-
1
-
-
0032214649
-
Databases for protein-ligand complexes
-
Pt 6 Pt 1
-
Hendlich, M. (1998) Databases for protein-ligand complexes. Acta Crystallogr D Biol Crystallogr, 54(Pt 6 Pt 1): 1178-1182.
-
(1998)
Acta Crystallogr D Biol Crystallogr
, vol.54
, pp. 1178-1182
-
-
Hendlich, M.1
-
2
-
-
23044480075
-
Binding MOAD (Mother Of All Databases)
-
Hu, L., Benson, M.L., Smith, R.D., Lerner, M.G., and Carlson, H.A. (2005) Binding MOAD (Mother Of All Databases). Proteins, 60(3): 333-340.
-
(2005)
Proteins
, vol.60
, Issue.3
, pp. 333-340
-
-
Hu, L.1
Benson, M.L.2
Smith, R.D.3
Lerner, M.G.4
Carlson, H.A.5
-
3
-
-
13844312649
-
ZINC - a free database of commercially available compounds for virtual screening
-
Irwin, J.J. and Shoichet, B.K. (2005) ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model, 45(1): 177-182.
-
(2005)
J Chem Inf Model
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
4
-
-
0033954256
-
The Protein Data Bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) The Protein Data Bank. Nucleic Acids Res, 28(1): 235-242.
-
(2000)
Nucleic Acids Res
, vol.28
, Issue.1
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
5
-
-
33745123321
-
Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery
-
Pozzan, A. (2006) Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery. Curr Pharm Des, 12(17): 2099-2110.
-
(2006)
Curr Pharm Des
, vol.12
, Issue.17
, pp. 2099-2110
-
-
Pozzan, A.1
-
6
-
-
33846212271
-
Comparison of shape-matching and docking as virtual screening tools
-
Hawkins, P.C., Skillman, A.G., and Nicholls, A. (2007) Comparison of shape-matching and docking as virtual screening tools. J Med Chem, 50(1): 74-82.
-
(2007)
J Med Chem
, vol.50
, Issue.1
, pp. 74-82
-
-
Hawkins, P.C.1
Skillman, A.G.2
Nicholls, A.3
-
7
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa, S.F., Fernandes, P.A., and Ramos, M.J. (2006) Protein-ligand docking: Current status and future challenges. Proteins, 65(1): 15-26.
-
(2006)
Proteins
, vol.65
, Issue.1
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
8
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris, G.M., Goodsell, D.S., Halliday, R.S., Huey, R., Hart, W.E., Belew, R.K., and Olson, A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem, 19: 1639-1662.
-
(1998)
J Comput Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
9
-
-
0030203710
-
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
-
Morris, G.M., Goodsell, D.S., Huey, R., and Olson, A.J. (1996) Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des, 10(4): 293-304.
-
(1996)
J Comput Aided Mol Des
, vol.10
, Issue.4
, pp. 293-304
-
-
Morris, G.M.1
Goodsell, D.S.2
Huey, R.3
Olson, A.J.4
-
10
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell, D.S. and Olson, A.J. (1990) Automated docking of substrates to proteins by simulated annealing. Proteins, 8(3): 195-202.
-
(1990)
Proteins
, vol.8
, Issue.3
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
11
-
-
6244283606
-
Critical evaluation of search algorithms for automated molecular docking and database screening
-
Ewing, T.J.A. and Kuntz, I.D. (1997) Critical evaluation of search algorithms for automated molecular docking and database screening. J Comput Chem, 18(9): 1175-1189.
-
(1997)
J Comput Chem
, vol.18
, Issue.9
, pp. 1175-1189
-
-
Ewing, T.J.A.1
Kuntz, I.D.2
-
12
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E. (1982) A geometric approach to macromolecule-ligand interactions. J Mol Biol, 161(2): 269-288.
-
(1982)
J Mol Biol
, vol.161
, Issue.2
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
13
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey, M., Kramer, B., Lengauer, T., and Klebe, G. (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol, 261(3): 470-489.
-
(1996)
J Mol Biol
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
14
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
Jones, G., Willett, P., Glen, R.C., Leach, A.R., and Taylor, R. (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol, 267(3): 727-748.
-
(1997)
J Mol Biol
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
15
-
-
0028854034
-
Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
-
Jones, G., Willett, P., and Glen, R.C. (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol, 245(1): 43-53.
