.A., Prati F., and Shoichet B.K. The deacylation mechanism of AmpC beta-lactamase at ultrahigh resolution. J. Am. Chem. Soc. 128 (2006) 2970-2976
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 2970-2976
-
-
Chen, Y.1
Minasov, G.2
Roth, T.A.3
Prati, F.4
Shoichet, B.K.5
-
20
-
-
0034835794
-
Protein side-chain rotamers from dipolar couplings in a liquid crystalline phase
-
Chou J.J., and Bax A. Protein side-chain rotamers from dipolar couplings in a liquid crystalline phase. J. Am. Chem. Soc. 123 (2001) 3844-3845
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 3844-3845
-
-
Chou, J.J.1
Bax, A.2
-
21
-
-
53549089920
-
Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects
-
Constantine K.L., Mueller L., Metzler W.J., McDonnell P.A., Todderud G., Goldfarb V., Fan Y., Newitt J.A., Keifer S.E., Gao M., et al. Multiple and single binding modes of fragment-like kinase inhibitors revealed by molecular modeling, residue type-selective protonation, and nuclear overhauser effects. J. Med. Chem. 51 (2008) 6225-6229
-
(2008)
J. Med. Chem.
, vol.51
, pp. 6225-6229
-
-
Constantine, K.L.1
Mueller, L.2
Metzler, W.J.3
McDonnell, P.A.4
Todderud, G.5
Goldfarb, V.6
Fan, Y.7
Newitt, J.A.8
Keifer, S.E.9
Gao, M.10
-
22
-
-
34247197110
-
Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0
-
Corbeil C.R., Englebienne P., and Moitessier N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 47 (2007) 435-449
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 435-449
-
-
Corbeil, C.R.1
Englebienne, P.2
Moitessier, N.3
-
23
-
-
54549098184
-
Target flexibility: an emerging consideration in drug discovery and design
-
Cozzini P., Kellogg G.E., Spyrakis F., Abraham D.J., Constntino G., Emerson A., Fanelli F., Gohlke H., Kuhn L.A., Morris G.M., et al. Target flexibility: an emerging consideration in drug discovery and design. J. Med. Chem. 51 (2008) 6237-6255
-
(2008)
J. Med. Chem.
, vol.51
, pp. 6237-6255
-
-
Cozzini, P.1
Kellogg, G.E.2
Spyrakis, F.3
Abraham, D.J.4
Constntino, G.5
Emerson, A.6
Fanelli, F.7
Gohlke, H.8
Kuhn, L.A.9
Morris, G.M.10
-
24
-
-
34547657456
-
Atypical protonation states in the active site of HIV-1 protease: a computational study
-
Czodrowski P., Sotriffer C.A., and Klebe G. Atypical protonation states in the active site of HIV-1 protease: a computational study. J. Chem. Inf. Model. 47 (2007) 1590-1598
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1590-1598
-
-
Czodrowski, P.1
Sotriffer, C.A.2
Klebe, G.3
-
25
-
-
33749238080
-
Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant
-
Deng Y., and Roux B. Calculation of standard binding free energies: aromatic molecules in the T4 lysozyme L99A mutant. J. Chem. Theory Comput. 2 (2006) 1255-1273
-
(2006)
J. Chem. Theory Comput.
, vol.2
, pp. 1255-1273
-
-
Deng, Y.1
Roux, B.2
-
26
-
-
0035799367
-
Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase
-
Deng H., Zhadin N., and Callender R. Dynamics of protein ligand binding on multiple time scales: NADH binding to lactate dehydrogenase. Biochemistry 40 (2001) 3767-3773
-
(2001)
Biochemistry
, vol.40
, pp. 3767-3773
-
-
Deng, H.1
Zhadin, N.2
Callender, R.3
-
27
-
-
0035955550
-
Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition
-
Dullweber F., Stubbs M.T., Musil D., Sturzebecher J., and Klebe G. Factorising ligand affinity: a combined thermodynamic and crystallographic study of trypsin and thrombin inhibition. J. Mol. Biol. 313 (2001) 593-614
-
(2001)
J. Mol. Biol.
, vol.313
, pp. 593-614
-
-
Dullweber, F.1
Stubbs, M.T.2
Musil, D.3
Sturzebecher, J.4
Klebe, G.5
-
29
-
-
27744499156
-
Intrinsic dynamics of an enzyme underlies catalysis
-
Eisenmesser E.Z., Millet O., Labeikovsky W., Korzhnev D.M., Wolf-Watz M., Bosco D.A., Skalicky J.J., Kay L.E., and Kern D. Intrinsic dynamics of an enzyme underlies catalysis. Nature 438 (2005) 117-121
-
(2005)
Nature
, vol.438
, pp. 117-121
-
-
Eisenmesser, E.Z.1
Millet, O.2
Labeikovsky, W.3
Korzhnev, D.M.4
Wolf-Watz, M.5
Bosco, D.A.6
Skalicky, J.J.7
Kay, L.E.8
Kern, D.9
-
30
-
-
1942471391
-
Assessing scoring functions for protein-ligand interactions
-
Ferrara P., Gohlke H., Price D.J., Klebe G., Charles L., and Brooks I.I.I. Assessing scoring functions for protein-ligand interactions. J. Med. Chem. 47 (2004) 3032-3047
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3032-3047
-
-
Ferrara, P.1
Gohlke, H.2
Price, D.J.3
Klebe, G.4
Charles, L.5
Brooks, I.I.I.6
-
31
-
-
33846230547
-
"Four-dimensional" protein structures: examples from metalloproteins
-
Fragai M., Luchinat C., and Parigi G. "Four-dimensional" protein structures: examples from metalloproteins. Acc. Chem. Res. 39 (2006) 909-917
-
(2006)
Acc. Chem. Res.
, vol.39
, pp. 909-917
-
-
Fragai, M.1
Luchinat, C.2
Parigi, G.3
-
32
-
-
33646415982
-
Direct calculation of the binding free energies of FKBP ligands
-
Fujitani H., Tanida Y., Ito M., Shirts M.R., Jayachandran G., Snow C.D., Sorin E.J., and Pande V.S. Direct calculation of the binding free energies of FKBP ligands. J. Chem. Phys. 123 (2005) 084108
-
(2005)
J. Chem. Phys.
, vol.123
, pp. 084108
-
-
Fujitani, H.1
Tanida, Y.2
Ito, M.3
Shirts, M.R.4
Jayachandran, G.5
Snow, C.D.6
Sorin, E.J.7
Pande, V.S.8
-
33
-
-
0037147768
-
Structure-based design and protein X-ray analysis of a protein kinase inhibitor
-
Furet P., Meyer T., Strauss A., Raccuglia S., and Rondeau J.M. Structure-based design and protein X-ray analysis of a protein kinase inhibitor. Bioorg. Med. Chem. Lett. 12 (2002) 221-224
-
(2002)
Bioorg. Med. Chem. Lett.
