-
1
-
-
0029836953
-
Discovering high-affinity ligands for proteins: SAR by NMR
-
DOI 10.1126/science.274.5292.1531
-
Shuker SB, Hajduk PJ, Meadows RP, Fesik SW (1996) Discovering high-affinity ligands for proteins: SAR by NMR. Science 274(5292):1531-1534 (Pubitemid 26403929)
-
(1996)
Science
, vol.274
, Issue.5292
, pp. 1531-1534
-
-
Shuker, S.B.1
Hajduk, P.J.2
Meadows, R.P.3
Fesik, S.W.4
-
2
-
-
1942453243
-
Ligand efficiency: A useful metric for lead selection
-
DOI 10.1016/S1359-6446(04)03069-7, PII S1359644604030697
-
Hopkins AL, Groom CR, Alex A (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov Today 9(10): 430-431. doi:10.1016/S1359-6446(04) 03069-7 (Pubitemid 38510559)
-
(2004)
Drug Discovery Today
, vol.9
, Issue.10
, pp. 430-431
-
-
Hopkins, A.L.1
Groom, C.R.2
Alex, A.3
-
3
-
-
58549087807
-
Scaffoldbased discovery of indeglitazar, a PPAR pan-active anti-diabetic agent
-
doi:10.1073/pnas.0811325106
-
Artis DR, Lin JJ, Zhang C, Wang W, Mehra U, Perreault M, Erbe D, Krupka HI, England BP, Arnold J, Plotnikov AN, Marimuthu A, Nguyen H, Will S, Signaevsky M, Kral J, Cantwell J, Settachatgull C, Yan DS, Fong D, Oh A, Shi S, Womack P, Powell B, Habets G, West BL, Zhang KY, Milburn MV, Vlasuk GP, Hirth KP, Nolop K, Bollag G, Ibrahim PN, Tobin JF (2009) Scaffoldbased discovery of indeglitazar, a PPAR pan-active anti-diabetic agent. Proc Natl Acad Sci USA 106(1):262-267. doi:10.1073/pnas.0811325106
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.1
, pp. 262-267
-
-
Artis, D.R.1
Lin, J.J.2
Zhang, C.3
Wang, W.4
Mehra, U.5
Perreault, M.6
Erbe, D.7
Krupka, H.I.8
England, B.P.9
Arnold, J.10
Plotnikov, A.N.11
Marimuthu, A.12
Nguyen, H.13
Will, S.14
Signaevsky, M.15
Kral, J.16
Cantwell, J.17
Settachatgull, C.18
Yan, D.S.19
Fong, D.20
Oh, A.21
Shi, S.22
Womack, P.23
Powell, B.24
Habets, G.25
West, B.L.26
Zhang, K.Y.27
Milburn, M.V.28
Vlasuk, G.P.29
Hirth, K.P.30
Nolop, K.31
Bollag, G.32
Ibrahim, P.N.33
Tobin, J.F.34
more..
