-
1
-
-
33744826819
-
MolDock: A new technique for high-accuracy molecular docking
-
DOI 10.1021/jm051197e
-
Thomsen, R.; Christensen, M. H. MolDock: a new technique for high-accuracy molecular docking. J. Med. Chem. 2006, 49 (11), 3315-3321. (Pubitemid 43830529)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.11
, pp. 3315-3321
-
-
Thomsen, R.1
Christensen, M.H.2
-
2
-
-
33749239216
-
M-score: A knowledge-based potential scoring function accounting for protein atom mobility
-
DOI 10.1021/jm050043w
-
Yang, C.-Y.; Wang, R.; Wang, S. M-Score: a knowledge-based potential scoring function accounting for protein atom mobility. J. Med. Chem. 2006, 49 (20), 5903-5911. (Pubitemid 44484937)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5903-5911
-
-
Yang, C.-Y.1
Wang, R.2
Wang, S.3
-
3
-
-
33750124980
-
Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes
-
DOI 10.1021/jm051256o
-
Friesner, R. A.; Murphy, R. B.; Repasky, M. P.; Frye, L. L.; Greenwood, J. R.; Halgren, T. A.; Sanschagrin, P. C.; Mainz, D. T. Extra precision Glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49 (21), 6177-6196. (Pubitemid 44595196)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.21
, pp. 6177-6196
-
-
Friesner, R.A.1
Murphy, R.B.2
Repasky, M.P.3
Frye, L.L.4
Greenwood, J.R.5
Halgren, T.A.6
Sanschagrin, P.C.7
Mainz, D.T.8
-
4
-
-
33749521613
-
EHiTS: An innovative approach to the docking and scoring function problems
-
DOI 10.2174/138920306778559412
-
Zsoldos, Z.; Reid, D.; Simon, A.; Sadjad, B. S.; Johnson, P. eHiTS: an innovative approach to the docking and scoring function problems. Curr. Protein Pept. Sci. 2006, 7 (5), 421-435. (Pubitemid 44524491)
-
(2006)
Current Protein and Peptide Science
, vol.7
, Issue.5
, pp. 421-435
-
-
Zsoldos, Z.1
Reid, D.2
Simon, A.3
Sadjad, B.S.4
Johnson, A.P.5
-
5
-
-
40749153054
-
Docking and hydropathic scoring of polysubstituted pyrrole compounds with anti-tubulin activity
-
doi:10.1016/j.bmc.2007.11.076
-
Tripathi, A.; Fornabaio, M.; Kellogg, G. E.; Gupton, J. T.; Gewirtz, D. A.; Yeudall, W. A.; Vega, N. E.; Mooberry, S. L. Docking and hydropathic scoring of polysubstituted pyrrole compounds with anti-tubulin activity. Bioorg. Med. Chem. 2007, doi:10.1016/j.bmc.2007.11.076.
-
(2007)
Bioorg. Med. Chem.
-
-
Tripathi, A.1
Fornabaio, M.2
Kellogg, G.E.3
Gupton, J.T.4
Gewirtz, D.A.5
Yeudall, W.A.6
Vega, N.E.7
Mooberry, S.L.8
-
6
-
-
40349106022
-
Ligand discovery and virtual screening using the program LIDAEUS
-
doi: 10.1038/sj.bjp.0707532
-
Taylor, P.; Blackburn, E.; Sheng, Y. G.; Harding, S.; Hsin, K.-Y.; Kan, D.; Shave, S.; Walkinshaw, M. D. Ligand discovery and virtual screening using the program LIDAEUS. Br. J. Pharmacol. 2007, doi: 10.1038/sj.bjp.0707532.
-
(2007)
Br. J. Pharmacol.