, vol.12
, pp. 221-224
-
-
Furet, P.1
Meyer, T.2
Strauss, A.3
Raccuglia, S.4
Rondeau, J.M.5
-
34
-
-
0027999378
-
The mobile flavin of 4-OH benzoate hydroxylase
-
Gatti D.L., Palfrey B.A., Lah M.S., Entsch B., Massey V., Ballou D.P., and Ludwig M.L. The mobile flavin of 4-OH benzoate hydroxylase. Science 266 (1994) 110-114
-
(1994)
Science
, vol.266
, pp. 110-114
-
-
Gatti, D.L.1
Palfrey, B.A.2
Lah, M.S.3
Entsch, B.4
Massey, V.5
Ballou, D.P.6
Ludwig, M.L.7
-
35
-
-
0028335096
-
Structural mechanisms for domain movements in proteins
-
Gerstein M., Lesk A.M., and Chothia C. Structural mechanisms for domain movements in proteins. Biochemistry 33 (1994) 6739-6749
-
(1994)
Biochemistry
, vol.33
, pp. 6739-6749
-
-
Gerstein, M.1
Lesk, A.M.2
Chothia, C.3
-
37
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
Gohlke H., and Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew. Chem. Int. Ed. 41 (2002) 2645-2676
-
(2002)
Angew. Chem. Int. Ed.
, vol.41
, pp. 2645-2676
-
-
Gohlke, H.1
Klebe, G.2
-
39
-
-
40649101151
-
Rescoring docking hit lists for model cavity sites: predictions and experimental testing
-
Graves A.P., Shivakumar D.M., Boyce S.E., Jacobson M.P., Case D.A., and Shoichet B.K. Rescoring docking hit lists for model cavity sites: predictions and experimental testing. J. Mol. Biol. 377 (2008) 914-934
-
(2008)
J. Mol. Biol.
, vol.377
, pp. 914-934
-
-
Graves, A.P.1
Shivakumar, D.M.2
Boyce, S.E.3
Jacobson, M.P.4
Case, D.A.5
Shoichet, B.K.6
-
40
-
-
0028297112
-
Application of the three-dimensional structures of protein target molecules in structure-based drug design
-
Greer J., Erickson J.W., Baldwin J.J., and Varney M.D. Application of the three-dimensional structures of protein target molecules in structure-based drug design. J. Med. Chem. 37 (1994) 1035-1047
-
(1994)
J. Med. Chem.
, vol.37
, pp. 1035-1047
-
-
Greer, J.1
Erickson, J.W.2
Baldwin, J.J.3
Varney, M.D.4
-
41
-
-
45749138489
-
MM-GB/SA rescoring of docking poses in structure-based lead optimization
-
Guimaraes C.R.W., and Cardozo M. MM-GB/SA rescoring of docking poses in structure-based lead optimization. J. Chem. Inf. Model. 48 (2008) 958-970
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 958-970
-
-
Guimaraes, C.R.W.1
Cardozo, M.2
-
42
-
-
12344307441
-
Conformational changes observed in enzyme crystal structures upon substrate binding
-
Gutteridge A., and Thornton J. Conformational changes observed in enzyme crystal structures upon substrate binding. J. Mol. Biol. 346 (2005) 21-28
-
(2005)
J. Mol. Biol.
, vol.346
, pp. 21-28
-
-
Gutteridge, A.1
Thornton, J.2
-
43
-
-
2942659093
-
Standard free energy of releasing a localized water molecule from the binding pockets of proteins: double-decoupling method
-
Hamelberg D., and 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. 126 (2004) 7683-7689
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 7683-7689
-
-
Hamelberg, D.1
McCammon, J.A.2
-
44
-
-
37249023634
-
Torsion angle preference and energetics of small-molecule ligands bound to proteins
-
Hao M.H., Haq O., and Muegge I. Torsion angle preference and energetics of small-molecule ligands bound to proteins. J. Chem. Inf. Model. 47 (2007) 2242-2252
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 2242-2252
-
-
Hao, M.H.1
Haq, O.2
Muegge, I.3
-
45
-
-
3843108916
-
A napthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase
-
Hazuda D.J., Anthony N.J., Gomez R.P., Jolly S.M., Wai J.S., Zhuang L., Fisher T.E., Embrey M., Guare Jr. J.P., Egbertson M.S., et al. A napthyridine carboxamide provides evidence for discordant resistance between mechanistically identical inhibitors of HIV-1 integrase. Proc. Natl. Acad. Sci. U.S.A. 101 (2004) 11233-11238
-
(2004)
Proc. Natl. Acad. Sci. U.S.A.
, vol.101
, pp. 11233-11238
-
-
Hazuda, D.J.1
Anthony, N.J.2
Gomez, R.P.3
Jolly, S.M.4
Wai, J.S.5
Zhuang, L.6
Fisher, T.E.7
Embrey, M.8
Guare Jr., J.P.9
Egbertson, M.S.10
-
46
-
-
0031079364
-
"Mining minima": direct computation of conformational free energy
-
Head M.S., Given J.A., and Gilson M.K. "Mining minima": direct computation of conformational free energy. J. Phys. Chem. A 101 (1997) 1609-1618
-
(1997)
J. Phys. Chem. A
, vol.101
, pp. 1609-1618
-
-
Head, M.S.1
Given, J.A.2
Gilson, M.K.3
-
47
-
-
0029160249
-
Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study
-
Helms V., and Wade R.C. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study. Biophys. J. 69 (1995) 810-824
-
(1995)
Biophys. J.
, vol.69
, pp. 810-824
-
-
Helms, V.1
Wade, R.C.2
-
48
-
-
0032054675
-
Computational alchemy to calculate absolute protein-ligand binding free energy
-
Helms V., and Wade R.C. Computational alchemy to calculate absolute protein-ligand binding free energy. J. Am. Chem. Soc. 120 (1998) 2710-2713
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 2710-2713
-
-
Helms, V.1
Wade, R.C.2
-
49
-
-
0032529586
-
Hydration energy landscape of the active site cavity in cytochrome P450cam
-
Helms V., and Wade R.C. Hydration energy landscape of the active site cavity in cytochrome P450cam. Proteins Struct. Funct. Genet. 32 (1998) 381-396
-
(1998)
Proteins Struct. Funct. Genet.
, vol.32
, pp. 381-396
-
-
Helms, V.1
Wade, R.C.2
-
50
-
-
37249032102
-
Dynamic personalities of proteins
-
Henzler-Wildman K., and Kern D. Dynamic personalities of proteins. Nature 450 (2007) 964-972
-
(2007)
Nature
, vol.450
, pp. 964-972
-
-
Henzler-Wildman, K.1
Kern, D.2
-
51
-
-
36849048228
-
Intrinsic motions along an enzymatic reaction trajectory
-
Henzler-Wildman K.A., Thai V., Lei M., Ott M., Wolf-Watz M., Fenn T., Pozharski E., Wilson M.A., Petsko G.A., Karplus M., et al. Intrinsic motions along an enzymatic reaction trajectory. Nature 450 (2007) 838-844
-
(2007)
Nature
, vol.450
, pp. 838-844
-
-
Henzler-Wildman, K.A.1
Thai, V.2
Lei, M.3
Ott, M.4
Wolf-Watz, M.5
Fenn, T.6
Pozharski, E.7
Wilson, M.A.8
Petsko, G.A.9
Karplus, M.10
-
52
-
-
85005687495
-
The free energy of xenon binding to myoglobin from molecular dynamics simulation
-
Hermans J., and Subramaniam S. The free energy of xenon binding to myoglobin from molecular dynamics simulation. Isr. J. Chem. 27 (1986) 225-227
-
(1986)
Isr. J. Chem.