-
4
-
-
20844437061
-
A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design
-
DOI 10.1038/nbt1059
-
Card GL, Blasdel L, England BP, Zhang C, Suzuki Y, Gillette S, Fong D, Ibrahim PN, Artis DR, Bollag G, Milburn MV, Kim SH, Schlessinger J, Zhang KY (2005) A family of phosphodiesterase inhibitors discovered by cocrystallography and scaffold-based drug design. Nat Biotechnol 23(2):201-207. doi:10.1038/nbt1059 (Pubitemid 40255330)
-
(2005)
Nature Biotechnology
, vol.23
, Issue.2
, pp. 201-207
-
-
Card, G.L.1
Blasdel, L.2
England, B.P.3
Zhang, C.4
Suzuki, Y.5
Gillette, S.6
Fong, D.7
Ibrahim, P.N.8
Artis, D.R.9
Bollag, G.10
Milburn, M.V.11
Kim, S.-H.12
Schlessinger, J.13
Zhang, K.Y.J.14
-
5
-
-
42949149240
-
Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity
-
DOI 10.1073/pnas.0711741105
-
Tsai J, Lee JT, Wang W, Zhang J, Cho H, Mamo S, Bremer R, Gillette S, Kong J, Haass NK, Sproesser K, Li L, Smalley KS, Fong D, Zhu YL, Marimuthu A, Nguyen H, Lam B, Liu J, Cheung I, Rice J, Suzuki Y, Luu C, Settachatgul C, Shellooe R, Cantwell J, Kim SH, Schlessinger J, Zhang KY, West BL, Powell B, Habets G, Zhang C, Ibrahim PN, Hirth P, Artis DR, Herlyn M, Bollag G (2008) Discovery of a selective inhibitor of oncogenic B-Raf kinase with potent antimelanoma activity. Proc Natl Acad Sci USA 105(8):3041-3046. doi:10.1073/pnas.0711741105 (Pubitemid 351723664)
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, Issue.8
, pp. 3041-3046
-
-
Tsai, J.1
Lee, J.T.2
Wang, W.3
Zhang, J.4
Cho, H.5
Mamo, S.6
Bremer, R.7
Gillette, S.8
Kong, J.9
Haass, N.K.10
Sproesser, K.11
Li, L.12
Smalley, K.S.M.13
Fong, D.14
Zhu, Y.-L.15
Marimuthu, A.16
Nguyen, H.17
Lam, B.18
Liu, J.19
Cheung, I.20
Rice, J.21
Suzuki, Y.22
Luu, C.23
Settachatgul, C.24
Shellooe, R.25
Cantwell, J.26
Kim, S.-H.27
Schlessinger, J.28
Zhang, K.Y.J.29
West, B.L.30
Powell, B.31
Habets, G.32
Zhang, C.33
Ibrahim, P.N.34
Hirth, P.35
Artis, D.R.36
Herlyn, M.37
Bollag, G.38
more..
-
6
-
-
46849089254
-
Recent developments in fragment-based drug discovery
-
DOI 10.1021/jm8000373
-
Congreve M, Chessari G, Tisi D, Woodhead AJ (2008) Recent developments in fragment-based drug discovery. J Med Chem 51(13):3661-3680. doi:10.1021/jm8000373 (Pubitemid 351956496)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.13
, pp. 3661-3680
-
-
Congreve, M.1
Chessari, G.2
Tisi, D.3
Woodhead, A.J.4
-
7
-
-
33847381100
-
A decade of fragment-based drug design: Strategic advances and lessons learned
-
DOI 10.1038/nrd2220, PII NRD2220
-
Hajduk PJ, Greer J (2007) A decade of fragment-based drug design: strategic advances and lessons learned. Nat Rev Drug Discov 6(3):211-219. doi:10.1038/nrd2220 (Pubitemid 46344625)
-
(2007)
Nature Reviews Drug Discovery
, vol.6
, Issue.3
, pp. 211-219
-
-
Hajduk, P.J.1
Greer, J.2
-
8
-
-
67849113794
-
The rise of fragment-based drug discovery
-
doi:10.1038/nchem.217
-
Murray CW, Rees DC (2009) The rise of fragment-based drug discovery. Nat Chem 1(3):187-192. doi:10.1038/nchem.217
-
(2009)
Nat Chem
, vol.1
, Issue.3
, pp. 187-192
-
-
Murray, C.W.1
Rees, D.C.2
-
9
-
-
67649494337
-
Transforming fragments into candidates: Small becomes big in medicinal chemistry
-
doi:10.1016/j.drudis. 2009.03.009
-
de Kloe GE, Bailey D, Leurs R, de Esch IJ (2009) Transforming fragments into candidates: small becomes big in medicinal chemistry. Drug Discov Today 14(13-14):630-646. doi:10.1016/j.drudis. 2009.03.009
-
(2009)
Drug Discov Today
