-
1
-
-
0035895505
-
The sequence of the human genome
-
Venter JC et al (2001) The sequence of the human genome. Science 291(5507): 1304-1351
-
(2001)
Science
, vol.291
, Issue.5507
, pp. 1304-1351
-
-
Venter, J.C.1
-
2
-
-
77649234756
-
How to improve R&D productivity: The pharmaceutical industry's grand challenge
-
Paul SM et al (2010) How to improve R&D productivity: the pharmaceutical industry's grand challenge. Nat Rev Drug Discov 9(3): 203-214
-
(2010)
Nat Rev Drug Discov
, vol.9
, Issue.3
, pp. 203-214
-
-
Paul, S.M.1
-
3
-
-
4344645978
-
Can the pharmaceutical industry reduce attrition rates?
-
Kola I, Landis J (2004) Can the pharmaceutical industry reduce attrition rates? Nat Rev Drug Discov 3(8): 711-715 (Pubitemid 39173511)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.8
, pp. 711-715
-
-
Kola, I.1
Landis, J.2
-
4
-
-
33750579770
-
Drug discovery in jeopardy
-
DOI 10.1172/JCI29999
-
Cuatrecasas P (2006) Drug discovery in jeopardy. J Clin Invest 116(11): 2837-2842 (Pubitemid 44684465)
-
(2006)
Journal of Clinical Investigation
, vol.116
, Issue.11
, pp. 2837-2842
-
-
Cuatrecasas, P.1
-
5
-
-
0035161543
-
Genomes OnLine Database (GOLD): A monitor of genome projects world-wide
-
Bernal A, Ear U, Kyrpides N (2001) Genomes OnLine Database (GOLD): a monitor of genome projects world-wide. Nucleic Acids Res 29(1): 126-127 (Pubitemid 32054425)
-
(2001)
Nucleic Acids Research
, vol.29
, Issue.1
, pp. 126-127
-
-
Bernal, A.1
Ear, U.2
Kyrpides, N.3
-
6
-
-
0037249497
-
The PEDANT genome database
-
DOI 10.1093/nar/gkg005
-
Frishman D et al (2003) The PEDANT genome database. Nucleic Acids Res 31(1): 207-211 (Pubitemid 36150366)
-
(2003)
Nucleic Acids Research
, vol.31
, Issue.1
, pp. 207-211
-
-
Frishman, D.1
Mokrejs, M.2
Kosykh, D.3
Kastenmuller, G.4
Kolesov, G.5
Zubrzycki, I.6
Gruber, C.7
Geier, B.8
Kaps, A.9
Albermann, K.10
Volz, A.11
Wagner, C.12
Fellenberg, M.13
Heumann, K.14
Mewes, H.-W.15
-
7
-
-
33646591220
-
The difficult road from sequence to function
-
DOI 10.1128/JB.188.10.3431-3432.2006
-
White RH (2006) The difficult road from sequence to function. J Bacteriol 188(10): 3431-3432 (Pubitemid 43726205)
-
(2006)
Journal of Bacteriology
, vol.188
, Issue.10
, pp. 3431-3432
-
-
White, R.H.1
-
8
-
-
33746664765
-
Can sequence determine function?
