-
1
-
-
66149134591
-
-
Orita, M.; Ohno, K.; Niimi, T. Two Golden ratio indices in fragment-based drug discovery. Drug Discovery Today,. in press.
-
Orita, M.; Ohno, K.; Niimi, T. Two "Golden ratio" indices in fragment-based drug discovery. Drug Discovery Today,. in press.
-
-
-
-
2
-
-
17144373303
-
Draggability indices for protein targets derived from NMR-based screening data
-
Hajduk, P. J.; Huth, J. R.; Fesik, S. W. Draggability indices for protein targets derived from NMR-based screening data. J. Med. Chem. 2005, 48, 2518-2525.
-
(2005)
J. Med. Chem
, vol.48
, pp. 2518-2525
-
-
Hajduk, P.J.1
Huth, J.R.2
Fesik, S.W.3
-
3
-
-
36248944181
-
An integrated approach to fragment-based lead generation: Philosophy, strategy and case studies from AstraZeneca's drag discovery programmes
-
Albert, J. S.; Blomberg, N.; Breeze, A. L.; Brown, A. J. H.; Burrows, J. N.; Edwards, P. D.; Folmer, R. H. A.; Geschwindner, S.; Griffen, E. J.; Kenny, P. W.; Nowak, T.; Olsson, L. L.; Sanganess, H.; Shapiro, A. B. An integrated approach to fragment-based lead generation: philosophy, strategy and case studies from AstraZeneca's drag discovery programmes. Curr. Top. Med. Chem. 2007, 7, 1600-1629.
-
(2007)
Curr. Top. Med. Chem
, vol.7
, pp. 1600-1629
-
-
Albert, J.S.1
Blomberg, N.2
Breeze, A.L.3
Brown, A.J.H.4
Burrows, J.N.5
Edwards, P.D.6
Folmer, R.H.A.7
Geschwindner, S.8
Griffen, E.J.9
Kenny, P.W.10
Nowak, T.11
Olsson, L.L.12
Sanganess, H.13
Shapiro, A.B.14
-
4
-
-
3042689621
-
Fragment-based drag discovery
-
Erlanson, D. A.; McDowell, R. S.; O'Brien, T. Fragment-based drag discovery. J. Med. Chem. 2004, 47, 3463-3482.
-
(2004)
J. Med. Chem
, vol.47
, pp. 3463-3482
-
-
Erlanson, D.A.1
McDowell, R.S.2
O'Brien, T.3
-
5
-
-
36248997755
-
Fragment-based drag discovery: What has it achieved so far
-
Alex, A. A.; Flocco, M. M. Fragment-based drag discovery: What has it achieved so far. Curr. Top. Med. Chem. 2007, 7, 1544-1567.
-
(2007)
Curr. Top. Med. Chem
, vol.7
, pp. 1544-1567
-
-
Alex, A.A.1
Flocco, M.M.2
-
6
-
-
33847381100
-
A decade of fragment-based drag design: Strategic advances and lessons learned
-
Hajduk, P. J.; Gréer, J. A decade of fragment-based drag design: strategic advances and lessons learned. Nat. Rev. Drug. Discovery 2007, 6, 211-219.
-
(2007)
Nat. Rev. Drug. Discovery
, vol.6
, pp. 211-219
-
-
Hajduk, P.J.1
Gréer, J.2
-
7
-
-
46849089254
-
Recent developments in fragment-based drag discovery
-
Congreve, M.; Chessari, G.; Tisi, D.; Woodhead, A. J. Recent developments in fragment-based drag discovery. J. Med. Chem. 2008, 51, 3661-3680.
-
(2008)
J. Med. Chem
, vol.51
, pp. 3661-3680
-
-
Congreve, M.1
Chessari, G.2
Tisi, D.3
Woodhead, A.J.4
-
8
-
-
37049231053
-
Computer-assisted design of complex organic syntheses
-
Corey, E. J.; Wipke, W. T. Computer-assisted design of complex organic syntheses. Science 1969, 166, 178-192.