, vol.14
, Issue.13-14
, pp. 630-646
-
-
De Kloe, G.E.1
Bailey, D.2
Leurs, R.3
De Esch, I.J.4
-
10
-
-
77956513286
-
Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma
-
doi:10.1038/nature09454
-
Bollag G, Hirth P, Tsai J, Zhang J, Ibrahim PN, Cho H, Spevak W, Zhang C, Zhang Y, Habets G, Burton EA, Wong B, Tsang G, West BL, Powell B, Shellooe R, Marimuthu A, Nguyen H, Zhang KY, Artis DR, Schlessinger J, Su F, Higgins B, Iyer R, D'Andrea K, Koehler A, Stumm M, Lin PS, Lee RJ, Grippo J, Puzanov I, Kim KB, Ribas A, McArthur GA, Sosman JA, Chapman PB, Flaherty KT, Xu X, Nathanson KL, Nolop K (2010) Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature 467(7315):596-599. doi:10.1038/nature09454
-
(2010)
Nature
, vol.467
, Issue.7315
, pp. 596-599
-
-
Bollag, G.1
Hirth, P.2
Tsai, J.3
Zhang, J.4
Ibrahim, P.N.5
Cho, H.6
Spevak, W.7
Zhang, C.8
Zhang, Y.9
Habets, G.10
Burton, E.A.11
Wong, B.12
Tsang, G.13
West, B.L.14
Powell, B.15
Shellooe, R.16
Marimuthu, A.17
Nguyen, H.18
Zhang, K.Y.19
Artis, D.R.20
Schlessinger, J.21
Su, F.22
Higgins, B.23
Iyer, R.24
D'Andrea, K.25
Koehler, A.26
Stumm, M.27
Lin, P.S.28
Lee, R.J.29
Grippo, J.30
Puzanov, I.31
Kim, K.B.32
Ribas, A.33
McArthur, G.A.34
Sosman, J.A.35
Chapman, P.B.36
Flaherty, K.T.37
Xu, X.38
Nathanson, K.L.39
Nolop, K.40
more..
-
11
-
-
36248932680
-
Practical aspects of NMR-based fragment discovery
-
DOI 10.2174/156802607782341055
-
Zartler ER, Mo H (2007) Practical aspects of NMR-based fragment discovery. Curr Top Med Chem 7(16):1592-1599 (Pubitemid 350131016)
-
(2007)
Current Topics in Medicinal Chemistry
, vol.7
, Issue.16
, pp. 1592-1599
-
-
Zartler, E.R.1
Mo, H.2
-
12
-
-
12344318177
-
Fragment-based lead discovery using X-ray crystallography
-
DOI 10.1021/jm0495778
-
Hartshorn MJ, Murray CW, Cleasby A, Frederickson M, Tickle IJ, Jhoti H (2005) Fragment-based lead discovery using X-ray crystallography. J Med Chem 48(2):403-413. doi:10.1021/jm0495778 (Pubitemid 40139783)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.2
, pp. 403-413
-
-
Hartshorn, M.J.1
Murray, C.W.2
Cleasby, A.3
Frederickson, M.4
Tickle, I.J.5
Jhoti, H.6
-
13
-
-
36249028775
-
SPR-based fragment screening: Advantages and applications
-
DOI 10.2174/156802607782341073
-
Neumann T, Junker HD, Schmidt K, Sekul R (2007) SPR-based fragment screening: advantages and applications. Curr Top Med Chem 7(16):1630-1642 (Pubitemid 350131018)
-
(2007)
Current Topics in Medicinal Chemistry
, vol.7
, Issue.16
, pp. 1630-1642
-
-
Neumann, T.1
Junker, H.-D.2
Schmidt, K.3
Sekul, R.4
-
14
-
-
70349768241
-
Docking and chemoinformatic screens for new ligands and targets
-
doi:10.1016/j.copbio.2009.08.003
-
Kolb P, Ferreira RS, Irwin JJ, Shoichet BK (2009) Docking and chemoinformatic screens for new ligands and targets. Curr Opin Biotechnol 20(4):429-436. doi:10.1016/j.copbio.2009.08.003
-
(2009)
Curr Opin Biotechnol
, vol.20
, Issue.4
, pp. 429-436
-
-
Kolb, P.1
Ferreira, R.S.2
Irwin, J.J.3
Shoichet, B.K.4
-
15
-
-
33947612966
-
Application of fragment screening by X-ray crystallography to β-secretase
-
DOI 10.1021/jm0611962
-
Murray CW, Callaghan O, Chessari G, Cleasby A, Congreve M, Frederickson M, Hartshorn MJ, McMenamin R, Patel S, Wallis N (2007) Application of fragment screening by X-ray crystallography to beta-secretase. J Med Chem 50(6):1116-1123. doi:10.1021/jm0611962 (Pubitemid 46496312)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.6