-
(1995)
J Mol Biol
, vol.245
, Issue.1
, pp. 43-53
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
-
16
-
-
84986522918
-
ICM - a new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan, R.A., Totrov, M.M., and Kuznetzov, D.A. (1994) ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. Journal of Computational Chemistry, 15: 488-506.
-
(1994)
Journal of Computational Chemistry
, vol.15
, pp. 488-506
-
-
Abagyan, R.A.1
Totrov, M.M.2
Kuznetzov, D.A.3
-
17
-
-
0036520840
-
A review of protein-small molecule docking methods
-
Taylor, R.D., Jewsbury, P.J., and Essex, J.W. (2002) A review of protein-small molecule docking methods. J Comput Aided Mol Des, 16(3): 151-166.
-
(2002)
J Comput Aided Mol Des
, vol.16
, Issue.3
, pp. 151-166
-
-
Taylor, R.D.1
Jewsbury, P.J.2
Essex, J.W.3
-
18
-
-
0034649618
-
Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations
-
Bissantz, C., Folkers, G., and Rognan, D. (2000) Protein-based virtual screening of chemical databases. 1. Evaluation of different docking/scoring combinations. J Med Chem, 43(25): 4759-4767.
-
(2000)
J Med Chem
, vol.43
, Issue.25
, pp. 4759-4767
-
-
Bissantz, C.1
Folkers, G.2
Rognan, D.3
-
19
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner, R.A., Banks, J.L., Murphy, R.B., Halgren, T.A., Klicic, J.J., Mainz, D.T., Repasky, M.R, Knoll, E.H., Shelley, M., Perry, J.K., Shaw, D.E., Francis, P., and Shenkin, P.S. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem, 47(7): 1739-1749.
-
(2004)
J Med Chem
, vol.47
, Issue.7
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.R.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
20
-
-
1642310340
-
Glide: A new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening
-
Halgren, T.A., Murphy, R.B., Friesner, R.A., Beard, H.S., Frye, L.L., Pollard, W.T., and Banks, J.L. (2004) Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem, 47(7): 1750-1759.
-
(2004)
J Med Chem
, vol.47
, Issue.7
, pp. 1750-1759
-
-
Halgren, T.A.1
Murphy, R.B.2
Friesner, R.A.3
Beard, H.S.4
Frye, L.L.5
Pollard, W.T.6
Banks, J.L.7
-
21
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger, E., Rodrigo, J., Muller, P., and Rognan, D. (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins, 57(2): 225-242.
-
(2004)
Proteins
, vol.57
, Issue.2
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
22
-
-
1642540577
-
Evaluation of docking performance: Comparative data on docking algorithms
-
Kontoyianni, M., McClellan, L.M., and Sokol, G.S. (2004) Evaluation of docking performance: comparative data on docking algorithms. J Med Chem, 47(3): 558-565.
-
(2004)
J Med Chem
, vol.47
, Issue.3
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
23
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
Perola, E., Walters, W.P., and Charifson, P.S. (2004) A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins, 56(2): 235-249.
-
(2004)
Proteins
, vol.56
, Issue.2
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
24
-
-
33745864845
-
Virtual screening of DNA minor groove binders
-
Evans, D.A. and Neidle, S. (2006) Virtual screening of DNA minor groove binders. J Med Chem, 49(14): 4232-4238.
-
(2006)
J Med Chem
, vol.49
, Issue.14
, pp. 4232-4238
-
-
Evans, D.A.1
Neidle, S.2
-
25
-
-
23944454816
-
Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols
-
Evers, A., Hessler, G., Matter, H., and Klabunde, T. (2005) Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein- and ligand-based virtual screening protocols. J Med Chem, 48(17): 5448-5465.
-
(2005)
J Med Chem
, vol.48
, Issue.17
, pp. 5448-5465
-
-
Evers, A.1
Hessler, G.2
Matter, H.3
Klabunde, T.4
-
26
-
-
13944263886
-
Comparison of automated docking programs as virtual screening tools
-
Cummings, M.D., DesJarlais, R.L., Gibbs, A.C., Mohan, V., and Jaeger, E.P. (2005) Comparison of automated docking programs as virtual screening tools. J Med Chem, 48(4): 962-976.