-
Gerlt JA, Babbitt PC (2000) Can sequence determine function? Genome Biol 1(5): REVIEWS0005
-
(2000)
Genome Biol
, vol.1
, Issue.5
-
-
Gerlt, J.A.1
Babbitt, P.C.2
-
9
-
-
0030756360
-
Reactive compounds and in vitro false positives in HTS
-
DOI 10.1016/S1359-6446(97)01083-0, PII S1359644697010830
-
Rishton GM (1997) Reactive compounds and in vitro false positives in HTS. Drug Discov Today 2(9): 382-384 (Pubitemid 27368216)
-
(1997)
Drug Discovery Today
, vol.2
, Issue.9
, pp. 382-384
-
-
Rishton, G.M.1
-
14
-
-
33645887230
-
Critical review of the role of HTS in drug discovery
-
Macarron R (2006) Critical review of the role of HTS in drug discovery. Drug Discov Today 11(7-8): 277-279
-
(2006)
Drug Discov Today
, vol.11
, Issue.7-8
, pp. 277-279
-
-
MacArron, R.1
-
15
-
-
70349392687
-
Advances in nuclear magnetic resonance for drug discovery
-
Powers R (2009) Advances in nuclear magnetic resonance for drug discovery. Expert Opin Drug Discov 4(10): 1077-1098
-
(2009)
Expert Opin Drug Discov
, vol.4
, Issue.10
, pp. 1077-1098
-
-
Powers, R.1
-
16
-
-
51249121331
-
Perspectives on NMR in drug discovery: A technique comes of age
-
Pellecchia M et al (2008) Perspectives on NMR in drug discovery: a technique comes of age. Nat Rev Drug Discov 7(9): 738-745
-
(2008)
Nat Rev Drug Discov
, vol.7
, Issue.9
, pp. 738-745
-
-
Pellecchia, M.1
-
17
-
-
0034212454
-
Applications of NMR in drug discovery
-
Roberts GCK (2000) Applications of NMR in drug discovery. Drug Discov Today 5(6): 230-240
-
(2000)
Drug Discov Today
, vol.5
, Issue.6
, pp. 230-240
-
-
Gck, R.1
-
18
-
-
11844253252
-
ALARM NMR: A rapid and robust experimental method to detect reactive false positives in biochemical screens
-
DOI 10.1021/ja0455547
-
Huth JR et al (2004) ALARM NMR: a rapid and robust experimental method to detect reactive false positives in biochemical screens. J Am Chem Soc 127(1): 217-224 (Pubitemid 40094385)
-
(2005)
Journal of the American Chemical Society
, vol.127
, Issue.1
, pp. 217-224
-
-
Huth, J.R.1
Mendoza, R.2
Olejniczak, E.T.3
Johnson, R.W.4
Cothron, D.A.5
Liu, Y.6
Lerner, C.G.7
Chen, J.8
Hajduk, P.J.9
-
19
-
-
33747827255
-
NMR-based quality control approach for the identification of false positives and false negatives in high throughput screening
-
DOI 10.2174/157016306778108875
-
Dalvit C et al (2006) NMR-based quality control approach for the identification of false positives and false negatives in high throughput screening. Curr Drug Discov Technol 3(2): 115-124 (Pubitemid 44285197)
-
(2006)
Current Drug Discovery Technologies
, vol.3
, Issue.2
, pp. 115-124
-
-
Dalvit, C.1
Caronni, D.2
Mongelli, N.3
Veronesi, M.4
Vulpetti, A.5
-
20
-
-
46849122376
-
Fragment-based lead discovery by NMR
-
Schade M (2007) Fragment-based lead discovery by NMR. Front Drug Des Discov 3: 105-119
-
(2007)
Front Drug des Discov
, vol.3
, pp. 105-119
-
-
Schade, M.1
-
21
-
-
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
-
22
-
-
70350422335
-
NMR methods in fragment screening: Theory and a comparison with other biophysical techniques
-
Dalvit C (2009) NMR methods in fragment screening: theory and a comparison with other biophysical techniques. Drug Discov Today 14(21/22): 1051-1057
-
(2009)
Drug Discov Today
, vol.14
, Issue.21-22
, pp. 1051-1057
-
-
Dalvit, C.1
-
23
-
-
0027604421
-
NMR structure-based drug design
-
Fesik SW (1993) NMR structure-based drug design. J Biomol NMR 3(3): 261-269
-
(1993)
J Biomol NMR
, vol.3
, Issue.3
, pp. 261-269
-
-
Fesik, S.W.1
-
24
-
-
0002716826
-
Structure-based design of enzyme inhibitors and receptor ligands
-
Kubinyi H (1998) Structure-based design of enzyme inhibitors and receptor ligands. Curr Opin Drug Discov Devel 1(1): 4-15 (Pubitemid 128731837)
-
(1998)