, pp. 1116-1123
-
-
Murray, C.W.1
Callaghan, O.2
Chessari, G.3
Cleasby, A.4
Congreve, M.5
Frederickson, M.6
Hartshorn, M.J.7
McMenamin, R.8
Patel, S.9
Wallis, N.10
-
16
-
-
56749182336
-
Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors
-
doi:10.1021/jm8006992
-
Huang JW, Zhang Z, Wu B, Cellitti JF, Zhang X, Dahl R, Shiau CW, Welsh K, Emdadi A, Stebbins JL, Reed JC, Pellecchia M (2008) Fragment-based design of small molecule X-linked inhibitor of apoptosis protein inhibitors. J Med Chem 51(22): 7111-7118. doi:10.1021/jm8006992
-
(2008)
J Med Chem
, vol.51
, Issue.22
, pp. 7111-7118
-
-
Huang, J.W.1
Zhang, Z.2
Wu, B.3
Cellitti, J.F.4
Zhang, X.5
Dahl, R.6
Shiau, C.W.7
Welsh, K.8
Emdadi, A.9
Stebbins, J.L.10
Reed, J.C.11
Pellecchia, M.12
-
17
-
-
65349195698
-
Molecular docking and ligand specificity in fragment-based inhibitor discovery
-
doi:10.1038/nchembio.155
-
Chen Y, Shoichet BK (2009) Molecular docking and ligand specificity in fragment-based inhibitor discovery. Nat Chem Biol 5(5):358-364. doi:10.1038/nchembio.155
-
(2009)
Nat Chem Biol
, vol.5
, Issue.5
, pp. 358-364
-
-
Chen, Y.1
Shoichet, B.K.2
-
18
-
-
66149158600
-
Docking for fragment inhibitors of AmpC beta-lactamase
-
doi:10.1073/pnas.0813029106
-
Teotico DG, Babaoglu K, Rocklin GJ, Ferreira RS, Giannetti AM, Shoichet BK (2009) Docking for fragment inhibitors of AmpC beta-lactamase. Proc Natl Acad Sci USA 106(18): 7455-7460. doi:10.1073/pnas.0813029106
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, Issue.18
, pp. 7455-7460
-
-
Teotico, D.G.1
Babaoglu, K.2
Rocklin, G.J.3
Ferreira, R.S.4
Giannetti, A.M.5
Shoichet, B.K.6
-
20
-
-
33751076241
-
Deconstructing fragment-based inhibitor discovery
-
DOI 10.1038/nchembio831, PII NCHEMBIO831
-
Babaoglu K, Shoichet BK (2006) Deconstructing fragment-based inhibitor discovery. Nat Chem Biol 2(12):720-723. doi:10.1038/nchembio831 (Pubitemid 44764214)
-
(2006)
Nature Chemical Biology
, vol.2
, Issue.12
, pp. 720-723
-
-
Babaoglu, K.1
Shoichet, B.K.2
-
21
-
-
45749139232
-
Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: Evaluation on kinase inhibitor cross docking
-
DOI 10.1021/jm800071v
-
May A, Zacharias M (2008) Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking. J Med Chem 51(12): 3499-3506. doi:10.1021/jm800071v (Pubitemid 351875006)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.12
, pp. 3499-3506
-
-
May, A.1
Zacharias, M.2
-
22
-
-
33750056673
-
ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility
-
DOI 10.1002/prot.21086
-
Meiler J, Baker D (2006) ROSETTALIGAND: protein-small molecule docking with full side-chain flexibility. Proteins 65(3):538-548. doi:10.1002/prot.21086 (Pubitemid 44583205)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.3
, pp. 538-548
-
-
Meiler, J.1
Baker, D.2
-
23
-
-
37349085453
-
A flexible approach to induced fit docking
-
DOI 10.1021/jm070593p
-
Nabuurs SB, Wagener M, de Vlieg J (2007) A flexible approach to induced fit docking. J Med Chem 50(26):6507-6518. doi:10.1021/jm070593p (Pubitemid 350309091)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.26
, pp. 6507-6518
-
-
Nabuurs, S.B.1
Wagener, M.2
De Vlieg, J.3
-
24
-
-
0034996721
-
Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking
-
DOI 10.1016/S1074-5521(01)00023-0, PII S1074552101000230
-
Anderson AC, O'Neil RH, Surti TS, Stroud RM (2001) Approaches to solving the rigid receptor problem by identifying a minimal set of flexible residues during ligand docking. Chem Biol 8(5):445-457 (Pubitemid 32455899)