-
(1969)
Science
, vol.166
, pp. 178-192
-
-
Corey, E.J.1
Wipke, W.T.2
-
9
-
-
0003981102
-
Computer-assisted mechanistic evaluation of organic reactions. 1. overview
-
Timothy, D.; Salatin, T. D.; Jorgensen, W. L. Computer-assisted mechanistic evaluation of organic reactions. 1. overview. J. Org. Chem. 1980, 45, 2043-2057.
-
(1980)
J. Org. Chem
, vol.45
, pp. 2043-2057
-
-
Timothy, D.1
Salatin, T.D.2
Jorgensen, W.L.3
-
10
-
-
0013050946
-
Computer-assisted organic synthesis design and reaction prediction system, "AIPHOS
-
Funatsu, K.; Sasaki, S. Computer-assisted organic synthesis design and reaction prediction system, "AIPHOS". Tetrahedron Comput. Methodol. 1988, 1, 27-38.
-
(1988)
Tetrahedron Comput. Methodol
, vol.1
, pp. 27-38
-
-
Funatsu, K.1
Sasaki, S.2
-
11
-
-
0020491251
-
A Geometric approach to macromolecule-ligand interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A Geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 1982, 161, 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
-
12
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489.
-
(1996)
J. Mol. Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
13
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G.; Willet, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748.
-
(1997)
J. Mol. Biol
, vol.267
, pp. 727-748
-
-
Jones, G.1
Willet, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
14
-
-
0032533791
-
Flexible docking using tabu search and an empirical estimate of binding affinity
-
Baxter, C. A.; Murray, C. W.; Clark, D. E.; Westhead, D. R.; Eldridge, M. D. Flexible docking using tabu search and an empirical estimate of binding affinity. Proteins 1998, 33, 367-382.
-
(1998)
Proteins
, vol.33
, pp. 367-382
-
-
Baxter, C.A.1
Murray, C.W.2
Clark, D.E.3
Westhead, D.R.4
Eldridge, M.D.5
-
15
-
-
0025135112
-
Automated Docking of Substrates to Proteins by Simulated Annealing
-
Goodsell, D. S.; Olson, A. J. Automated Docking of Substrates to Proteins by Simulated Annealing. Proteins 1990, 8, 195-202.
-
(1990)
Proteins
, vol.8
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
16
-
-
84986522918
-
ICM: A new method for structure modeling and design: application to docking and structure prediction from the disordered native conformation
-
Abagyan, R.; Totrov, M.; Kuznetsov, D. ICM: a new method for structure modeling and design: application to docking and structure prediction from the disordered native conformation. J. Comput. Chem. 1994, 15, 488-506.
-
(1994)
J. Comput. Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
17
-
-
0028584446
-
Structure-based drug design
-
Colman, P. M. Structure-based drug design. Curr. Opin. Struct. Biol. 1994, 4, 868-874.
-
(1994)
Curr. Opin. Struct. Biol
, vol.4
, pp. 868-874
-
-
Colman, P.M.1
-
18
-
-
15244346501
-
-
Kramer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
-
Kramer, A.; Kirchhoff, P. D.; Jiang, X.; Venkatachalam, C. M.; Waldman, M. LigScore: a novel scoring function for predicting binding affinities. J. Mol. Graphics Modell. 2005, 23, 395-407.
-
-
-
-
19
-
-
24944576105
-
Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening
-
Fukunishi, Y.; Mikami, Y.; Nakamura, H. Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graphics Modell. 2005, 24, 34-45.
-
(2005)
J. Mol. Graphics Modell
, vol.24
, pp. 34-45
-
-
Fukunishi, Y.1
Mikami, Y.2
Nakamura, H.3
-
20
-
-
17144383951
-
A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes
-
Zhang, C.; Liu, S.; Zhu, Q.; Zhou, Y. A knowledge-based energy function for protein-ligand, protein-protein, and protein-DNA complexes. J. Med. Chem. 2005, 48, 2325-2335.