, vol.27
, pp. 225-227
-
-
Hermans, J.1
Subramaniam, S.2
-
53
-
-
0030887944
-
Inclusion of the loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme
-
Hermans J., and Wang L. Inclusion of the loss of translational and rotational freedom in theoretical estimates of free energies of binding. Application to a complex of benzene and mutant T4 lysozyme. J. Am. Chem. Soc. 119 (1997) 2707-2714
-
(1997)
J. Am. Chem. Soc.
, vol.119
, pp. 2707-2714
-
-
Hermans, J.1
Wang, L.2
-
54
-
-
34347235156
-
Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins
-
Hilser V.J., and Thompson E.B. Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins. Proc. Natl. Acad. Sci. U.S.A. 104 (2007) 8311-8315
-
(2007)
Proc. Natl. Acad. Sci. U.S.A.
, vol.104
, pp. 8311-8315
-
-
Hilser, V.J.1
Thompson, E.B.2
-
55
-
-
34249040810
-
Physics-based methods for studying protein-ligand interactions
-
Huang N., and Jacobson M.P. Physics-based methods for studying protein-ligand interactions. Curr. Opin. Drug Discov. Dev. 10 (2007) 325-331
-
(2007)
Curr. Opin. Drug Discov. Dev.
, vol.10
, pp. 325-331
-
-
Huang, N.1
Jacobson, M.P.2
-
57
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
Huey R., Morris G.M., Olson A.J., and Goodsell D.S. A semiempirical free energy force field with charge-based desolvation. J. Comput. Chem. 28 (2007) 1145-1152
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
58
-
-
0037187412
-
Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design
-
Huo S., Wang J., Cieplak P., Kollman P.A., and Kuntz I.D. Molecular dynamics and free energy analyses of cathepsin D-inhibitor interactions: insight into structure-based ligand design. J. Med. Chem. 45 (2002) 1412-1419
-
(2002)
J. Med. Chem.
, vol.45
, pp. 1412-1419
-
-
Huo, S.1
Wang, J.2
Cieplak, P.3
Kollman, P.A.4
Kuntz, I.D.5
-
59
-
-
33748267063
-
Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics
-
Jayachandran G., Shirts M.R., Park S., and Pande V.S. Parallelized-over-parts computation of absolute binding free energy with docking and molecular dynamics. J. Chem. Phys. 125 (2006) 084901
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 084901
-
-
Jayachandran, G.1
Shirts, M.R.2
Park, S.3
Pande, V.S.4
-
60
-
-
44049091290
-
Calculation of protein-ligand binding free energy using a polarizable potential
-
Jiao D., Golubkov P.A., Darden T.A., and Ren P. Calculation of protein-ligand binding free energy using a polarizable potential. Proc. Nat. Acad. Sci U.S.A. 105 (2008) 6290-6295
-
(2008)
Proc. Nat. Acad. Sci U.S.A.
, vol.105
, pp. 6290-6295
-
-
Jiao, D.1
Golubkov, P.A.2
Darden, T.A.3
Ren, P.4
-
61
-
-
1642357706
-
The many roles of computation in drug discovery
-
Jorgensen W.L. The many roles of computation in drug discovery. Science 303 (2004) 1813-1818
-
(2004)
Science
, vol.303
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
62
-
-
0034824313
-
Electrostatic complementarity at ligand binding sites: application to chorismate mutase
-
Kangas E., and Tidor B. Electrostatic complementarity at ligand binding sites: application to chorismate mutase. J. Phys. Chem. B 105 (2001) 880-888
-
(2001)
J. Phys. Chem. B
, vol.105
, pp. 880-888
-
-
Kangas, E.1
Tidor, B.2
-
63
-
-
34548785534
-
Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?
-
Kim K.H. Outliers in SAR and QSAR: 2. Is a flexible binding site a possible source of outliers?. J. Comput. Aided Mol. Des. 21 (2007) 421-435
-
(2007)
J. Comput. Aided Mol. Des.
, vol.21
, pp. 421-435
-
-
Kim, K.H.1
-
64
-
-
33947195392
-
Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?
-
Kim K.H. Outliers in SAR and QSAR: Is unusual binding mode a possible source of outliers?. J. Comput. Aided Mol. Des. 21 (2007) 63-86
-
(2007)
J. Comput. Aided Mol. Des.
, vol.21
, pp. 63-86
-
-
Kim, K.H.1
-
65
-
-
0034521981
-
Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models
-
Kollman P.A., Massova I., Reyes C., Kuhn B., Huo S., Chong L., Lee M., Lee T., Duan Y., Wang W., et al. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 33 (2000) 889-897
-
(2000)
Acc. Chem. Res.
, vol.33
, pp. 889-897
-
-
Kollman, P.A.1
Massova, I.2
Reyes, C.3
Kuhn, B.4
Huo, S.5
Chong, L.6
Lee, M.7
Lee, T.8
Duan, Y.9
Wang, W.10
-
66
-
-
84961980685
-
Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
-
Kuhn B., and Kollman P.A. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 43 (2000) 3786-3791
-
(2000)
J. Med. Chem.
, vol.43
, pp. 3786-3791
-
-
Kuhn, B.1
Kollman, P.A.2
-
67
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., and 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
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
68
-
-
0141990820
-
Specific empirical free energy function for automated docking of carbohydrates to proteins
-
Laederach A., and Reilly P.J. Specific empirical free energy function for automated docking of carbohydrates to proteins. J. Comput. Chem. 24 (2003) 1748-1757
-
(2003)
J. Comput. Chem.
, vol.24
, pp. 1748-1757
-
-
Laederach, A.1
Reilly, P.J.2
-
69
-
-
0028206116
-
X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites
-
LaLonde J.M., Bernlohr D.A., and Banaszak L.J. X-ray crystallographic structures of adipocyte lipid-binding protein complexed with palmitate and hexadecanesulfonic acid. Properties of cavity binding sites. Biochemistry 33 (1994) 4885-4895
-
(1994)
Biochemistry
, vol.33
, pp. 4885-4895
-
-
LaLonde, J.M.1
Bernlohr, D.A.2
Banaszak, L.J.3
-
70
-
-
0036568354
-
Contributions to the binding free energy of ligands to avidin and streptavidin
-
Lazaridis T., Matsunov A., and Gandolfo F. Contributions to the binding free energy of ligands to avidin and streptavidin. Proteins 47 (2002) 194-208
-
(2002)
Proteins
, vol.47
, pp. 194-208
-
-
Lazaridis, T.1
Matsunov, A.2
Gandolfo, F.3
-
71
-
-
0028158936
-
Ligand docking to proteins with discrete side-chain flexibility
-
Leach A.R. Ligand docking to proteins with discrete side-chain flexibility. J. Mol. Biol. 235 (1994) 345-356
-
(1994)
J. Mol. Biol.
, vol.235
, pp. 345-356
-
-
Leach, A.R.1
-
72
-
-
33646178918
-
Calculation of absolute protein-ligand binding affinity using path and endpoint approaches
-
Lee M.S., and Olson M.A. Calculation of absolute protein-ligand binding affinity using path and endpoint approaches. Biophys. J. 90 (2006) 864-877
-
(2006)
Biophys. J.