-
(2005)
J Med Chem
, vol.48
, Issue.4
, pp. 962-976
-
-
Cummings, M.D.1
DesJarlais, R.L.2
Gibbs, A.C.3
Mohan, V.4
Jaeger, E.P.5
-
27
-
-
24644481912
-
Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models
-
Cotesta, S., Giordanetto, F., Trosset, J.Y., Crivori, P., Kroemer, R.T., Stouten, P.F., and Vulpetti, A. (2005) Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. Proteins, 60(4): 629-643.
-
(2005)
Proteins
, vol.60
, Issue.4
, pp. 629-643
-
-
Cotesta, S.1
Giordanetto, F.2
Trosset, J.Y.3
Crivori, P.4
Kroemer, R.T.5
Stouten, P.F.6
Vulpetti, A.7
-
28
-
-
23044513878
-
Comparing protein-ligand docking programs is difficult
-
Cole, J.C., Murray, C.W., Nissink, J.W., Taylor, R.D., and Taylor, R. (2005) Comparing protein-ligand docking programs is difficult. Proteins, 60(3): 325-332.
-
(2005)
Proteins
, vol.60
, Issue.3
, pp. 325-332
-
-
Cole, J.C.1
Murray, C.W.2
Nissink, J.W.3
Taylor, R.D.4
Taylor, R.5
-
29
-
-
0346731233
-
Multiple active site corrections for docking and virtual screening
-
Vigers, G.P. and Rizzi, J.P. (2004) Multiple active site corrections for docking and virtual screening. J Med Chem, 47(1): 80-89.
-
(2004)
J Med Chem
, vol.47
, Issue.1
, pp. 80-89
-
-
Vigers, G.P.1
Rizzi, J.P.2
-
31
-
-
0026136104
-
A globally convergent augmented Lagrangian pattern search algorithm for optimization with general constraints and simple bounds
-
Conn, A.R., Gould, N.I.M., and Toint, P.L. (1991) A globally convergent augmented Lagrangian pattern search algorithm for optimization with general constraints and simple bounds. SIAM Journal on Numerical Analysis, 28(2): 545-572.
-
(1991)
SIAM Journal on Numerical Analysis
, vol.28
, Issue.2
, pp. 545-572
-
-
Conn, A.R.1
Gould, N.I.M.2
Toint, P.L.3
-
32
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S., C. D. Gelatt, J., and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220(4598): 671-680.
-
(1983)
Science
, vol.220
, Issue.4598
, pp. 671-680
-
-
Kirkpatrick, S.C.D.1
Gelatt, J.2
Vecchi, M.P.3
-
34
-
-
0003722376
-
-
1st ed, Boston, MA: Addison-Wesley Longman Publishing Co, Inc
-
Goldberg, D.E., Genetic Algorithms in Search, Optimization and Machine Learning. 1st ed. 1989, Boston, MA: Addison-Wesley Longman Publishing Co., Inc. 372.
-
(1989)
Genetic Algorithms in Search, Optimization and Machine Learning
, pp. 372
-
-
Goldberg, D.E.1
-
36
-
-
33646107162
-
Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking
-
de Graaf, C., Oostenbrink, C., Keizers, P.H., van der Wijst, T., Jongejan, A., and Vermeulen, N.P. (2006) Catalytic site prediction and virtual screening of cytochrome P450 2D6 substrates by consideration of water and rescoring in automated docking. J Med Chem, 49(8): 2417-2430.
-
(2006)
J Med Chem
, vol.49
, Issue.8
, pp. 2417-2430
-
-
de Graaf, C.1
Oostenbrink, C.2
Keizers, P.H.3
van der Wijst, T.4
Jongejan, A.5
Vermeulen, N.P.6
-
37
-
-
0142028937
-
Kinases, homology models, and high throughput docking
-
Diller, D.J. and Li, R. (2003) Kinases, homology models, and high throughput docking. J Med Chem, 46(22): 4638-4647.
-
(2003)
J Med Chem
, vol.46
, Issue.22
, pp. 4638-4647
-
-
Diller, D.J.1
Li, R.2
-
38
-
-
13944255377
-
Structure-based drug discovery using GPCR homology modeling: Successful virtual screening for antagonists of the alphalA adrenergic receptor
-
Evers, A. and Klabunde, T. (2005) Structure-based drug discovery using GPCR homology modeling: successful virtual screening for antagonists of the alphalA adrenergic receptor. J Med Chem, 48(4): 1088-1097.