Current Opinion in Drug Discovery and Development
, vol.1
, Issue.1
, pp. 4-15
-
-
Kubinyi, H.1
-
25
-
-
68949219758
-
Identification of urinary biomarkers useful for distinguishing a difference in mechanism of toxicity in rat model of cholestasis
-
Ishihara K et al (2009) Identification of urinary biomarkers useful for distinguishing a difference in mechanism of toxicity in rat model of cholestasis. Basic Clin Pharmacol Toxicol 105(3): 156-166
-
(2009)
Basic Clin Pharmacol Toxicol
, vol.105
, Issue.3
, pp. 156-166
-
-
Ishihara, K.1
-
26
-
-
39049195153
-
Nuclear magnetic resonance metabonomics: Methods for drug discovery and development
-
Ott K-H, Aranibar N (2007) Nuclear magnetic resonance metabonomics: methods for drug discovery and development. Methods Mol Biol 358: 247-271
-
(2007)
Methods Mol Biol
, vol.358
, pp. 247-271
-
-
Ott, K.-H.1
Aranibar, N.2
-
27
-
-
72249116728
-
NMR metabolomics and drug discovery
-
Powers R (2009) NMR metabolomics and drug discovery. Magn Reson Chem 47(S1): S2-S11
-
(2009)
Magn Reson Chem
, vol.47
, Issue.S1
-
-
Powers, R.1
-
28
-
-
39149084666
-
The application of FAST-NMR for the identification of novel drug discovery targets
-
Powers R, Mercier KA, Copeland JC (2008) The application of FAST-NMR for the identification of novel drug discovery targets. Drug Discov Today 13(3-4): 172-179
-
(2008)
Drug Discov Today
, vol.13
, Issue.3-4
, pp. 172-179
-
-
Powers, R.1
Mercier, K.A.2
Copeland, J.C.3
-
29
-
-
33845231983
-
FAST-NMR: Functional annotation screening technology using NMR spectroscopy
-
DOI 10.1021/ja0651759
-
Mercier KA et al (2006) FAST-NMR: functional annotation screening technology using NMR spectroscopy. J Am Chem Soc 128(47): 15292-15299 (Pubitemid 44853540)
-
(2006)
Journal of the American Chemical Society
, vol.128
, Issue.47
, pp. 15292-15299
-
-
Mercier, K.A.1
Baran, M.2
Ramanathan, V.3
Revesz, P.4
Xiao, R.5
Montelione, G.T.6
Powers, R.7
-
30
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: Methods and applications
-
DOI 10.1038/nrd1549
-
Kitchen DB et al (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov 3(11): 935-949 (Pubitemid 39529931)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.11
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
32
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren GL et al (2006) A critical assessment of docking programs and scoring functions. J Med Chem 49(20): 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
-
33
-
-
33847347192
-
Diverse, high-quality test set for the validation of protein-ligand docking performance
-
DOI 10.1021/jm061277y
-
Hartshorn MJ et al (2007) Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem 50(4): 726-741 (Pubitemid 46332985)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.4
, pp. 726-741
-
-
Hartshorn, M.J.1
Verdonk, M.L.2
Chessari, G.3
Brewerton, S.C.4
Mooij, W.T.M.5
Mortenson, P.N.6
Murray, C.W.7
-
35
-
-
67651002876
-
Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation
-
Loving K, Salam NK, Sherman W (2009) Energetic analysis of fragment docking and application to structure-based pharmacophore hypothesis generation. J Comput Aided Mol Des 23(8): 541-554
-
(2009)
J Comput Aided Mol des
, vol.23
, Issue.8
, pp. 541-554
-
-
Loving, K.1
Salam, N.K.2
Sherman, W.3
-
37
-
-
4944222323
-
Application of semiempirical quantum chemical methods as a scoring function in docking
-
DOI 10.1007/s00214-004-0589-9
-
Vasilyev V, Bliznyuk A (2004) Application of semiempirical quantum chemical methods as a scoring function in docking. Theor Chem Acc 112(4): 313-317 (Pubitemid 39329354)
-
(2004)
Theoretical Chemistry Accounts
, vol.112
, Issue.4
, pp. 313-317
-
-
Vasilyev, V.1
Bliznyuk, A.2
-
38
-
-
77958565592
-
Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening
-