-
-
Taylor, P.1
Blackburn, E.2
Sheng, Y.G.3
Harding, S.4
Hsin, K.-Y.5
Kan, D.6
Shave, S.7
Walkinshaw, M.D.8
-
7
-
-
33846889763
-
Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery
-
DOI 10.1021/ci600357t
-
Catana, C.; Stouten, P. F. W. Novel, customizable scoring functions, parameterized using N-PLS, for structure-based drug discovery. J. Chem. Inf. Model. 2007, 47 (1), 85-91. (Pubitemid 46225563)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.1
, pp. 85-91
-
-
Catana, C.1
Stouten, P.F.W.2
-
8
-
-
34247197110
-
Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0
-
DOI 10.1021/ci6002637
-
Corbeil, C. R.; Englebienne, P.; Moitessier, N. Docking ligands into flexible and solvated macromolecules. 1. Development and validation of FITTED 1.0. J. Chem. Inf. Model. 2007, 47 (2), 435-449. (Pubitemid 46615946)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 435-449
-
-
Corbeil, C.R.1
Englebienne, P.2
Moitessier, N.3
-
9
-
-
33846630833
-
SODOCK: Swarm optimization for highly flexible protein-ligand docking
-
DOI 10.1002/jcc.20542
-
Chen, H.-M.; Liu, B.-F.; Huang, H.-L.; Hwang, S.-F.; Ho, S.-Y. SODOCK: swarm optimization for highly flexible protein-ligand docking. J. Comput. Chem. 2007, 28 (2), 612-623. (Pubitemid 46181836)
-
(2007)
Journal of Computational Chemistry
, vol.28
, Issue.2
, pp. 612-623
-
-
Chen, H.-M.1
Liu, B.-F.2
Huang, H.-L.3
Hwang, S.-F.4
Ho, S.-Y.5
-
10
-
-
34247343346
-
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
-
DOI 10.1007/s10822-007-9114-2
-
Jain, A. N. Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. J. Comput.-Aided Mol. Des. 2007, 21 (5), 281-306. (Pubitemid 46630055)
-
(2007)
Journal of Computer-Aided Molecular Design
, vol.21
, Issue.5
, pp. 281-306
-
-
Jain, A.N.1
-
11
-
-
3042806401
-
A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance
-
DOI 10.1002/prot.20088
-
Perola, E.; Walters, W.; Charifson, P. A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance. Proteins 2004, 56 (2), 235-249. (Pubitemid 38850158)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.56
, Issue.2
, pp. 235-249
-
-
Perola, E.1
Walters, W.P.2
Charifson, P.S.3
-
12
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G. L.; Andrews, C. W.; 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. (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, 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
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
13
-
-
41349090342
-
Can we use docking and scoring for hit-to-lead optimization?
-
doi:10.1007/s10822-007-9165-9174
-
Enyedy, I.; Egan, W. Can we use docking and scoring for hit-to-lead optimization? J. Comput.-Aided Mol. Des. 2008, doi:10.1007/s10822-007-9165-9174
-
(2008)
J. Comput.-Aided Mol. Des.
-
-
Enyedy, I.1
Egan, W.2
-
14
-
-
1642380461
-
The problem of overfitting
-
Hawkins, D. M. The problem of overfitting. J. Chem. Inf. Comput. Sci. 2004, 44 (1), 1-12.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, Issue.1
, pp. 1-12
-
-
Hawkins, D.M.1
-
15
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
DOI 10.1021/jm0003992
-
Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem. 2001, 44 (7), 1035-1042. (Pubitemid 32852130)
-
(2001)
Journal of Medicinal Chemistry
, vol.44
, Issue.7
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
17
-
-
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.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models. Acc. Chem. Res. 2000, 33 (12), 889-897.
-
(2000)
Acc. Chem. Res.