, vol.90
, pp. 864-877
-
-
Lee, M.S.1
Olson, M.A.2
-
73
-
-
0029894436
-
Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4
-
Lee H., Reyes V.M., and Kraut J. Crystal structures of Escherichia coli dihydrofolate reductase complexed with 5-formyltetrahydrofolate (folinic acid) in two space groups: evidence for enolization of pteridine O4. Biochemistry 35 (1996) 7012-7020
-
(1996)
Biochemistry
, vol.35
, pp. 7012-7020
-
-
Lee, H.1
Reyes, V.M.2
Kraut, J.3
-
74
-
-
41849092643
-
Molecular modeling based approach to potent P2-P4 macrocyclic inhibitors of hepatitis C NS3/4A protease
-
Liverton N.J., Holloway M.K., McCauley J.A., Rudd M.T., Butcher J.W., Carroll S.S., DiMuzio J., Fandozzi C., Gilbert K.F., Mao S.-S., et al. Molecular modeling based approach to potent P2-P4 macrocyclic inhibitors of hepatitis C NS3/4A protease. J. Am. Chem. Soc. 130 (2008) 4607-4609
-
(2008)
J. Am. Chem. Soc.
, vol.130
, pp. 4607-4609
-
-
Liverton, N.J.1
Holloway, M.K.2
McCauley, J.A.3
Rudd, M.T.4
Butcher, J.W.5
Carroll, S.S.6
DiMuzio, J.7
Fandozzi, C.8
Gilbert, K.F.9
Mao, S.-S.10
-
75
-
-
33748513468
-
Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes
-
Lu Y., Wang C.-Y., and Wang S. Binding free energy contributions of interfacial waters in HIV-1 protease/inhibitor complexes. J. Am. Chem. Soc. 128 (2006) 11830-11839
-
(2006)
J. Am. Chem. Soc.
, vol.128
, pp. 11830-11839
-
-
Lu, Y.1
Wang, C.-Y.2
Wang, S.3
-
76
-
-
0036147568
-
Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations
-
Ma B., Shatsky M., Wolfson H.J., and Nussinov R. Multiple diverse ligands binding at a single protein site: a matter of pre-existing populations. Protein Sci. 11 (2002) 184-197
-
(2002)
Protein Sci.
, vol.11
, pp. 184-197
-
-
Ma, B.1
Shatsky, M.2
Wolfson, H.J.3
Nussinov, R.4
-
77
-
-
0035367150
-
Interpreting trends in the binding of cyclic ureas to HIV-1 protease
-
Mardis K.L., Luo R., and Gilson M.K. Interpreting trends in the binding of cyclic ureas to HIV-1 protease. J. Mol. Biol. 309 (2001) 507-517
-
(2001)
J. Mol. Biol.
, vol.309
, pp. 507-517
-
-
Mardis, K.L.1
Luo, R.2
Gilson, M.K.3
-
78
-
-
33750056673
-
ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility
-
Meiler J., and Baker D.A. ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65 (2006) 538-548
-
(2006)
Proteins
, vol.65
, pp. 538-548
-
-
Meiler, J.1
Baker, D.A.2
-
79
-
-
20444387545
-
ERbeta ligands. 3. Exploiting two binding orientations of 2-phenylnapthalene scaffold to achieve ERbeta selectivity
-
Mewshaw R.E., Edsall Jr. R.J., Yang C., Manas E.S., Xu Z.B., Henderson R.A., Keith Jr. J.C., and Harris H.A. ERbeta ligands. 3. Exploiting two binding orientations of 2-phenylnapthalene scaffold to achieve ERbeta selectivity. J. Med. Chem. 48 (2005) 3953-3979
-
(2005)
J. Med. Chem.
, vol.48
, pp. 3953-3979
-
-
Mewshaw, R.E.1
Edsall Jr., R.J.2
Yang, C.3
Manas, E.S.4
Xu, Z.B.5
Henderson, R.A.6
Keith Jr., J.C.7
Harris, H.A.8
-
80
-
-
0030867610
-
Ligand binding to proteins: the binding landscape model
-
Miller D.W., and Dill K.A. Ligand binding to proteins: the binding landscape model. Protein Sci. 6 (1997) 2166-2179
-
(1997)
Protein Sci.
, vol.6
, pp. 2166-2179
-
-
Miller, D.W.1
Dill, K.A.2
-
81
-
-
30944460113
-
Fluctuating enzymes: lessons from single-molecule studies
-
Min W., English B.P., Luo G., Cherayil B.J., Kou S.C., and Xie X.S. Fluctuating enzymes: lessons from single-molecule studies. Acc. Chem. Res. 38 (2005) 923-931
-
(2005)
Acc. Chem. Res.
, vol.38
, pp. 923-931
-
-
Min, W.1
English, B.P.2
Luo, G.3
Cherayil, B.J.4
Kou, S.C.5
Xie, X.S.6
-
82
-
-
27144465458
-
Observation of a power-law memory kernel for fluctuations within a single protein molecule
-
Min W., Luo G., Cherayil B.J., Kou S.C., and Xie X.S. Observation of a power-law memory kernel for fluctuations within a single protein molecule. Phys. Rev. Lett. 94 (2005) 198302
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 198302
-
-
Min, W.1
Luo, G.2
Cherayil, B.J.3
Kou, S.C.4
Xie, X.S.5
-
83
-
-
33748252631
-
On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
-
Mobley D.L., Chodera J.D., and Dill K.A. On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. J. Chem. Phys. 125 (2006) 084902
-
(2006)
J. Chem. Phys.
, vol.125
, pp. 084902
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
84
-
-
36049017659
-
Confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change
-
Mobley D.L., Chodera J.D., and Dill K.A. Confine-and-release method: obtaining correct binding free energies in the presence of protein conformational change. J. Chem. Theory Comput. 3 (2007) 1231-1235
-
(2007)
J. Chem. Theory Comput.
, vol.3
, pp. 1231-1235
-
-
Mobley, D.L.1
Chodera, J.D.2
Dill, K.A.3
-
85
-
-
34547110591
-
Predicting absolute ligand binding free energies to a simple model site
-
Mobley D.L., Graves A.P., Chodera J.D., McReynolds A.C., Shoichet B.K., and Dill K.A. Predicting absolute ligand binding free energies to a simple model site. J. Mol. Biol. 371 (2007) 1118-1134
-
(2007)