-
(2001)
Chemistry and Biology
, vol.8
, Issue.5
, pp. 445-457
-
-
Anderson, A.C.1
O'Neil, R.H.2
Surti, T.S.3
Stroud, R.M.4
-
25
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
doi:10.1016/j.sbi.2008.01.004
-
Totrov M, Abagyan R (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr Opin Struct Biol 18(2):178-184. doi:10.1016/j.sbi.2008.01.004
-
(2008)
Curr Opin Struct Biol
, vol.18
, Issue.2
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
26
-
-
58149094776
-
RosettaLigand docking with full ligand and receptor flexibility
-
doi:10.1016/j.jmb.2008.11.010
-
Davis IW, Baker D (2009) RosettaLigand docking with full ligand and receptor flexibility. J Mol Biol 385(2):381-392. doi: 10.1016/j.jmb.2008.11.010
-
(2009)
J Mol Biol
, vol.385
, Issue.2
, pp. 381-392
-
-
Davis, I.W.1
Baker, D.2
-
27
-
-
69249127027
-
Blind docking of pharmaceutically relevant compounds using RosettaLigand
-
doi:10.1002/pro.192
-
Davis IW, Raha K, Head MS, Baker D (2009) Blind docking of pharmaceutically relevant compounds using RosettaLigand. Protein Sci 18(9):1998-2002. doi:10.1002/pro.192
-
(2009)
Protein Sci
, vol.18
, Issue.9
, pp. 1998-2002
-
-
Davis, I.W.1
Raha, K.2
Head, M.S.3
Baker, D.4
-
28
-
-
67650997041
-
Virtual fragment screening: An exploration of various docking and scoring protocols for fragments using Glide
-
doi:10.1007/s10822-009-9281-4
-
Kawatkar S, Wang H, Czerminski R, Joseph-McCarthy D (2009) Virtual fragment screening: an exploration of various docking and scoring protocols for fragments using Glide. J Comput Aided Mol Des 23:527-539. doi:10.1007/s10822- 009-9281-4
-
(2009)
J Comput Aided Mol Des
, vol.23
, pp. 527-539
-
-
Kawatkar, S.1
Wang, H.2
Czerminski, R.3
Joseph-McCarthy, D.4
-
29
-
-
77954036921
-
Virtual fragment docking by Glide: A validation study on 190 protein-fragment complexes
-
doi:10.1021/ci1000407
-
Sandor M, Kiss R, Keseru GM (2010) Virtual fragment docking by Glide: a validation study on 190 protein-fragment complexes. J Chem Inf Model 50(6):1165-1172. doi:10.1021/ci1000407
-
(2010)
J Chem Inf Model
, vol.50
, Issue.6
, pp. 1165-1172
-
-
Sandor, M.1
Kiss, R.2
Keseru, G.M.3
-
31
-
-
84872612809
-
-
Santa Fe, NM, USA
-
OpenEye Scientific Software, Inc., Santa Fe, NM, USA. www.eyesopen.com
-
-
-
-
32
-
-
84863087869
-
High throughput fragment screeningTrypsin
-
this issue
-
Peat TS, Newman J (2012) High throughput fragment screeningTrypsin. J Comput Aided Mol Des, this issue
-
(2012)
J Comput Aided Mol Des
-
-
Peat, T.S.1
Newman, J.2
-
33
-
-
71949100268
-
Practical aspects of the SAMPL challenge: Providing an extensive experimental data set for the modeling community
-
doi:10.1177/108705710934 8220
-
Newman J, Fazio VJ, Caradoc-Davies TT, Branson K, Peat TS (2009) Practical aspects of the SAMPL challenge: providing an extensive experimental data set for the modeling community. J Biomol Screen 14(10):1245-1250. doi:10.1177/108705710934 8220
-
(2009)
J Biomol Screen
, vol.14
, Issue.10
, pp. 1245-1250
-
-
Newman, J.1
Fazio, V.J.2
Caradoc-Davies, T.T.3
Branson, K.4
Peat, T.S.5
-
34
-
-
0033954256
-
The protein data bank
-
Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235-242 (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, 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
-
35
-
-
0141726877
-
A 'Rule of Three' for fragment-based lead discovery?