, vol.33
, Issue.12
, 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
Donini, O.11
Cieplak, P.12
Srinivasan, J.13
Case, D.A.14
Cheatham, T.E.15
-
18
-
-
33745405015
-
High-throughput calculation of protein-ligand binding affinities: Modification and adaptation of the MM-PBSA protocol to enterprise grid computing
-
DOI 10.1021/ci050488t
-
Brown, S. P.; Muchmore, S. W. High-throughput calculation of protein-ligand binding affinities: modification and adaptation of the MM-PBSA protocol to enterprise grid computing. J. Chem. Inf. Model. 2006, 46 (3), 999-1005. (Pubitemid 43999143)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.3
, pp. 999-1005
-
-
Brown, S.P.1
Muchmore, S.W.2
-
19
-
-
0030788411
-
The urokinase-type plasminogen activator system in cancer metastasis: A review
-
DOI 10.1002/(SICI)1097-0215(19970703)72:1<1::AID-IJC1>3.0.CO;2-Z
-
Andreasen, P. A.; Kjoller, L.; Christensen, L.; Duffy, M. J. The urokinase-type plasminogen activator system in cancer metastasis: a review. Int. J. Cancer 1997, 72 (1), 1-22. (Pubitemid 27314632)
-
(1997)
International Journal of Cancer
, vol.72
, Issue.1
, pp. 1-22
-
-
Andreasen, P.A.1
Kjoller, L.2
Christensen, L.3
Duffy, M.J.4
-
20
-
-
0033026635
-
Urokinase plasminogen activator: A prognostic marker in multiple types of cancer
-
DOI 10.1002/(SICI)1096-9098(199906)71:2<130::AID-JSO14>3.0.CO;2-9
-
Duffy, M. J.; Maguire, T. M.; McDermott, E. W.; O'Higgins, N. Urokinase plasminogen activator: a prognostic marker in multiple types of cancer. J. Surg. Oncol. 1999, 71 (2), 130-135. (Pubitemid 29288493)
-
(1999)
Journal of Surgical Oncology
, vol.71
, Issue.2
, pp. 130-135
-
-
Duffy, M.J.1
Maguire, T.M.2
Mcdermott, E.W.3
O'Higgins, N.4
-
21
-
-
0033525870
-
Increased insulin sensitivity and obesity resistance in mice lacking the protein tyrosine phosphatase-1B gene
-
Elchebly, M.; Payette, P.; Michaliszyn, E.; Cromlish, W.; Collins, S.; Loy, A. L.; Normandin, D.; Cheng, A.; Himms-Hagen, J.; Chan, C.-C.; Ramachandran, C.; Gresser, M. J.; Tremblay, M. L.; Kennedy, B. P. Increased insulin sensitivity and obesity resistance in mice lacking the protein tyrosine phosphatase-1B gene. Science 1999, 283 (5407), 1544.
-
(1999)
Science
, vol.283
, Issue.5407
, pp. 1544
-
-
Elchebly, M.1
Payette, P.2
Michaliszyn, E.3
Cromlish, W.4
Collins, S.5
Loy, A.L.6
Normandin, D.7
Cheng, A.8
Himms-Hagen, J.9
Chan, C.-C.10
Ramachandran, C.11
Gresser, M.J.12
Tremblay, M.L.13
Kennedy, B.P.14
-
22
-
-
0037143754
-
PTP1B antisense oligonucleotide lowers PTP1B protein, normalizes blood glucose, and improves insulin sensitivity in diabetic mice
-
Zinker, B. A.; Rondinone, C. M.; Trevillyan, J. M.; Gum, R. J.; Clampit, J. E.; Waring, J. F.; Xie, N.; Wilcox, D.; Jacobson, P.; Frost, L.; Kroeger, P. E.; Reilly, R. M.; Koterski, S.; Opgenorth, T. J.; Ulrich, R. G.; Crosby, S.; Butler, M.; Murray, S. F.; McKay, R. A.; Bhanot, S.; Monia, B. P.; Jirousek, M. R. PTP1B antisense oligonucleotide lowers PTP1B protein, normalizes blood glucose, and improves insulin sensitivity in diabetic mice. Proc. Natl. Acad. Sci. U.S.A. 2002, 99 (17), 11357-11362.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, Issue.17
, pp. 11357-11362
-
-
Zinker, B.A.1
Rondinone, C.M.2
Trevillyan, J.M.3
Gum, R.J.4
Clampit, J.E.5
Waring, J.F.6
Xie, N.7
Wilcox, D.8
Jacobson, P.9
Frost, L.10
Kroeger, P.E.11
Reilly, R.M.12
Koterski, S.13
Opgenorth, T.J.14
Ulrich, R.G.15
Crosby, S.16
Butler, M.17
Murray, S.F.18
McKay, R.A.19
Bhanot, S.20
Monia, B.P.21
Jirousek, M.R.22
more..