Wei D et al (2010) Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening. J Chem Inf Model 50(10): 1855-1864
-
(2010)
J Chem Inf Model
, vol.50
, Issue.10
, pp. 1855-1864
-
-
Wei, D.1
-
39
-
-
67650236889
-
Scoring ligand similarity in structure-based virtual screening
-
Zavodszky MI et al (2009) Scoring ligand similarity in structure-based virtual screening. J Mol Recognit 22(4): 280-292
-
(2009)
J Mol Recognit
, vol.22
, Issue.4
, pp. 280-292
-
-
Zavodszky, M.I.1
-
40
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
Morris GM et al (2009) AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J Comput Chem 30(16): 2785-2791
-
(2009)
J Comput Chem
, vol.30
, Issue.16
, pp. 2785-2791
-
-
Morris, G.M.1
-
42
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
DOI 10.1006/jmbi.1996.0477
-
Rarey M et al (1996) A fast flexible docking method using an incremental construction algorithm. J Mol Biol 261(3): 470-489 (Pubitemid 26335901)
-
(1996)
Journal of Molecular Biology
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
43
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
DOI 10.1021/jm0306430
-
Friesner RA et al (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 (Pubitemid 38380917)
-
(2004)
Journal of Medicinal Chemistry
, 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.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
44
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
DOI 10.1021/ja026939x
-
Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein dockingapproach based on biochemical or biophysical information. J Am Chem Soc 125(7): 1731-1737 (Pubitemid 36232568)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.7
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.J.J.3
-
45
-
-
0027027467
-
LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
-
Bohm HJ (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J Comput Aided Mol Des 6(6): 593-606
-
(1992)
J Comput Aided Mol des
, vol.6
, Issue.6
, pp. 593-606
-
-
Bohm, H.J.1
-
46
-
-
0026813925
-
The computer program LUDI: A new method for the de novo design of enzyme inhibitors
-
Bohm HJ (1992) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J Comput Aided Mol Des 6(1): 61-78
-
(1992)
J Comput Aided Mol des
, vol.6
, Issue.1
, pp. 61-78
-
-
Bohm, H.J.1
-
47
-
-
79952110876
-
Virtual screening of compound libraries
-
Ligand-Macromolecular Interactions in Drug Discovery
-
Cerqueira NMFSA et al. (2010) Virtual screening of compound libraries. Methods Mol Biol 572: 57-70 (Ligand-Macromolecular Interactions in Drug Discovery)
-
(2010)
Methods Mol Biol
, vol.572
, pp. 57-70
-
-
Cerqueira, N.M.F.S.A.1
-
48
-
-
78650352933
-
Quo vadis, virtual screening? A comprehensive survey of prospective applications
-
Ripphausen P et al (2010) Quo vadis, virtual screening? A comprehensive survey of prospective applications. J Med Chem 53(24): 8461-8467
-
(2010)
J Med Chem
, vol.53
, Issue.24
, pp. 8461-8467
-
-
Ripphausen, P.1
-
49
-
-
77955767207
-
Virtual screening in drug design and development
-
Sousa SF et al (2010) Virtual screening in drug design and development. Comb Chem High Throughput Screen 13(5): 442-453
-
(2010)
Comb Chem High Throughput Screen
, vol.13
, Issue.5
, pp. 442-453
-
-
Sousa, S.F.1
-
50
-
-
33847207834
-
Molecular similarity analysis in virtual screening: Foundations, limitations and novel approaches
-
Eckert H, Bajorath J (2007) Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discov Today 12(5-6): 225-233
-
(2007)
Drug Discov Today
, vol.12
, Issue.5-6
, pp. 225-233
-
-
Eckert, H.1
Bajorath, J.2
-
51
-
-
77952387014
-
Limits of free energy computation for protein-ligand interactions
-
Merz KM Jr (2010) Limits of free energy computation for protein-ligand interactions. J Chem Theory Comput 6(5): 1769-1776