-
DOI 10.1016/S1359-6446(03)02831-9, PII S1359644603028319
-
Congreve M, Carr R, Murray C, Jhoti H (2003) A 'rule of three' for fragment-based lead discovery? Drug Discov Today 8(19):876-877 (Pubitemid 37194496)
-
(2003)
Drug Discovery Today
, vol.8
, Issue.19
, pp. 876-877
-
-
Congreve, M.1
Carr, R.2
Murray, C.3
Jhoti, H.4
-
37
-
-
65249157397
-
Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
-
doi:10.1002/prot.22234
-
Labute P (2009) Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures. Proteins 75(1):187-205. doi:10.1002/prot.22234
-
(2009)
Proteins
, vol.75
, Issue.1
, pp. 187-205
-
-
Labute, P.1
-
38
-
-
77952756998
-
LowModeMD - Implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops
-
doi:10.1021/ci900508k
-
Labute P (2010) LowModeMD - implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops. J Chem Inf Model 50(5):792-800. doi:10.1021/ci900508k
-
(2010)
J Chem Inf Model
, vol.50
, Issue.5
, pp. 792-800
-
-
Labute, P.1
-
39
-
-
5544242529
-
MMFF VI. MMFF94s option for energy minimization studies
-
Halgren TA (1999) MMFF VI. MMFF94s option for energy minimization studies. J Comput Chem 20(7):720-729. doi:10.1002/(sici)1096-987x(199905)20:7\ 720::aid-jcc7[3.0.co;2-x (Pubitemid 129652635)
-
(1999)
Journal of Computational Chemistry
, vol.20
, Issue.7
, pp. 720-729
-
-
Halgren, T.A.1
-
40
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
DOI 10.1021/ci600342e
-
Marcou G, Rognan D (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J Chem Inf Model 47(1):195-207. doi:10.1021/ci600342e (Pubitemid 46237537)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.1
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
41
-
-
37049239596
-
A computer program for classifying plants
-
doi:10.1126/science.132.3434.1115
-
Rogers DJ, Tanimoto TT (1960) A computer program for classifying plants. Science 132(3434):1115-1118. doi:10.1126/science.132.3434.1115
-
(1960)
Science
, vol.132
, Issue.3434
, pp. 1115-1118
-
-
Rogers, D.J.1
Tanimoto, T.T.2
-
42
-
-
2542530042
-
The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
-
DOI 10.1021/jm030580l
-
Wang R, Fang X, Lu Y, Wang S (2004) The PDBbind database: collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J Med Chem 47(12):2977-2980. doi:10.1021/jm030580l (Pubitemid 38702694)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.12
, pp. 2977-2980
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Wang, S.4
-
43
-
-
20444422149
-
The PDBbind database: Methodologies and updates
-
DOI 10.1021/jm048957q
-
Wang R, Fang X, Lu Y, Yang CY, Wang S (2005) The PDBbind database: methodologies and updates. J Med Chem 48(12): 4111-4119. doi:10.1021/jm048957q (Pubitemid 40800619)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.12
, pp. 4111-4119
-
-
Wang, R.1
Fang, X.2
Lu, Y.3
Yang, C.-Y.4
Wang, S.5
-
44
-
-
79952709519
-
Proc: An open-source package for R and S? To analyze and compare ROC curves
-
doi:10.1186/1471-2105-12-77
-
Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Muller M (2011) pROC: an open-source package for R and S? to analyze and compare ROC curves. BMC Bioinforma 12:77. doi: 10.1186/1471-2105-12-77
-
(2011)
BMC Bioinforma
, vol.12
, pp. 77
-
-
Robin, X.1
Turck, N.2