-
23
-
-
0030867582
-
Conservation of the Chk1 checkpoint pathway in mammals: Linkage of DNA damage to Cdk regulation through Cdc25
-
DOI 10.1126/science.277.5331.1497
-
Sanchez, Y.; Wong, C.; Thoma, R. S.; Richman, R.; Wu, Z.; Piwnica-Worms, H.; Elledge, S. J. Conservation of the Chk1 checkpoint pathway in mammals: linkage of DNA damage to Cdk regulation through Cdc25. Science 1997, 277 (5331), 1497-1501. (Pubitemid 27449236)
-
(1997)
Science
, vol.277
, Issue.5331
, pp. 1497-1501
-
-
Sanchez, Y.1
Wong, C.2
Thoma, R.S.3
Richman, R.4
Wu, Z.5
Piwnica-Worms, H.6
Elledge, S.J.7
-
25
-
-
0034629461
-
Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite
-
DOI 10.1074/jbc.275.10.7239
-
Nienaber, V.; Wang, J.; Davidson, D.; Henkin, J. Re-engineering of human urokinase provides a system for structure-based drug design at high resolution and reveals a novel structural subsite. J. Biol. Chem. 2000, 275 (10), 7239-7248. (Pubitemid 30146275)
-
(2000)
Journal of Biological Chemistry
, vol.275
, Issue.10
, pp. 7239-7248
-
-
Nienaber, V.1
Wang, J.2
Davidson, D.3
Henkin, J.4
-
26
-
-
0141680857
-
Fragment screening and assembly: A highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor
-
DOI 10.1021/jm034122o
-
Liu, G.; Xin, Z.; Pei, Z.; Hajduk, P. J.; Abad-Zapatero, C.; Hutchins, C. W.; Zhao, H.; Lubben, T. H.; Ballaron, S. J.; Haasch, D. L.; Kaszubska, W.; Rondinone, C. M.; Trevillyan, J. M.; Jirousek, M. R. Fragment screening and assembly: a highly efficient approach to a selective and cell active protein tyrosine phosphatase 1B inhibitor. J. Med. Chem. 2003, 46 (20), 4232-4235. (Pubitemid 37153003)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.20
, pp. 4232-4235
-
-
Liu, G.1
Xin, Z.2
Pei, Z.3
Hajduk, P.J.4
Abad-Zapatero, C.5
Hutchins, C.W.6
Zhao, H.7
Lubben, T.H.8
Ballaron, S.J.9
Haasch, D.L.10
Kaszubska, W.11
Rondinone, C.M.12
Trevillyan, J.M.13
Jirousek, M.R.14
-
27
-
-
33644790240
-
Synthesis and biological evaluation of 1-(2,4,5-trisubstituted phenyl)-3-(5-cyanopyrazin-2-yl)ureas as potent Chk1 kinase inhibitors
-
Li, G.; Hasvold, L. A.; Tao, Z. F.; Wang, G. T.; Gwaltney, S. L., 2nd; Patel, J.; Kovar, P.; Credo, R. B.; Chen, Z.; Zhang, H.; Park, C.; Sham, H. L.; Sowin, T.; Rosenberg, S. H.; Lin, N. H. Synthesis and biological evaluation of 1-(2,4,5-trisubstituted phenyl)-3-(5-cyanopyrazin-2-yl)ureas as potent Chk1 kinase inhibitors. Bioorg. Med. Chem. Lett. 2006, 16 (8), 2293-2298.
-
(2006)
Bioorg. Med. Chem. Lett.