-
(2010)
J Chem Theory Comput
, vol.6
, Issue.5
, pp. 1769-1776
-
-
Merz Jr., K.M.1
-
52
-
-
37649005977
-
Shapelets: Possibilities and limitations of shape-based virtual screening
-
Proschak E et al (2007) Shapelets: possibilities and limitations of shape-based virtual screening. J Comput Chem 29(1): 108-114
-
(2007)
J Comput Chem
, vol.29
, Issue.1
, pp. 108-114
-
-
Proschak, E.1
-
54
-
-
4344711355
-
Theory and applications of NMR-based screening in pharmaceutical research
-
Lepre CA, Moore JM, Peng JW (2004) Theory and applications of NMR-based screening in pharmaceutical research. Chem Rev 104(8): 3641-3676
-
(2004)
Chem Rev
, vol.104
, Issue.8
, pp. 3641-3676
-
-
Lepre, C.A.1
Moore, J.M.2
Peng, J.W.3
-
55
-
-
22144493017
-
Determining the optimal size of small molecule mixtures for high throughput NMR screening
-
DOI 10.1007/s10858-005-0948-4
-
Mercier KA, Powers R (2005) Determining the optimal size of small molecule mixtures for high throughput NMR screening. J Biomol NMR 31(3): 243-258 (Pubitemid 41348928)
-
(2005)
Journal of Biomolecular NMR
, vol.31
, Issue.3
, pp. 243-258
-
-
Mercier, K.A.1
Powers, R.2
-
56
-
-
0031576702
-
One-dimensional relaxation- and diffusion-edited NMR methods for screening compounds that bind to macromolecules
-
DOI 10.1021/ja9715962
-
Hajduk PJ, Olejniczak ET, Fesik SW (1997) One-dimensional relaxation- and diffusionedited NMR methods for screening compounds that bind to macromolecules. J Am Chem Soc 119: 12257-12261 (Pubitemid 28078713)
-
(1997)
Journal of the American Chemical Society
, vol.119
, Issue.50
, pp. 12257-12261
-
-
Hajduk, P.J.1
Olejniczak, E.T.2
Fesik, S.W.3
-
57
-
-
0033553844
-
Characterization of ligand binding by saturation transfer difference NMR spectroscopy
-
DOI 10.1002/(SICI)1521-3773(19990614)38: 12<1784::AID-ANIE1784>3.0. CO;2-Q
-
Mayer M, Meyer B (1999) Characterization of ligand binding by saturation transfer difference NMR spectroscopy. Angew Chem Int Ed 38(12): 1784-1788 (Pubitemid 29290947)
-
(1999)
Angewandte Chemie - International Edition
, vol.38
, Issue.12
, pp. 1784-1788
-
-
Mayer, M.1
Meyer, B.2
-
58
-
-
0033789206
-
Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water
-
Dalvit C et al (2000) Identification of compounds with binding affinity to proteins via magnetization transfer from bulk water. J Biomol NMR 18(1): 65-68
-
(2000)
J Biomol NMR
, vol.18
, Issue.1
, pp. 65-68
-
-
Dalvit, C.1
-
60
-
-
14144250362
-
TINS, target immobilized NMR screening: An efficient and sensitive method for ligand discovery
-
DOI 10.1016/j.chembiol.2004.12.004
-
Vanwetswinkel S et al (2005) TINS, target immobilized NMR screening: an efficient and sensitive method for ligand discovery. Chem Biol 12(2): 207-216 (Pubitemid 40281328)
-
(2005)
Chemistry and Biology
, vol.12
, Issue.2
, pp. 207-216
-
-
Vanwetswinkel, S.1
Heetebrij, R.J.2
Van Duynhoven, J.3
Hollander, J.G.4
Filippov, D.V.5
Hajduk, P.J.6
Siegal, G.7
-
62
-
-
0038207989
-
Fluorine-NMR experiments for high-throughput screening: Theoretical aspects, practical considerations, and range of applicability
-
DOI 10.1021/ja034646d
-
Dalvit C et al (2003) Fluorine-NMR experiments for high-throughput screening: theoretical aspects, practical considerations, and range of applicability. J Am Chem Soc 125(25): 7696-7703 (Pubitemid 36750291)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.25
, pp. 7696-7703
-
-
Dalvit, C.1
Fagerness, P.E.2
Hadden, D.T.A.3
Sarver, R.W.4
Stockman, B.J.5
-
64
-
-
0344012137
-
A general NMR method for rapid, efficient, and reliable biochemical screening
-
DOI 10.1021/ja038128e
-
Dalvit C et al (2003) A general NMR method for rapid, efficient, and reliable biochemical screening. J Am Chem Soc 125(47): 14620-14625 (Pubitemid 37452398)
-
(2003)