Hainard, A.3
Tiberti, N.4
Lisacek, F.5
Sanchez, J.C.6
Muller, M.7
-
45
-
-
5344244656
-
-
R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0
-
R Development Core Team (2008) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. http://www.R-project.org
-
(2008)
R: A Language and Environment for Statistical Computing
-
-
-
46
-
-
79956201474
-
Systematic exploitation of multiple receptor conformations for virtual ligand screening
-
doi:10.1371/journal.pone.0018845
-
Bottegoni G, Rocchia W, Rueda M, Abagyan R, Cavalli A (2011) Systematic exploitation of multiple receptor conformations for virtual ligand screening. PLoS One 6(5):e18845. doi:10.1371/journal.pone.0018845
-
(2011)
PLoS One
, vol.6
, Issue.5
-
-
Bottegoni, G.1
Rocchia, W.2
Rueda, M.3
Abagyan, R.4
Cavalli, A.5
-
47
-
-
77951992987
-
Ensemble docking into multiple crystallographically derived protein structures: An evaluation based on the statistical analysis of enrichments
-
doi:10.1021/ci900407c
-
Craig IR, Essex JW, Spiegel K (2010) Ensemble docking into multiple crystallographically derived protein structures: an evaluation based on the statistical analysis of enrichments. J Chem Inf Model 50(4):511-524. doi:10.1021/ci900407c
-
(2010)
J Chem Inf Model
, vol.50
, Issue.4
, pp. 511-524
-
-
Craig, I.R.1
Essex, J.W.2
Spiegel, K.3
-
48
-
-
33846000313
-
Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
-
DOI 10.1002/prot.21214
-
Huang SY, Zou X (2007) Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins 66(2):399-421. doi:10.1002/prot.21214 (Pubitemid 46053470)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.2
, pp. 399-421
-
-
Huang, S.-Y.1
Zou, X.2
-
49
-
-
50249130736
-
Improving database enrichment through ensemble docking
-
doi:10.1007/s10822-008-9182-y
-
Rao S, Sanschagrin PC, Greenwood JR, Repasky MP, Sherman W, Farid R (2008) Improving database enrichment through ensemble docking. J Comput Aided Mol Des 22(9):621-627. doi: 10.1007/s10822-008-9182-y
-
(2008)
J Comput Aided Mol Des
, vol.22
, Issue.9
, pp. 621-627
-
-
Rao, S.1
Sanschagrin, P.C.2
Greenwood, J.R.3
Repasky, M.P.4
Sherman, W.5
Farid, R.6
-
50
-
-
75749093371
-
Recipes for the selection of experimental protein conformations for virtual screening
-
doi:10.1021/ci9003943
-
Rueda M, Bottegoni G, Abagyan R (2010) Recipes for the selection of experimental protein conformations for virtual screening. J Chem Inf Model 50(1):186-193. doi:10.1021/ci9003943
-
(2010)
J Chem Inf Model
, vol.50
, Issue.1
, pp. 186-193
-
-
Rueda, M.1
Bottegoni, G.2
Abagyan, R.3
-
51
-
-
57349156167
-
In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
-
DOI 10.1002/prot.22081
-
Bolstad ES, Anderson AC (2008) In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking. Proteins 73(3):566-580. doi:10.1002/prot.22081 (Pubitemid 352788641)
-
(2008)
Proteins: Structure, Function and Genetics
, vol.73
, Issue.3
, pp. 566-580
-
-
Bolstad, E.S.D.1
Anderson, A.C.2
-
52
-
-
79251524915
-
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
-
doi:10.1002/jcc.21643
-
Plewczynski D, Lazniewski M, Augustyniak R, Ginalski K (2011) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J Comput Chem 32(4):742-755. doi:10.1002/jcc.21643
-
(2011)
J Comput Chem