, vol.16
, Issue.8
, pp. 2293-2298
-
-
Li, G.1
Hasvold, L.A.2
Tao, Z.F.3
Wang, G.T.4
Gwaltney II, S.L.5
Patel, J.6
Kovar, P.7
Credo, R.B.8
Chen, Z.9
Zhang, H.10
Park, C.11
Sham, H.L.12
Sowin, T.13
Rosenberg, S.H.14
Lin, N.H.15
-
28
-
-
9144246951
-
Identification of Novel Binding Interactions in the Development of Potent, Selective 2-Naphthamidine Inhibitors of Urokinase. Synthesis, Structural Analysis, and SAR of N-Phenyl Amide 6-Substitution
-
DOI 10.1021/jm0300072
-
Wendt, M. D.; Rockway, T. W.; Geyer, A.; McClellan, W.; Weitzberg, M.; Zhao, X.; Mantei, R.; Nienaber, V. L.; Stewart, K.; Klinghofer, V.; Giranda, V. L. Identification of novel binding interactions in the development of potent, selective 2-naphthamidine inhibitors of urokinase. Synthesis, structural analysis, and SAR of N-phenyl amide 6-substitution. J. Med. Chem. 2004, 47 (2), 303-324. (Pubitemid 38057876)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.2
, pp. 303-324
-
-
Wendt, M.D.1
Rockway, T.W.2
Geyer, A.3
McClellan, W.4
Weitzberg, M.5
Zhao, X.6
Mantei, R.7
Nienaber, V.L.8
Stewart, K.9
Klinghofer, V.10
Giranda, V.L.11
-
29
-
-
0242417581
-
Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy
-
DOI 10.1021/ja0296733
-
Szczepankiewicz, B. G.; Liu, G.; Hajduk, P. J.; Abad-Zapatero, C.; Pei, Z.; Xin, Z.; Lubben, T. H.; Trevillyan, J. M.; Stashko, M. A.; Ballaron, S. J.; Liang, H.; Huang, F.; Hutchins, C. W.; Fesik, S. W.; Jirousek, M. R. Discovery of a potent, selective protein tyrosine phosphatase 1B inhibitor using a linked-fragment strategy. J. Am. Chem. Soc. 2003, 125 (14), 4087-4096. (Pubitemid 36512302)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.14
, pp. 4087-4096
-
-
Szczepankiewicz, B.G.1
Liu, G.2
Hajduk, P.J.3
Abad-Zapatero, C.4
Pei, Z.5
Xin, Z.6
Lubben, T.H.7
Trevillyan, J.M.8
Stashko, M.A.9
Ballaron, S.J.10
Liang, H.11
Huang, F.12
Hutchins, C.W.13
Fesik, S.W.14
Jirousek, M.R.15
-
30
-
-
33751581196
-
Selective Chk1 inhibitors differentially sensitize p53-deficient cancer cells to cancer therapeutics
-
DOI 10.1002/ijc.22198
-
Chen, Z.; Xiao, Z.; Gu, W. Z.; Xue, J.; Bui, M. H.; Kovar, P.; Li, G.; Wang, G.; Tao, Z. F.; Tong, Y.; Lin, N. H.; Sham, H. L.; Wang, J. Y.; Sowin, T. J.; Rosenberg, S. H.; Zhang, H. Selective Chk1 inhibitors differentially sensitize p53-deficient cancer cells to cancer therapeutics. Int. J. Cancer 2006, 119 (12), 2784-2794. (Pubitemid 44846229)
-
(2006)
International Journal of Cancer
, vol.119
, Issue.12
, pp. 2784-2794
-
-
Chen, Z.1
Xiao, Z.2
Gu, W.-Z.3
Xue, J.4
Bui, M.H.5
Kovar, P.6
Li, G.7
Wang, G.8
Tao, Z.-F.9
Tong, Y.10
Lin, N.-H.11
Sham, H.L.12
Wang, J.Y.J.13
Sowin, T.J.14
Rosenberg, S.H.15
Zhang, H.16
-
31
-
-
33749598013
-
Cheminformatics analysis and learning in a data pipelining environment
-
Hassan, M.; Brown, R. D.; Varma-O'brien, S.; Rogers, D. Cheminformatics analysis and learning in a data pipelining environment. Mol. Diversity 2006, 10 (3), 283-299.