J. Mol. Biol.
, vol.371
, pp. 1118-1134
-
-
Mobley, D.L.1
Graves, A.P.2
Chodera, J.D.3
McReynolds, A.C.4
Shoichet, B.K.5
Dill, K.A.6
-
86
-
-
38949212628
-
Treating entropy and conformational changes in implicit solvent simulations of small molecules
-
Mobley D.L., Dill K.A., and Chodera J.D. Treating entropy and conformational changes in implicit solvent simulations of small molecules. J. Phys. Chem. B 112 (2008) 938-946
-
(2008)
J. Phys. Chem. B
, vol.112
, pp. 938-946
-
-
Mobley, D.L.1
Dill, K.A.2
Chodera, J.D.3
-
87
-
-
0025311258
-
Structure, multiple site binding, and segmental accomodation in thymidylate synthase on binding dUMP and an anti-folate
-
Montfort W.R., Perry K.M., Fauman E.B., Finer-Moore J.S., Maley G.F., Hardy L., Maley F., and Stroud R.M. Structure, multiple site binding, and segmental accomodation in thymidylate synthase on binding dUMP and an anti-folate. Biochemistry 29 (1990) 6964-6977
-
(1990)
Biochemistry
, vol.29
, pp. 6964-6977
-
-
Montfort, W.R.1
Perry, K.M.2
Fauman, E.B.3
Finer-Moore, J.S.4
Maley, G.F.5
Hardy, L.6
Maley, F.7
Stroud, R.M.8
-
88
-
-
0029067489
-
Specificity of ligand binding in a buried nonpolar cavity of {T4} lysozyme: linkage of dynamics and structural plasticity
-
Morton A., and Matthews B.W. Specificity of ligand binding in a buried nonpolar cavity of {T4} lysozyme: linkage of dynamics and structural plasticity. Biochemistry 34 (1995) 8576-8588
-
(1995)
Biochemistry
, vol.34
, pp. 8576-8588
-
-
Morton, A.1
Matthews, B.W.2
-
89
-
-
0026474757
-
The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations
-
Murthy K.H.M., Winborne E.L., Minnich M.D., Culp J.S., and Debouck C. The crystal structures at 2.2-A resolution of hydroxyethylene-based inhibitors bound to human immunodeficiency virus type 1 protease show that the inhibitors are present in two distinct orientations. J. Biol. Chem. 267 (1992) 22770-22778
-
(1992)
J. Biol. Chem.
, vol.267
, pp. 22770-22778
-
-
Murthy, K.H.M.1
Winborne, E.L.2
Minnich, M.D.3
Culp, J.S.4
Debouck, C.5
-
91
-
-
1642323740
-
Protein kinase inhibitors: insights into drug design from structure
-
Noble M.E., Endicott J.A., and Johnson L.N. Protein kinase inhibitors: insights into drug design from structure. Science 303 (2004) 1800-1805
-
(2004)
Science
, vol.303
, pp. 1800-1805
-
-
Noble, M.E.1
Endicott, J.A.2
Johnson, L.N.3
-
92
-
-
3042592839
-
Hydration free energies and entropies for water in protein interiors
-
Olano L.R., and Rick S.W. Hydration free energies and entropies for water in protein interiors. J. Am. Chem. Soc. 126 (2004) 7991-8000
-
(2004)
J. Am. Chem. Soc.
, vol.126
, pp. 7991-8000
-
-
Olano, L.R.1
Rick, S.W.2
-
93
-
-
0346458810
-
Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation
-
Oostenbrink C., and van Gunsteren W.F. Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation. Proteins 54 (2004) 237-246
-
(2004)
Proteins
, vol.54
, pp. 237-246
-
-
Oostenbrink, C.1
van Gunsteren, W.F.2
-
94
-
-
0030874393
-
Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site
-
Orville A.M., Elango N., Lipscomb J.D., and Ohlendorf D.H. Structures of competitive inhibitor complexes of protocatechuate 3,4-dioxygenase: multiple exogenous ligand binding orientations within the active site. Biochemistry 36 (1997) 10039-10051
-
(1997)
Biochemistry
, vol.36
, pp. 10039-10051
-
-
Orville, A.M.1
Elango, N.2
Lipscomb, J.D.3
Ohlendorf, D.H.4
-
95
-
-
34249027590
-
Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor
-
Pan C., Mezei M., Mujtaba S., Muller M., Zeng L., Li J., Wang Z., and Zhou M.M. Structure-guided optimization of small molecules inhibiting human immunodeficiency virus 1 Tat association with the human coactivator p300/CREB binding protein-associated factor. J. Med. Chem. 50 (2007) 2285-2288
-
(2007)
J. Med. Chem.
, vol.50
, pp. 2285-2288
-
-
Pan, C.1
Mezei, M.2
Mujtaba, S.3
Muller, M.4
Zeng, L.5
Li, J.6
Wang, Z.7
Zhou, M.M.8
-
96
-
-
0026936915
-
Predicting the product specificity and coupling of cytochrome P450cam
-
Paulsen M.D., and Ornstein R.L. Predicting the product specificity and coupling of cytochrome P450cam. J. Comput. Aided Mol. Des. 6 (1992) 449-460
-
(1992)
J. Comput. Aided Mol. Des.
, vol.6
, pp. 449-460
-
-
Paulsen, M.D.1
Ornstein, R.L.2
-
97
-
-
28144441347
-
Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase
-
Pearlman D.A. Evaluating the molecular mechanics poisson-boltzmann surface area free energy method using a congeneric series of ligands to p38 MAP kinase. J. Med. Chem. 48 (2005) 7796-7807
-
(2005)
J. Med. Chem.
, vol.48
, pp. 7796-7807
-
-
Pearlman, D.A.1
-
98
-
-
0035846166
-
Are free energy calculations useful in practice? A comparison with rapid scoring functions for the p38 MAP kinase protein system
-
Pearlman D.A., and 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. 44 (2001) 3417-3423
-
(2001)
J. Med. Chem.
, vol.44
, pp. 3417-3423
-
-
Pearlman, D.A.1
Charifson, P.S.2
-
99
-
-
33745148202
-
Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors
-
Pei Z., Li X., Longenecker K., Geldern T.W., Wiedeman P.E., Lubben T.H., Zinker B.A., Stewart K., Ballaron S.J., Stashko M.A., Mika A.K., Beno D.W., et al. Discovery, structure-activity relationship, and pharmacological evaluation of (5-substituted-pyrrolidinyl-2-carbonyl)-2-cyanopyrrolidines as potent dipeptidyl peptidase IV inhibitors. J. Med. Chem. 49 (2006) 3520-3535
-
(2006)