-
(2005)
J Med Chem
, vol.48
, Issue.4
, pp. 1088-1097
-
-
Evers, A.1
Klabunde, T.2
-
39
-
-
0036680148
-
Lead discovery using molecular docking
-
Shoichet, B.K., McGovern, S.L., Wei, B., and Irwin, J.J. (2002) Lead discovery using molecular docking. Curr Opin Chem Biol, 6(4): 439-446.
-
(2002)
Curr Opin Chem Biol
, vol.6
, Issue.4
, pp. 439-446
-
-
Shoichet, B.K.1
McGovern, S.L.2
Wei, B.3
Irwin, J.J.4
-
40
-
-
0032718788
-
The sensitivity of the results of molecular docking to induced fit effects: Application to thrombin, thermolysin and neuraminidase
-
Murray, C.W., Baxter, C.A., and Frenkel, A.D. (1999) The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. J Comput Aided Mol Des, 13(6): 547-562.
-
(1999)
J Comput Aided Mol Des
, vol.13
, Issue.6
, pp. 547-562
-
-
Murray, C.W.1
Baxter, C.A.2
Frenkel, A.D.3
-
41
-
-
33751423377
-
How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding
-
Gunasekaran, K. and Nussinov, R. (2007) How different are structurally flexible and rigid binding sites? Sequence and structural features discriminating proteins that do and do not undergo conformational change upon ligand binding. J Mol Biol, 365(1): 257-273.
-
(2007)
J Mol Biol
, vol.365
, Issue.1
, pp. 257-273
-
-
Gunasekaran, K.1
Nussinov, R.2
-
42
-
-
33747200808
-
Combining docking and molecular dynamic simulations in drug design
-
Alonso, H., Bliznyuk, A.A., and Gready, J.E. (2006) Combining docking and molecular dynamic simulations in drug design. Med Res Rev, 26(5): 531-568.
-
(2006)
Med Res Rev
, vol.26
, Issue.5
, pp. 531-568
-
-
Alonso, H.1
Bliznyuk, A.A.2
Gready, J.E.3
-
43
-
-
0037157153
-
Computational drug design accommodating receptor flexibility: The relaxed complex scheme
-
Lin, J.H., Perryman, A.L., Schames, J.R., and McCammon, J.A. (2002) Computational drug design accommodating receptor flexibility: The relaxed complex scheme. J Am Chem Soc, 124(20): 5632-5633.
-
(2002)
J Am Chem Soc
, vol.124
, Issue.20
, pp. 5632-5633
-
-
Lin, J.H.1
Perryman, A.L.2
Schames, J.R.3
McCammon, J.A.4
-
44
-
-
0004023353
-
-
University of California: San Francisco
-
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, T.E., III, Ross, W.S., Simmerling, C.L., Darden, T.A., Merz, K.M., Stanton, R.V., Cheng, A.L., Vincent, J.J., Crowley, M., Ferguson, D.M., Radmer, R.J., Seibel, G.L., Singh, U.C., Weiner, P.K., and Kollman, P.A. (1997) AMBER 5 University of California: San Francisco.
-
(1997)
AMBER 5
-
-
Case, D.A.1
Pearlman, D.A.2
Caldwell, J.W.3
Cheatham III, T.E.4
Ross, W.S.5
Simmerling, C.L.6
Darden, T.A.7
Merz, K.M.8
Stanton, R.V.9
Cheng, A.L.10
Vincent, J.J.11
Crowley, M.12
Ferguson, D.M.13
Radmer, R.J.14
Seibel, G.L.15
Singh, U.C.16
Weiner, P.K.17
Kollman, P.A.18
-
45
-
-
85069135109
-
-
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, TE., III, J., W., Ross, W.S., C., S., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., V., T., Gohlke, R.R., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, C., Weiner, P., and Kollman, P.A. (2002) AMBER 7 University of California: San Francisco.
-
Case, D.A., Pearlman, D.A., Caldwell, J.W., Cheatham, TE., III, J., W., Ross, W.S., C., S., Darden, T., Merz, K.M., Stanton, R.V., Cheng, A., Vincent, J.J., Crowley, M., V., T., Gohlke, R.R., Duan, Y., Pitera, J., Massova, I., Seibel, G.L., Singh, C., Weiner, P., and Kollman, P.A. (2002) AMBER 7 University of California: San Francisco.
-
-
-
-
46
-
-
27344436659
-
Scalable molecular dynamics with NAMD
-
Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., and Schulten, K. (2005) Scalable molecular dynamics with NAMD. J Comput Chem, 26: 1781-1802.