-
(2006)
Mol. Diversity
, vol.10
, Issue.3
, pp. 283-299
-
-
Hassan, M.1
Brown, R.D.2
Varma-O'Brien, S.3
Rogers, D.4
-
32
-
-
45749116266
-
Application of belief theory to similarity data fusion for use in analog searching and lead hopping
-
Muchmore, S. W.; Debe, D. A.; Metz, J. T.; Brown, S. P.; Martin, Y. C.; Hajduk, P. J. Application of belief theory to similarity data fusion for use in analog searching and lead hopping. J. Chem. Inf. Model. 2008, 48 (5), 941-948.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, Issue.5
, pp. 941-948
-
-
Muchmore, S.W.1
Debe, D.A.2
Metz, J.T.3
Brown, S.P.4
Martin, Y.C.5
Hajduk, P.J.6
-
33
-
-
0001041959
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model I: Method
-
Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model I: method. J. Comput. Chem. 2000, 21 (2), 132-146.
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.2
, pp. 132-146
-
-
Jakalian, A.1
Bush, B.L.2
Jack, D.B.3
Bayly, C.I.4
-
34
-
-
66249099911
-
-
Santa Fe, NM (accessed October 31, 2008)
-
OpenEye Scientific Software, Santa Fe, NM. http://www.eyesopen.com/ (accessed October 31, 2008).
-
-
-
-
35
-
-
34547666868
-
Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA
-
DOI 10.1021/ci700041j
-
Brown, S. P.; Muchmore, S. W. Rapid estimation of relative protein-ligand binding affinities using a high-throughput version of MM-PBSA. J. Chem. Inf. Model. 2007, 47 (4), 1493-1503. (Pubitemid 47210052)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.4
, pp. 1493-1503
-
-
Brown, S.P.1
Muchmore, S.W.2
-
36
-
-
0023779259
-
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis
-
Gilson, M. K.; Honig, B. Calculation of the total electrostatic energy of a macromolecular system: solvation energies, binding energies, and conformational analysis. Proteins 1988, 4 (1), 7-18.
-
(1988)
Proteins
, vol.4
, Issue.1
, pp. 7-18
-
-
Gilson, M.K.1
Honig, B.2
-
37
-
-
20544433165
-
Van der Waals volumes and radii
-
Bondi, A. van der Waals volumes and radii. J. Phys. Chem. 1964, 68 (3), 441-451.
-
(1964)
J. Phys. Chem.
, vol.68
, Issue.3
, pp. 441-451
-
-
Bondi, A.1
-
38
-
-
32844457567
-
Accurate calculation of hydration free energies using macroscopic solvent models
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate calculation of hydration free energies using macroscopic solvent models. J. Phys. Chem. 1994, 98, 1978-1988.
-
(1994)
J. Phys. Chem.
, vol.98
, pp. 1978-1988
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
39
-
-
0000398347
-
Empirical correlation between hydrophobic free energy and aqueous cavity surface area
-
Reynolds, J. A.; Gilbert, D. B.; Tanford, C. Empirical correlation between hydrophobic free energy and aqueous cavity surface area. Proc. Natl. Acad. Sci. U.S.A. 1974, 71 (8), 2925-2927.
-
(1974)
Proc. Natl. Acad. Sci. U.S.A.
, vol.71
, Issue.8
, pp. 2925-2927
-
-
Reynolds, J.A.1
Gilbert, D.B.2
Tanford, C.3
-
40
-
-
0027936280
-
Correlating solvation free energies and surface tensions of hydrocarbon solutes
-
DOI 10.1016/0301-4622(94)00062-X
-
Sitkoff, D.; Sharp, K. A.; Honig, B. Correlating solvation free energies and surface tensions of hydrocarbon solutes. Biophys. Chem. 1994, 51 (2-3), 397-409. (Pubitemid 24244015)
-
(1994)
Biophysical Chemistry
, vol.51
, Issue.2-3
, pp. 397-409
-
-
Sitkoff, D.1
Sharp, K.A.2
Honig, B.3
-
41
-
-
0028331255
-
Normal mode analysis of protein dynamics
-
Case, D. A. Normal mode analysis of protein dynamics. Curr. Opin. Struct. Biol. 1994, 4, 285-290. (Pubitemid 24116915)
-
(1994)
Current Opinion in Structural Biology
, vol.4
, Issue.2
, pp. 285-290
-
-
Case, D.A.1
-
42
-
-
0029633186
-
AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structureal and energetic properties of molecules
-
Pearlman, D. A.; Case, D. A.; Caldwell, J. W.; Ross, W. S.; Cheatham, T. E., III; DeBolt, S.; Ferguson, D.; Seibel, G.; Kollman, P. AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structureal and energetic properties of molecules. Comput. Phys. Commun. 1995, 91, 1-41.