-
(2005)
J. Med. Chem
, vol.48
, pp. 2325-2335
-
-
Zhang, C.1
Liu, S.2
Zhu, Q.3
Zhou, Y.4
-
21
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
Muegge, I.; Martin, Y. C. A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J. Med. Chem. 1999, 42, 791-804.
-
(1999)
J. Med. Chem
, vol.42
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
22
-
-
33748594188
-
Multiple target screening method for robust and accurate in silico ligand screening
-
Fukunishi, Y.; Mikami, Y.; Kubota, S.; Nakamura, H. Multiple target screening method for robust and accurate in silico ligand screening. J. Mol. Graphics Modell. 2005, 25, 61-70.
-
(2005)
J. Mol. Graphics Modell
, vol.25
, pp. 61-70
-
-
Fukunishi, Y.1
Mikami, Y.2
Kubota, S.3
Nakamura, H.4
-
23
-
-
33750303121
-
Noise reduction method for molecular interaction energy: Application to in silico drug screening and in silico target protein screening
-
Fukunishi, Y.; Kubota, S.; Nakamura, H. Noise reduction method for molecular interaction energy: application to in silico drug screening and in silico target protein screening. J. Chem. Inf. Model. 2006, 46, 2071-2084.
-
(2006)
J. Chem. Inf. Model
, vol.46
, pp. 2071-2084
-
-
Fukunishi, Y.1
Kubota, S.2
Nakamura, H.3
-
24
-
-
49149147973
-
Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges
-
Gasteiger, J.; Marsili, M. Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 1980, 36, 3219-3228.
-
(1980)
Tetrahedron
, vol.36
, pp. 3219-3228
-
-
Gasteiger, J.1
Marsili, M.2
-
25
-
-
0000125764
-
A new model for calculating atomic charges in molecules
-
Gasteiger, J.; Marsili, M. A new model for calculating atomic charges in molecules. Tetrahedron Lett. 1978, 3181-3184.
-
(1978)
Tetrahedron Lett
, pp. 3181-3184
-
-
Gasteiger, J.1
Marsili, M.2
-
26
-
-
2942532422
-
Development and testing of a general amber force field
-
Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. "Development and testing of a general amber force field". J. Comput. Chem. 2004, 25, 1157-1174.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
27
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking. J. Med. Chem. 2006, 49, 6789-6801.
-
(2006)
J. Med. Chem
, vol.49
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
28
-
-
0344121638
-
The filling potential method: A method for estimating the free energy surface for protein-ligand docking
-
Fukunishi, Y.; Mikami, Y.; Nakamura, H. The filling potential method: A method for estimating the free energy surface for protein-ligand docking. J. Phys. Chem. B 2003, 107, 13201-13210.
-
(2003)
J. Phys. Chem. B
, vol.107
, pp. 13201-13210
-
-
Fukunishi, Y.1
Mikami, Y.2
Nakamura, H.3
-
29
-
-
0013133162
-
A new test set for validating predictions of protein-ligand interaction
-
Nissink, J. W. M.; Murray, C.; Hartshorn, M.; Verdonk, M. L.; Cole, J. C.; Taylor, R. A new test set for validating predictions of protein-ligand interaction. Proteins 2002, 49, 457-471.
-
(2002)
Proteins
, vol.49
, pp. 457-471
-
-
Nissink, J.W.M.1
Murray, C.2
Hartshorn, M.3
Verdonk, M.L.4
Cole, J.C.5
Taylor, R.6
-
30
-
-
9244260409
-
-
University of California: San Francisco, CA
-
Case, D. A.; Darden, T. A.; Cheatham, T. E., III; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Merz, K. M.; Wang, B.; Pearlman, D. A.; Crowley, M.; Brozell, S.; Tsui, V.; Gohlke, H.; Mongan, J.; Hornak, V.; Cui, G.; Beroza, P.; Schafmeister, C.; Caldwell, J. W.; Ross, W. S.; Kollman, P. A. AMBER 8; University of California: San Francisco, CA, 2004.