-
(2005)
J Comput Chem
, vol.26
, pp. 1781-1802
-
-
Phillips, J.C.1
Braun, R.2
Wang, W.3
Gumbart, J.4
Tajkhorshid, E.5
Villa, E.6
Chipot, C.7
Skeel, R.D.8
Kale, L.9
Schulten, K.10
-
47
-
-
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. (2004) Discovery of a novel binding trench in HIV integrase. J Med Chem, 47(8): 1879-1881.
-
(2004)
J Med Chem
, vol.47
, Issue.8
, 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
-
48
-
-
33947585518
-
Ultrafast de novo docking: Combining pharmacophores and combinatorics
-
in press
-
Gastreich, M., Lilienthal, M., Briem, H., and Claussen, H. (2006) Ultrafast de novo docking: combining pharmacophores and combinatorics. J Comput Aided Mol Des, in press.
-
(2006)
J Comput Aided Mol Des
-
-
Gastreich, M.1
Lilienthal, M.2
Briem, H.3
Claussen, H.4
-
49
-
-
0000125764
-
A new model for calculating atomic charges in molecules
-
Gasteiger, J. and Marsili, M. (1978) A new model for calculating atomic charges in molecules. Tetrahedron Lett., 34: 3181-3184.
-
(1978)
Tetrahedron Lett
, vol.34
, pp. 3181-3184
-
-
Gasteiger, J.1
Marsili, M.2
-
50
-
-
33746214602
-
Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(l → 2)-mannosidase I to elucidate the pathway to the substrate transition state
-
Mulakala, C., Nerinckx, W., and Reilly, P.J. (2006) Docking studies on glycoside hydrolase Family 47 endoplasmic reticulum alpha-(l → 2)-mannosidase I to elucidate the pathway to the substrate transition state. Carbohydrate Research, 341(13): 2233-2245.
-
(2006)
Carbohydrate Research
, vol.341
, Issue.13
, pp. 2233-2245
-
-
Mulakala, C.1
Nerinckx, W.2
Reilly, P.J.3
-
52
-
-
0034257149
-
Automated docking of alpha-(1 → 4)-and alpha-(1 → 6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site
-
Rockey, W.M., Laederach, A., and Reilly, P.J. (2000) Automated docking of alpha-(1 → 4)-and alpha-(1 → 6)-linked glucosyl trisaccharides and maltopentaose into the soybean beta-amylase active site. Proteins-Structure Function and Genetics, 40(2): 299-309.
-
(2000)
Proteins-Structure Function and Genetics
, vol.40
, Issue.2
, pp. 299-309
-
-
Rockey, W.M.1
Laederach, A.2
Reilly, P.J.3
-
53
-
-
0029197510
-
Time-efficient docking of flexible ligands into active sites of proteins
-
Rarey, M., Kramer, B., and Lengauer, T. (1995) Time-efficient docking of flexible ligands into active sites of proteins. Proc Int Conf Intell Syst Mol Biol, 3: 300-308.
-
(1995)
Proc Int Conf Intell Syst Mol Biol
, vol.3
, pp. 300-308
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
-
54
-
-
85069129488
-
-
3.4, Molecular Networks GmbH: Erlangen, Germany
-
Gasteiger, J. and Sadowski, J. (1992) CORINA 3.4, Molecular Networks GmbH: Erlangen, Germany, http://www.molecular-networks.com/online- demos/corina-demo.html.
-
(1992)
CORINA
-
-
Gasteiger, J.1
Sadowski, J.2
-
55
-
-
31444452744
-
Automatic generation of 3D-atomic coordinates for organic molecules
-
Gasteiger, J., Rudolph, C., and Sadowski, J. (1992) Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comput. Methodol., 3: 537-547.
-
(1992)
Tetrahedron Comput. Methodol
, vol.3
, pp. 537-547
-
-
Gasteiger, J.1
Rudolph, C.2
Sadowski, J.3
-
57
-
-
34250900654
-
-
Ten Eyck, L.F., Mandell, J., Roberts, V.A., and Pique, M.E., Surveying Molecular Interactions With DOT. 1995.
-
(1995)
Surveying Molecular Interactions With DOT
-
-
Ten Eyck, L.F.1
Mandell, J.2
Roberts, V.A.3
Pique, M.E.4
-
58
-
-
0031296607
-
Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex
-
Vakser, I.A. (1997) Evaluation of GRAMM low-resolution docking methodology on the hemagglutinin-antibody complex. Proteins, Suppl 1: 226-230.