J. Med. Chem.
, vol.49
, pp. 3520-3535
-
-
Pei, Z.1
Li, X.2
Longenecker, K.3
Geldern, T.W.4
Wiedeman, P.E.5
Lubben, T.H.6
Zinker, B.A.7
Stewart, K.8
Ballaron, S.J.9
Stashko, M.A.10
Mika, A.K.11
Beno, D.W.12
-
100
-
-
2342586724
-
Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding
-
Perola E., and Charifson P.S. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J. Med. Chem. 47 (2004) 2499-2510
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.S.2
-
102
-
-
0025761693
-
Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation
-
Raag R., and Poulos T.L. Crystal structures of cytochrome P-450CAM complexed with camphane, thiocamphor, and adamantane: factors controlling P-450 substrate hydroxylation. Biochemistry 30 (1991) 2674-2684
-
(1991)
Biochemistry
, vol.30
, pp. 2674-2684
-
-
Raag, R.1
Poulos, T.L.2
-
103
-
-
33847795359
-
Intrinsic disorder and functional proteomics
-
Radivojac P., Iakoucheva L.M., Oldfield C.J., Obradovic Z., Uversky V.N., and Dunker A.K. Intrinsic disorder and functional proteomics. Biophys. J. 92 (2007) 1439-1456
-
(2007)
Biophys. J.
, vol.92
, pp. 1439-1456
-
-
Radivojac, P.1
Iakoucheva, L.M.2
Oldfield, C.J.3
Obradovic, Z.4
Uversky, V.N.5
Dunker, A.K.6
-
104
-
-
0034801307
-
Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach
-
Reddy M.R., and Erion M.D. Calculation of relative binding free energy differences for fructose 1,6-bisphosphatase inhibitors using the thermodynamic cycle perturbation approach. J. Am. Chem. Soc. 123 (2001) 6246-6252
-
(2001)
J. Am. Chem. Soc.
, vol.123
, pp. 6246-6252
-
-
Reddy, M.R.1
Erion, M.D.2
-
105
-
-
0028921611
-
Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease
-
Reich S.H., Melnick II M., Davies J.F., Appelt K., Lewis K.K., Fuhry M.A., Pino M., Trippe A.J., Nguyen D., Dawson H., et al. Protein structure-based design of potent orally bioavailable, nonpeptide inhibitors of human immunodeficiency virus protease. Proc. Natl. Acad. Sci. U.S.A. 92 (1995) 3298-3303
-
(1995)
Proc. Natl. Acad. Sci. U.S.A.
, vol.92
, pp. 3298-3303
-
-
Reich, S.H.1
Melnick II, M.2
Davies, J.F.3
Appelt, K.4
Lewis, K.K.5
Fuhry, M.A.6
Pino, M.7
Trippe, A.J.8
Nguyen, D.9
Dawson, H.10
-
106
-
-
0033606250
-
OPLS all-atom model for amines: resolution of the amine hydration problem
-
Rizzo R.C., and Jorgensen W.L. OPLS all-atom model for amines: resolution of the amine hydration problem. J. Am. Chem. Soc. 121 (1999) 4827-4836
-
(1999)
J. Am. Chem. Soc.
, vol.121
, pp. 4827-4836
-
-
Rizzo, R.C.1
Jorgensen, W.L.2
-
107
-
-
2542586266
-
A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations
-
Rizzo R.C., Toba S., and Kuntz I.D. A molecular basis for the selectivity of thiadiazole urea inhibitors with stromelysin-1 and gelatinase-A from generalized born molecular dynamics simulations. J. Med. Chem. 47 (2004) 3065-3074
-
(2004)
J. Med. Chem.
, vol.47
, pp. 3065-3074
-
-
Rizzo, R.C.1
Toba, S.2
Kuntz, I.D.3
-
108
-
-
0029757992
-
Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study
-
Roux B., Nina M., Poms R., and Smith J.C. Thermodynamic stability of water molecules in the bacteriorhodopsin proton channel: a molecular dynamics free energy perturbation study. Biophys. J. 71 (1996) 670-681
-
(1996)
Biophys. J.
, vol.71
, pp. 670-681
-
-
Roux, B.1
Nina, M.2
Poms, R.3
Smith, J.C.4
-
109
-
-
22844440711
-
New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy
-
Ruvinsky A.M., and Kozintsev A.V. New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. J. Comput. Chem. 26 (2005) 1089-1095
-
(2005)
J. Comput. Chem.
, vol.26
, pp. 1089-1095
-
-
Ruvinsky, A.M.1
Kozintsev, A.V.2
-
110
-
-
1842607357
-
Discovery of a novel binding trench in HIV integrase
-
Schames J.R., Henchman R.H., Siegel J.S., Sotriffer C.A., Ni H., and McCammon J.A. Discovery of a novel binding trench in HIV integrase. J. Med. Chem. 47 (2004) 1879-1881
-
(2004)
J. Med. Chem.
, vol.47
, pp. 1879-1881
-
-
Schames, J.R.1
Henchman, R.H.2
Siegel, J.S.3
Sotriffer, C.A.4
Ni, H.5
McCammon, J.A.6
-
111
-
-
0036722785
-
Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?
-
Schwarzl S.M., Tschopp T.B., Smith J.C., and Fischer S. Can the calculation of ligand binding free energies be improved with continuum solvent electrostatics and an ideal-gas entropy correction?. J. Comput. Chem. 23 (2002) 1143-1149
-
(2002)
J. Comput. Chem.
, vol.23
, pp. 1143-1149
-
-
Schwarzl, S.M.1
Tschopp, T.B.2
Smith, J.C.3
Fischer, S.4
-
112
-
-
64049112859
-
Important considerations impacting molecular docking
-
Shoichet B.K., and Alvarez J. (Eds), CRC Press, Boca Raton, FL
-
Sharp K.A. Important considerations impacting molecular docking. In: Shoichet B.K., and Alvarez J. (Eds). Virtual Screening in Drug Discovery (2005), CRC Press, Boca Raton, FL
-
(2005)
Virtual Screening in Drug Discovery
-
-
Sharp, K.A.1
-
113
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W., Day T., Jacobson M.P., Friesner R.A., and Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 49 (2006) 534-553
-
(2006)
J. Med. Chem.
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
114
-
-
79958862887
-
Free energy calculations in structure-based drug design
-
Merz K.M., Ringe D., and Reynolds C.H. (Eds), Cambridge University Press, Cambridge
-
Shirts M.R., Mobley D.L., and Brown S.P. Free energy calculations in structure-based drug design. In: Merz K.M., Ringe D., and Reynolds C.H. (Eds). Structure Based Drug Discovery (2009), Cambridge University Press, Cambridge
-
(2009)
Structure Based Drug Discovery
-
-
Shirts, M.R.1
Mobley, D.L.2
Brown, S.P.3
-
118
-
-
33748276474
-
Protein-ligand docking: current status and future challenges
-
Sousa S.F., Fernandes P.A., and Ramos M.J. Protein-ligand docking: current status and future challenges. Proteins 65 (2006) 15-26
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
119
-
-
0032560959
-
Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices
-
Srinivasan J., Cheatham III T.E., Cieplak P., Kollman P.A., and Case D.A. Continuum solvent studies of the stability of DNA, RNA, and phosphoramidate-DNA helices. J. Am. Chem. Soc. 120 (1998) 9401-9409
-
(1998)
J. Am. Chem. Soc.
, vol.120
, pp. 9401-9409
-
-
Srinivasan, J.1
Cheatham III, T.E.2
Cieplak, P.3
Kollman, P.A.4
Case, D.A.5
-
120
-
-
33847029846
-
Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind [beta]-secretase in a N-terminal 10s-loop down conformation
-
Stauffer S.R., Stanton M.G., Gregro A.R., Steinbeiser M.A., Shaffer J.R., Nantermet P.G., Barrow J.C., Rittle K.E., Collusi D., Espeseth A.S., et al. Discovery and SAR of isonicotinamide BACE-1 inhibitors that bind [beta]-secretase in a N-terminal 10s-loop down conformation. Bioorg. Med. Chem. Lett. 17 (2007) 1788-1792
-
(2007)
Bioorg. Med. Chem. Lett.