, vol.32
, Issue.4
, pp. 742-755
-
-
Plewczynski, D.1
Lazniewski, M.2
Augustyniak, R.3
Ginalski, K.4
-
53
-
-
0036890178
-
Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation
-
DOI 10.1002/jcc.10128
-
Jakalian A, Jack DB, Bayly CI (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem 23(16):1623-1641. doi: 10.1002/jcc.10128 (Pubitemid 35330860)
-
(2002)
Journal of Computational Chemistry
, vol.23
, Issue.16
, pp. 1623-1641
-
-
Jakalian, A.1
Jack, D.B.2
Bayly, C.I.3
-
54
-
-
49149147973
-
Iterative partial equalization of orbital electronegativity - A rapid access to atomic charges
-
Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electronegativity - a rapid access to atomic charges. Tetrahedron 36(22):3219-3228
-
(1980)
Tetrahedron
, vol.36
, Issue.22
, pp. 3219-3228
-
-
Gasteiger, J.1
Marsili, M.2
-
55
-
-
0025135112
-
Automated docking of substrates to proteins by simulated annealing
-
Goodsell DS, Olson AJ (1990) Automated docking of substrates to proteins by simulated annealing. Proteins 8(3):195-202. doi: 10.1002/prot.340080302 (Pubitemid 20363304)
-
(1990)
Proteins: Structure, Function and Genetics
, vol.8
, Issue.3
, pp. 195-202
-
-
Goodsell, D.S.1
Olson, A.J.2
-
56
-
-
0030203710
-
Distributed automated docking of flexible ligands to proteins: Parallel applications of AutoDock 2.4
-
Morris GM, Goodsell DS, Huey R, Olson AJ (1996) Distributed automated docking of flexible ligands to proteins: parallel applications of AutoDock 2.4. J Comput Aided Mol Des 10(4):293-304 (Pubitemid 126712824)
-
(1996)
Journal of Computer-Aided Molecular Design
, vol.10
, Issue.4
, pp. 293-304
-
-
Morris, G.M.1
Goodsell, D.S.2
Huey, R.3
Olson, A.J.4
-
57
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, Belew RK, Olson AJ (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14):1639-1662. doi:10.1002/(sici)1096-987x (19981115)19:14\1639:aid-jcc10[3.0.co;2-b (Pubitemid 128590223)
-
(1998)
Journal of Computational Chemistry
, vol.19
, Issue.14
, 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
-
58
-
-
80054943835
-
DSX: A knowledge-based scoring function for the assessment of protein-ligand complexes
-
doi:10.1021/ci200274q
-
Neudert G, Klebe G (2011) DSX: a knowledge-based scoring function for the assessment of protein-ligand complexes. J Chem Inf Model. doi:10.1021/ci200274q
-
(2011)
J Chem Inf Model
-
-
Neudert, G.1
Klebe, G.2
-
59
-
-
0034645763
-
Knowledge-based scoring function to predict protein-ligand interactions
-
DOI 10.1006/jmbi.1999.3371
-
Gohlke H, Hendlich M, Klebe G (2000) Knowledge-based scoring function to predict protein-ligand interactions. J Mol Biol 295(2):337-356 (Pubitemid 30045364)
-
(2000)
Journal of Molecular Biology
, vol.295
, Issue.2
, pp. 337-356
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
60
-
-
77950979053
-
Trypsin-ligand binding free energy calculation with AMOEBA
-
doi:10.1109/IEMBS.2009. 5335108
-
Shi Y, Jiao D, Schnieders MJ, Ren P (2009) Trypsin-ligand binding free energy calculation with AMOEBA. Conf Proc IEEE Eng Med Biol Soc 2009:2328-2331. doi:10.1109/IEMBS.2009. 5335108
-
(2009)
Conf Proc IEEE Eng Med Biol Soc
, vol.2009
, pp. 2328-2331
-
-
Shi, Y.1
Jiao, D.2
Schnieders, M.J.3
Ren, P.4
|