-
(1997)
Proteins
, Issue.SUPPL. 1
, pp. 226-230
-
-
Vakser, I.A.1
-
59
-
-
33747840389
-
GRAMM-X public web server for protein-protein docking
-
Web Server issue, W310-314
-
Tovchigrechko, A. and Vakser, I.A. (2006) GRAMM-X public web server for protein-protein docking. Nucleic Acids Res, 34(Web Server issue): W310-314.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Tovchigrechko, A.1
Vakser, I.A.2
-
60
-
-
0037093643
-
Docking unbound proteins using shape complementarity, desolvation, and electrostatics
-
Chen, R. and Weng, Z. (2002) Docking unbound proteins using shape complementarity, desolvation, and electrostatics. Proteins, 47(3): 281-294.
-
(2002)
Proteins
, vol.47
, Issue.3
, pp. 281-294
-
-
Chen, R.1
Weng, Z.2
-
61
-
-
14044262243
-
Docking: Successes and challenges
-
Mohan, V., Gibbs, A.C., Cummings, M.D., Jaeger, E.P., and DesJarlais, R.L. (2005) Docking: successes and challenges. Curr Pharm Des, 11(3): 323-333.
-
(2005)
Curr Pharm Des
, vol.11
, Issue.3
, pp. 323-333
-
-
Mohan, V.1
Gibbs, A.C.2
Cummings, M.D.3
Jaeger, E.P.4
DesJarlais, R.L.5
-
62
-
-
0029011701
-
A second 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, J., Kenneth M., Ferguson, D.M., Spellmeyer, D.C., Fox, T., Caldwell, J.W., and Kollman, P.A. (1995) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc., 117: 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, J.5
Kenneth, M.6
Ferguson, D.M.7
Spellmeyer, D.C.8
Fox, T.9
Caldwell, J.W.10
Kollman, P.A.11
-
63
-
-
33947716119
-
A semiempirical free energy force field with charge-based desolvation
-
Huey, R., Morris, G.M., Olson, A.J., and Goodsell, D.S. (2007) A semiempirical free energy force field with charge-based desolvation. J Comput Chem, 28(6): 1145-1152.
-
(2007)
J Comput Chem
, vol.28
, Issue.6
, pp. 1145-1152
-
-
Huey, R.1
Morris, G.M.2
Olson, A.J.3
Goodsell, D.S.4
-
64
-
-
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. (1994) 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(3): 243-256.
-
(1994)
J Comput Aided Mol Des
, vol.8
, Issue.3
, pp. 243-256
-
-
Böhm, H.-J.1
-
65
-
-
0346264740
-
Automated docking of ligands to an artificial active site: Augmenting crystallographic analysis with computer modeling
-
Rosenfeld, R.J., Goodsell, D.S., Musah, R.A., Morris, G.M., Goodin, D.B., and Olson, A.J. (2003) Automated docking of ligands to an artificial active site: augmenting crystallographic analysis with computer modeling. Journal of Computer-Aided Molecular Design, 17(8): 525-536.
-
(2003)
Journal of Computer-Aided Molecular Design
, vol.17
, Issue.8
, pp. 525-536
-
-
Rosenfeld, R.J.1
Goodsell, D.S.2
Musah, R.A.3
Morris, G.M.4
Goodin, D.B.5
Olson, A.J.6
-
66
-
-
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. (2005) New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy. Journal of Computational Chemistry, 26(11): 1089-1095.
-
(2005)
Journal of Computational Chemistry
, vol.26
, Issue.11
, pp. 1089-1095
-
-
Ruvinsky, A.M.1
Kozintsev, A.V.2
-
67
-
-
30344467833
-
Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions
-
Ruvinsky, A.M. and Kozintsev, A.V. (2006) Novel statistical-thermodynamic methods to predict protein-ligand binding positions using probability distribution functions. Proteins-Structure Function and Bioinformatics, 62(1): 202-208.
-
(2006)
Proteins-Structure Function and Bioinformatics
, vol.62
, Issue.1
, pp. 202-208
-
-
Ruvinsky, A.M.1
Kozintsev, A.V.2
-
68
-
-
0027013007
-
AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution
-
Cramer, C.J. and Truhlar, D.G. (1992) AM1-SM2 and PM3-SM3 parameterized SCF solvation models for free energies in aqueous solution. J Comput Aided Mol Des, 6(6): 629-666.