, vol.17
, pp. 1788-1792
-
-
Stauffer, S.R.1
Stanton, M.G.2
Gregro, A.R.3
Steinbeiser, M.A.4
Shaffer, J.R.5
Nantermet, P.G.6
Barrow, J.C.7
Rittle, K.E.8
Collusi, D.9
Espeseth, A.S.10
-
121
-
-
33645400172
-
A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase
-
Steinbrecher T., Case D.A., and Labahn A. A multistep approach to structure-based drug design: studying ligand binding at the human neutrophil elastase. J. Med. Chem. 49 (2006) 1837-1844
-
(2006)
J. Med. Chem.
, vol.49
, pp. 1837-1844
-
-
Steinbrecher, T.1
Case, D.A.2
Labahn, A.3
-
122
-
-
35148897726
-
Tracing changes in protonation: a prerequisite to binding to aldose reductase
-
Steuber H., Czodrowski P., Sotriffer C.A., and Klebe G. Tracing changes in protonation: a prerequisite to binding to aldose reductase. J. Mol. Biol. 373 (2007) 1305-1320
-
(2007)
J. Mol. Biol.
, vol.373
, pp. 1305-1320
-
-
Steuber, H.1
Czodrowski, P.2
Sotriffer, C.A.3
Klebe, G.4
-
123
-
-
0037469141
-
Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series
-
Stoll V., Stewart K.D., Maring C.J., Muchmore S., Giranda V., Gu Y.G., Wang G., Chen Y., Sun M., Zhao C., et al. Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series. Biochemistry 42 (2003) 718-727
-
(2003)
Biochemistry
, vol.42
, pp. 718-727
-
-
Stoll, V.1
Stewart, K.D.2
Maring, C.J.3
Muchmore, S.4
Giranda, V.5
Gu, Y.G.6
Wang, G.7
Chen, Y.8
Sun, M.9
Zhao, C.10
-
124
-
-
0033514283
-
Structure-based design of inhibitors specific for bacterial thymidylate synthase
-
Stout T.J., Tondi D., Rinaldi M., Barlocco D., Pecorari P., Santi D.V., Kuntz I.D., Stroud R.M., Shoichet B.K., and Costi M.P. Structure-based design of inhibitors specific for bacterial thymidylate synthase. Biochemistry 38 (1999) 1607-1617
-
(1999)
Biochemistry
, vol.38
, pp. 1607-1617
-
-
Stout, T.J.1
Tondi, D.2
Rinaldi, M.3
Barlocco, D.4
Pecorari, P.5
Santi, D.V.6
Kuntz, I.D.7
Stroud, R.M.8
Shoichet, B.K.9
Costi, M.P.10
-
125
-
-
0036523422
-
pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design
-
Stubbs M.T., Reyda S., Dullweber F., Moller M., Klebe G., Dorsch D., Mederski W.W.K.R., and Wurziger H. pH-dependent binding modes observed in trypsin crystals: lessons for structure-based drug design. Chembiochem 3 (2002) 246-249
-
(2002)
Chembiochem
, vol.3
, pp. 246-249
-
-
Stubbs, M.T.1
Reyda, S.2
Dullweber, F.3
Moller, M.4
Klebe, G.5
Dorsch, D.6
Mederski, W.W.K.R.7
Wurziger, H.8
-
126
-
-
34249727188
-
Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP)
-
Sulsky R., Magnin D.R., Huang Y., Simpkins L., Taunk P., Patel M., Zhu Y., Stouch T.R., Bassolino-Klimas D., Parker R., et al. Potent and selective biphenyl azole inhibitors of adipocyte fatty acid binding protein (aFABP). Bioorg. Med. Chem. Lett. 17 (2007) 3511-3515
-
(2007)
Bioorg. Med. Chem. Lett.
, vol.17
, pp. 3511-3515
-
-
Sulsky, R.1
Magnin, D.R.2
Huang, Y.3
Simpkins, L.4
Taunk, P.5
Patel, M.6
Zhu, Y.7
Stouch, T.R.8
Bassolino-Klimas, D.9
Parker, R.10
-
127
-
-
35548976322
-
Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR
-
Tang C., Schweiters C.D., and Clore G.M. Open-to-closed transition in apo maltose-binding protein observed by paramagnetic NMR. Nature 449 (2007) 1078-1082
-
(2007)
Nature
, vol.449
, pp. 1078-1082
-
-
Tang, C.1
Schweiters, C.D.2
Clore, G.M.3
-
129
-
-
0037666888
-
Implications of protein flexibility for drug discovery
-
Teague S.J. Implications of protein flexibility for drug discovery. Nat. Rev. Drug Discov. 2 (2003) 527-541
-
(2003)
Nat. Rev. Drug Discov.
, vol.2
, pp. 527-541
-
-
Teague, S.J.1
-
130
-
-
0021582448
-
Ligand-receptor interactions
-
Tembe B.L., and McCammon J.A. Ligand-receptor interactions. Comput. Chem. 8 (1984) 281-283
-
(1984)
Comput. Chem.
, vol.8
, pp. 281-283
-
-
Tembe, B.L.1
McCammon, J.A.2
-
131
-
-
33748603755
-
Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic
-
Thomson J.A., and Perni R.B. Hepatitis C virus NS3-4A protease inhibitors: countering viral subversion in vitro and showing promise in the clinic. Curr. Opin. Drug Discov. Devel. 9 (2006) 606-617
-
(2006)
Curr. Opin. Drug Discov. Devel.
, vol.9
, pp. 606-617
-
-
Thomson, J.A.1
Perni, R.B.2
-
132
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
Tirado-Rives J., and Jorgensen W.L. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J. Med. Chem. 49 (2006) 5880-5884
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
133
-
-
0036315480
-
Two 1:1 binding modes for distamycin in the minor groove of d(GGCCAATTGG)
-
Uytterhoeven K., Sponer J., and Meervelt L.V. Two 1:1 binding modes for distamycin in the minor groove of d(GGCCAATTGG). Eur. J. Biochem. 269 (2002) 2868-2877
-
(2002)
Eur. J. Biochem.