-
(1995)
Comput. Phys. Commun.
, vol.91
, pp. 1-41
-
-
Pearlman, D.A.1
Case, D.A.2
Caldwell, J.W.3
Ross, W.S.4
Cheatham III, T.E.5
Debolt, S.6
Ferguson, D.7
Seibel, G.8
Kollman, P.9
-
43
-
-
0001398008
-
How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
-
Wang, J.; Cieplak, P.; Kollman, P. A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 2000, 21 (12), 1049-1074.
-
(2000)
J. Comput. Chem.
, vol.21
, Issue.12
, pp. 1049-1074
-
-
Wang, J.1
Cieplak, P.2
Kollman, P.A.3
-
44
-
-
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 (9), 1157-1174.
-
(2004)
J. Comput. Chem.
, vol.25
, Issue.9
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
45
-
-
33748538349
-
Automatic atom type and bond type perception in molecular mechanical calculations
-
DOI 10.1016/j.jmgm.2005.12.005, PII S1093326305001737
-
Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. Automatic atom type and bond type perception in molecular mechanical calculations. J. Mol. Graphics Modell. 2006, 25 (2), 247-260. (Pubitemid 44363172)
-
(2006)
Journal of Molecular Graphics and Modelling
, vol.25
, Issue.2
, pp. 247-260
-
-
Wang, J.1
Wang, W.2
Kollman, P.A.3
Case, D.A.4
-
46
-
-
33646940952
-
Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes
-
Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 1977, 23, 327-341.
-
(1977)
J. Comput. Phys.
, vol.23
, pp. 327-341
-
-
Ryckaert, J.P.1
Ciccotti, G.2
Berendsen, H.J.C.3
-
47
-
-
1842479952
-
Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
-
DOI 10.1002/prot.20033
-
Onufriev, A.; Bashford, D.; Case, D. A. Exploring protein native states and large-scale conformational changes with a modified generalized born model. Proteins: Struct., Funct., Bioinf. 2004, 55 (2), 383-394. (Pubitemid 38437495)
-
(2004)
Proteins: Structure, Function and Genetics
, vol.55
, Issue.2
, pp. 383-394
-
-
Onufriev, A.1
Bashford, D.2
Case, D.A.3
-
48
-
-
23944463367
-
-
John Wiley & Sons Inc.: Hoboken, NJ
-
Thain, D.; Tannenbaum, T.; Livny, M. Condor and the Grid; John Wiley & Sons Inc.: Hoboken, NJ, 2003; p 1080.
-
(2003)
Condor and the Grid
, pp. 1080
-
-
Thain, D.1
Tannenbaum, T.2
Livny, M.3
-
49
-
-
0037763817
-
Comparative evaluation of 11 scoring functions for molecular docking
-
DOI 10.1021/jm0203783
-
Wang, R.; Lu, Y.; Wang, S. Comparative evaluation of 11 scoring functions for molecular docking. J. Med. Chem. 2003, 46 (12), 2287-2303. (Pubitemid 36637914)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.12
, pp. 2287-2303
-
-
Wang, R.1
Lu, Y.2
Wang, S.3
-
50
-
-
66249126516
-
-
St. Louis, MO. (accessed October 31, 2008)
-
Tripos Inc., St. Louis, MO. http://www.tripos.com/ (accessed October 31, 2008).
-
-
-
-
51
-
-
0008093096
-
Many faces of the correlation coefficient
-
Falk, R.; Well, A. D. Many faces of the correlation coefficient. J. Stat. Educ. 1997, 5 (3), 1-12.
-
(1997)
J. Stat. Educ.
, vol.5
, Issue.3
, pp. 1-12
-
-
Falk, R.1
Well, A.D.2
|