-
(1992)
J Comput Aided Mol Des
, vol.6
, Issue.6
, pp. 629-666
-
-
Cramer, C.J.1
Truhlar, D.G.2
-
69
-
-
85069132884
-
-
Hawkins, G.D., Giesen, D.J., Lynch, G.C., Chambers, C.C., Rossi, I., Storer, J.W., Li, J., Zhu, T., Thompson, J.D., Winget, P., Lynch, B.J., Rinaldi, D., Liotard, D.A., Cramer, C.J., and Truhlar, D.G. (2007) AMSOL 7.1, Department of Chemistry and Supercomputer Institute, University of Minnesota: Minneapolis, Minnesota, http://comp.chem.umn.edu/amsol/.
-
Hawkins, G.D., Giesen, D.J., Lynch, G.C., Chambers, C.C., Rossi, I., Storer, J.W., Li, J., Zhu, T., Thompson, J.D., Winget, P., Lynch, B.J., Rinaldi, D., Liotard, D.A., Cramer, C.J., and Truhlar, D.G. (2007) AMSOL 7.1, Department of Chemistry and Supercomputer Institute, University of Minnesota: Minneapolis, Minnesota, http://comp.chem.umn.edu/amsol/.
-
-
-
-
70
-
-
33748173818
-
BDT: An easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock
-
2006
-
Vaque, M., Arola, A., Aliagas, C., and Pujadas, G. (2006) BDT: an easy-to-use front-end application for automation of massive docking tasks and complex docking strategies with AutoDock. Bioinformatics, 22(14): 1803-1804.
-
(1803)
Bioinformatics
, vol.22
, Issue.14
-
-
Vaque, M.1
Arola, A.2
Aliagas, C.3
Pujadas, G.4
-
71
-
-
33645886036
-
Exploring protein-ligand recognition with Binding MOAD
-
Smith, R.D., Hu, L., Falkner, J.A., Benson, M.L., Nerothin, J.P., and Carlson, H.A. (2006) Exploring protein-ligand recognition with Binding MOAD. J Mol Graph Model, 24(6): 414-425.
-
(2006)
J Mol Graph Model
, vol.24
, Issue.6
, pp. 414-425
-
-
Smith, R.D.1
Hu, L.2
Falkner, J.A.3
Benson, M.L.4
Nerothin, J.P.5
Carlson, H.A.6
-
72
-
-
0031473847
-
SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
-
Guex, N. and Peitsch, M.C. (1997) SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18(15): 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, Issue.15
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
73
-
-
3242886389
-
-
Davis, I.W., Murray, L.W., Richardson, J.S., and Richardson, D.C. (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res, 32(Web Server issue): W615-619.
-
Davis, I.W., Murray, L.W., Richardson, J.S., and Richardson, D.C. (2004) MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res, 32(Web Server issue): W615-619.
-
-
-
-
74
-
-
0037441653
-
Structure validation by Calpha geometry: Phi,psi and Cbeta deviation
-
Lovell, S.C., Davis, I.W., Arendall, W.B., 3rd, de Bakker, P.I., Word, J.M., Prisant, M.G., Richardson, J.S., and Richardson, D.C. (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins, 50(3): 437-450.
-
(2003)
Proteins
, vol.50
, Issue.3
, pp. 437-450
-
-
Lovell, S.C.1
Davis, I.W.2
Arendall 3rd, W.B.3
de Bakker, P.I.4
Word, J.M.5
Prisant, M.G.6
Richardson, J.S.7
Richardson, D.C.8
-
75
-
-
0004117251
-
-
Daylight Chemical Information Systems, Inc
-
Weininger, D., Daylight Theory Manual. 2006, Daylight Chemical Information Systems, Inc.
-
(2006)
Daylight Theory Manual
-
-
Weininger, D.1
-
76
-
-
0001708959
-
Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited
-
Dalby, A., Nourse, J.G., Hounshell, W.D., Gushurst, A.K.I., Grier, D.L., Leland, B.A., and Laufer, J. (1992) Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited. J Chem Inf Comput Sci, 32: 244-255.