, vol.269
, pp. 2868-2877
-
-
Uytterhoeven, K.1
Sponer, J.2
Meervelt, L.V.3
-
134
-
-
49649108911
-
Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib
-
Vajpai N., Strauss A., Cowan-Jacob S.W., Manley P.W., Crzesiek S., and Jahnke W. Solution conformations and dynamics of ABL kinase-inhibitor complexes determined by NMR substantiate the different binding modes of imatinib/nilotinib and dasatinib. J. Biol. Chem. 283 (2008) 18292-18302
-
(2008)
J. Biol. Chem.
, vol.283
, pp. 18292-18302
-
-
Vajpai, N.1
Strauss, A.2
Cowan-Jacob, S.W.3
Manley, P.W.4
Crzesiek, S.5
Jahnke, W.6
-
135
-
-
0035937443
-
Two-state allosteric behavior in a single-domain signaling protein
-
Volkman B.F., Lipson D., Wemmer D.E., and Kern D. Two-state allosteric behavior in a single-domain signaling protein. Science 291 (2001) 2429-2433
-
(2001)
Science
, vol.291
, pp. 2429-2433
-
-
Volkman, B.F.1
Lipson, D.2
Wemmer, D.E.3
Kern, D.4
-
136
-
-
0027287506
-
Rational design of potent sialidase-based inhibitors of influenza virus replication
-
von Itzstein M., Wu W.Y., Kok G.B., Pegg M.S., Dyason J.C., Jin B., Van Phan T., Smythe M.L., White H.F., Oliver S.W., et al. Rational design of potent sialidase-based inhibitors of influenza virus replication. Nature 363 (1993) 418-423
-
(1993)
Nature
, vol.363
, pp. 418-423
-
-
von Itzstein, M.1
Wu, W.Y.2
Kok, G.B.3
Pegg, M.S.4
Dyason, J.C.5
Jin, B.6
Van Phan, T.7
Smythe, M.L.8
White, H.F.9
Oliver, S.W.10
-
137
-
-
0033003955
-
ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
-
Vorobjev Y.N., and Hermans J. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78 (1999) 195-205
-
(1999)
Biophys. Chem.
, vol.78
, pp. 195-205
-
-
Vorobjev, Y.N.1
Hermans, J.2
-
138
-
-
33749532284
-
Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials
-
Wang J., Deng Y., and Roux B. Absolute binding free energy calculations using molecular dynamics simulations with restraining potentials. Biophys. J. 91 (2006) 2798-2814
-
(2006)
Biophys. J.
, vol.91
, pp. 2798-2814
-
-
Wang, J.1
Deng, Y.2
Roux, B.3
-
139
-
-
33749260698
-
A critial assessment of docking programs and scoring functions
-
Warren G.L., Andrews C.W., Capelli A.M., Clarke B., LaLonde J., Lambert M.H., Lindvall M., Nevins N., Semus S.F., Sender S., et al. A critial assessment of docking programs and scoring functions. J. Med. Chem. 49 (2006) 5912-5931
-
(2006)
J. Med. Chem.
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Sender, S.10
-
140
-
-
64049099723
-
-
March 16-19, Santa Fe, NM. Available online at
-
Warren, G., and Perola, E. (2008). Field of extremes: if you re-refine them, they will come down. Paper presented at CUP IX, March 16-19, 2008, Santa Fe, NM. Available online at http://www.eyesopen.com/about/events/cups-2008/pdfs-CUP/CUP9-Field-of-Extremes.pdf.
-
(2008)
Paper presented at CUP IX, Field of extremes: If you re-refine them, they will come down
-
-
Warren, G.1
Perola, E.2
-
141
-
-
0023060081
-
Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process
-
Warshel A., Sussman F., and King G. Free energy of charges in solvated proteins: microscopic calculations using a reversible charging process. Biochemistry 25 (1986) 8368-8372
-
(1986)
Biochemistry
, vol.25
, pp. 8368-8372
-
-
Warshel, A.1
Sussman, F.2
King, G.3
-
142
-
-
1842471241
-
Testing a flexible-receptor docking algorithm in a model binding site
-
Wei B.Q., Weaver L.H., Ferrari A.M., Matthews B.W., and Shoichet B.K. Testing a flexible-receptor docking algorithm in a model binding site. J. Mol. Biol. 337 (2004) 1161-1182
-
(2004)
J. Mol. Biol.
, vol.337
, pp. 1161-1182
-
-
Wei, B.Q.1
Weaver, L.H.2
Ferrari, A.M.3
Matthews, B.W.4
Shoichet, B.K.5
-
143
-
-
34247470836
-
Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia
-
Weisberg E., Manley P.W., Cowan-Jacob S.W., Hochhaus A., and Griffin J.D. Second generation inhibitors of BCR-ABL for the treatment of imatinib-resistant chronic myeloid leukaemia. Nat. Rev. Cancer 7 (2007) 345-356
-
(2007)
Nat. Rev. Cancer
, vol.7
, pp. 345-356
-
-
Weisberg, E.1
Manley, P.W.2
Cowan-Jacob, S.W.3
Hochhaus, A.4
Griffin, J.D.5
-
144
-
-
0001486087
-
Dynamics and design of enzymes and inhibitors
-
Wong C.F., and McCammon J.A. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108 (1986) 3830-3832
-
(1986)
J. Am. Chem. Soc.
, vol.108
, pp. 3830-3832
-
-
Wong, C.F.1
McCammon, J.A.2
-
145
-
-
0032749078
-
Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm
-
Wright P.E., and Dyson H.J. Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. J. Mol. Biol. 293 (1999) 321-331
-
(1999)
J. Mol. Biol.
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
147
-
-
0029150760
-
Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme
-
Zhang X.J., Wozniak J.A., and Matthews B.W. Protein flexibility and adaptability seen in 25 crystal forms of T4 lysozyme. J. Mol. Biol. 250 (1995) 527-552
-
(1995)
J. Mol. Biol.
, vol.250
, pp. 527-552
-
-
Zhang, X.J.1
Wozniak, J.A.2
Matthews, B.W.3
-
148
-
-
17944384967
-
The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core
-
Zhou G., Ferrer M., Chopra R., Kapoor T.M., Strassmaier T., Weissenhorn W., Skehel J.J., Oprian D., Schreiber S.L., Harrison S.C., and Wiley D.C. The structure of an HIV-1 specific cell entry inhibitor in complex with the HIV-1 gp41 trimeric core. Bioorg. Med. Chem. 8 (2000) 2219-2227
-
(2000)
Bioorg. Med. Chem.
, vol.8
, pp. 2219-2227
-
-
Zhou, G.1
Ferrer, M.2
Chopra, R.3
Kapoor, T.M.4
Strassmaier, T.5
Weissenhorn, W.6
Skehel, J.J.7
Oprian, D.8
Schreiber, S.L.9
Harrison, S.C.10
Wiley, D.C.11
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