-
(2004)
AMBER 8
-
-
Case, D.A.1
Darden, T.A.2
Cheatham III, T.E.3
Simmerling, C.L.4
Wang, J.5
Duke, R.E.6
Luo, R.7
Merz, K.M.8
Wang, B.9
Pearlman, D.A.10
Crowley, M.11
Brozell, S.12
Tsui, V.13
Gohlke, H.14
Mongan, J.15
Hornak, V.16
Cui, G.17
Beroza, P.18
Schafmeister, C.19
Caldwell, J.W.20
Ross, W.S.21
Kollman, P.A.22
more..
-
31
-
-
0033594911
-
Nonsteroid drug selectivities for cyclo-oxygenase-1 rather than cyclo-oxygenase-2 are associated with human gastrointestinal toxicity: A full in vitro analysis
-
Warner, T. D.; Giuliano, F.; Vojnovic, I.; Bukasa, A.; Mitchell, J. A.; Vane, J. R. Nonsteroid drug selectivities for cyclo-oxygenase-1 rather than cyclo-oxygenase-2 are associated with human gastrointestinal toxicity: A full in vitro analysis. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 7563-7568.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 7563-7568
-
-
Warner, T.D.1
Giuliano, F.2
Vojnovic, I.3
Bukasa, A.4
Mitchell, J.A.5
Vane, J.R.6
-
32
-
-
0029911267
-
Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2
-
Luong, C.; Miller, A.; Barnett, J.; Chow, J.; Ramesha, C.; Browner, M. F. Flexibility of the NSAID binding site in the structure of human cyclooxygenase-2. Nat. Struct. Biol. 1996, 3, 927-933.
-
(1996)
Nat. Struct. Biol
, vol.3
, pp. 927-933
-
-
Luong, C.1
Miller, A.2
Barnett, J.3
Chow, J.4
Ramesha, C.5
Browner, M.F.6
-
33
-
-
0033827093
-
Recent advances in inducible cyclooxygenase (COX-2) inhibition
-
Levai, X.; Delarge, J.; Somers, F.; Tullio, P.; Henrotin, Y.; Pirotte, B.; Dogne, J. M. Recent advances in inducible cyclooxygenase (COX-2) inhibition. Curr. Med. Chem. 2000, 7, 1041-1062.
-
(2000)
Curr. Med. Chem
, vol.7
, pp. 1041-1062
-
-
Levai, X.1
Delarge, J.2
Somers, F.3
Tullio, P.4
Henrotin, Y.5
Pirotte, B.6
Dogne, J.M.7
-
34
-
-
3242748214
-
Design, synthesis, and structure-activity relationship studies of 3,4,6-triphenylpyran-2-ones as selective cyclooxygenase-2 inhibitors
-
Rao, P. N. P.; Uddin, M. J.; Knaus, E. E. Design, synthesis, and structure-activity relationship studies of 3,4,6-triphenylpyran-2-ones as selective cyclooxygenase-2 inhibitors. J. Med. Chem. 2004, 47, 3972-3990.
-
(2004)
J. Med. Chem
, vol.47
, pp. 3972-3990
-
-
Rao, P.N.P.1
Uddin, M.J.2
Knaus, E.E.3
-
35
-
-
33749260698
-
A Critical Assessment of Docking Programs and Scoring Functions
-
Warren, G. L.; Webster Andrews, C.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A Critical Assessment of Docking Programs and Scoring Functions. J. Med. Chem. 2006, 49, 5912-5931.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5912-5931
-
-
Warren, G.L.1
Webster Andrews, C.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
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
|