-
(1992)
J Chem Inf Comput Sci
, vol.32
, pp. 244-255
-
-
Dalby, A.1
Nourse, J.G.2
Hounshell, W.D.3
Gushurst, A.K.I.4
Grier, D.L.5
Leland, B.A.6
Laufer, J.7
-
77
-
-
84934437594
-
-
2.00, Department of Chemistry, University of Kuopio: Kuopio, Finland
-
Acton, A., Banck, M., Bréfort, J., Cruz, M., Curtis, D., Hassinen, T., Heikkilä, V., Hutchison, G., Huuskonen, J., Jensen, J., Liboska, R., and Rowley, C. (2006) Ghemical 2.00, Department of Chemistry, University of Kuopio: Kuopio, Finland, http://www.uku.fi/~thassine/projects/ghemical/.
-
(2006)
Ghemical
-
-
Acton, A.1
Banck, M.2
Bréfort, J.3
Cruz, M.4
Curtis, D.5
Hassinen, T.6
Heikkilä, V.7
Hutchison, G.8
Huuskonen, J.9
Jensen, J.10
Liboska, R.11
Rowley, C.12
-
78
-
-
0035451848
-
New energy terms for reduced protein models implemented in an off-lattice force field
-
Hassinen, T. and Peräkylä, M. (2001) New energy terms for reduced protein models implemented in an off-lattice force field. J Comput Chem, 22(12): 1229-1242.
-
(2001)
J Comput Chem
, vol.22
, Issue.12
, pp. 1229-1242
-
-
Hassinen, T.1
Peräkylä, M.2
-
79
-
-
85069133567
-
-
2.10, Department of Chemistry, University of Iowa, Iowa City, IA
-
Hassinen, T., Hutchison, G., Cruz, M., Banck, M., Rowley, C., and Curtis, D. (2007) Ghemical-GMS 2.10, Department of Chemistry, University of Iowa.: Iowa City, IA, http://www.uiowa.edu/~ghemical/ghemical.shtml.
-
(2007)
Ghemical-GMS
-
-
Hassinen, T.1
Hutchison, G.2
Cruz, M.3
Banck, M.4
Rowley, C.5
Curtis, D.6
-
80
-
-
85069134294
-
-
University of Dundee: Dundee, Scotland
-
van Aalten, D. and Oswald, S. (2007) PRODRG 2, University of Dundee: Dundee, Scotland, http://davapcl.bioch.dundee.ac.uk/programs/prodrg/.
-
(2007)
PRODRG
, pp. 2
-
-
van Aalten, D.1
Oswald, S.2
-
81
-
-
0030158429
-
PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules
-
van Aalten, D.M., Bywater, R., Findlay, J.B., Hendlich, M., Hooft, R.W., and Vriend, G. (1996) PRODRG, a program for generating molecular topologies and unique molecular descriptors from coordinates of small molecules. J Comput Aided Mol Des, 10(3): 255-262.
-
(1996)
J Comput Aided Mol Des
, vol.10
, Issue.3
, pp. 255-262
-
-
van Aalten, D.M.1
Bywater, R.2
Findlay, J.B.3
Hendlich, M.4
Hooft, R.W.5
Vriend, G.6
-
82
-
-
7544226311
-
PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
-
Schuttelkopf, A.W. and van Aalten, D.M. (2004) PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr D Biol Crystallogr, 60(Pt 8): 1355-1363.
-
(2004)
Acta Crystallogr D Biol Crystallogr
, vol.60
, Issue.PART 8
, pp. 1355-1363
-
-
Schuttelkopf, A.W.1
van Aalten, D.M.2
-
84
-
-
0036084259
-
Efficient docking of peptides to proteins without prior knowledge of the binding site
-
Hetenyi, C. and van der Spoel, D. (2002) Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci, 11(7): 1729-1737.
-
(2002)
Protein Sci
, vol.11
, Issue.7
, pp. 1729-1737
-
-
Hetenyi, C.1
van der Spoel, D.2
-
85
-
-
0031592453
-
Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm
-
Raymer, M.L., Sanschagrin, P.C., Punch, W.F., Venkataraman, S., Goodman, E.D., and Kuhn, L.A. (1997) Predicting conserved water-mediated and polar ligand interactions in proteins using a K-nearest-neighbors genetic algorithm. J Mol Biol, 265(4): 445-464.
-
(1997)
J Mol Biol
, vol.265
, Issue.4
, pp. 445-464
-
-
Raymer, M.L.1
Sanschagrin, P.C.2
Punch, W.F.3
Venkataraman, S.4
Goodman, E.D.5
Kuhn, L.A.6
|