Journal of the American Chemical Society
, vol.125
, Issue.47
, pp. 14620-14625
-
-
Dalvit, C.1
Ardini, E.2
Flocco, M.3
Fogliatto, G.P.4
Mongelli, N.5
Veronesit, M.6
-
66
-
-
0031498272
-
Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion: Part 1. Basic theory
-
Price SW (1997) Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion: part 1. Basic theory. Concepts Magn Reson 9: 299-336
-
(1997)
Concepts Magn Reson
, vol.9
, pp. 299-336
-
-
Price, S.W.1
-
67
-
-
0032352438
-
Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion: Part II. Experimental aspects
-
Price SW (1998) Pulsed-field gradient nuclear magnetic resonance as a tool for studying translational diffusion: part II. Experimental aspects. Concepts Magn Reson 10: 197-237
-
(1998)
Concepts Magn Reson
, vol.10
, pp. 197-237
-
-
Price, S.W.1
-
68
-
-
57549085603
-
Estimating protein-ligand binding affinity using high-throughput screening by NMR
-
Shortridge MD et al (2008) Estimating protein-ligand binding affinity using high-throughput screening by NMR. J Comb Chem 10(6): 948-958
-
(2008)
J Comb Chem
, vol.10
, Issue.6
, pp. 948-958
-
-
Shortridge, M.D.1
-
69
-
-
58149396562
-
Saturation transfer difference nuclear magnetic resonance study on the specific binding of ligand to protein
-
Ji Z, Yao Z, LiuM(2009) Saturation transfer difference nuclear magnetic resonance study on the specific binding of ligand to protein. Anal Biochem 385(2): 380-382
-
(2009)
Anal Biochem
, vol.385
, Issue.2
, pp. 380-382
-
-
Ji, Z.1
Yao, Z.2
Liu, M.3
-
70
-
-
0000179899
-
A gradient 13C NOESY-HSQC experiment for recording NOESY spectra of 13C-labeled proteins dissolved in H2O
-
Muhandiram DR et al (1993) A gradient 13C NOESY-HSQC experiment for recording NOESY spectra of 13C-labeled proteins dissolved in H2O. J Magn Reson B 102(3): 317-321
-
(1993)
J Magn Reson B
, vol.102
, Issue.3
, pp. 317-321
-
-
Muhandiram, D.R.1
-
71
-
-
0001350902
-
Gradient-tailored water suppression for proton-nitrogen-15 HSQC experiments optimized to retain full sensitivity
-
Sklenar V et al (1993) Gradient-tailored water suppression for proton-nitrogen-15 HSQC experiments optimized to retain full sensitivity. J Magn Reson A 102(2): 241-245
-
(1993)
J Magn Reson A
, vol.102
, Issue.2
, pp. 241-245
-
-
Sklenar, V.1
-
72
-
-
0030612833
-
Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution
-
Per VK et al (1997) Attenuated T2 relaxation by mutual cancellation of dipole-dipole coupling and chemical shift anisotropy indicates an avenue to NMR structures of very large biological macromolecules in solution. Proc Natl Acad Sci USA 94(23): 12366-12371
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, Issue.23
, pp. 12366-12371
-
-
Per, V.K.1
-
73
-
-
0029836953
-
Discovering high-affinity ligands for proteins: SAR by NMR
-
DOI 10.1126/science.274.5292.1531
-
Shuker SB et al (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
-
74
-
-
35948942349
-
NMR methods for the determination of protein-ligand dissociation constants
-
DOI 10.1016/j.pnmrs.2007.04.001, PII S0079656507000258
-
Fielding L (2007) NMR methods for the determination of protein-ligand dissociation constants. Prog Nucl Magn Reson Spectrosc 51: 219-242 (Pubitemid 350064300)
-
(2007)
Progress in Nuclear Magnetic Resonance Spectroscopy
, vol.51
, Issue.4
, pp. 219-242
-
-
Fielding, L.1
-
76
-
-
0038043169
-
Library design
-
Stoll F (2003) Library design. Chimia 57(5): 224-228 (Pubitemid 36707182)
-
(2003)
Chimia
, vol.57
, Issue.5
, pp. 224-228
-
-
Stoll, F.1
-
78
-
-
36549033318
-
Integration of fragment screening and library design
-
DOI 10.1016/j.drudis.2007.08.005, PII S1359644607003108
-
Siegal G, Ab E, Schultz J (2007) Integration of fragment screening and library design. Drug Discov Today 12(23-24): 1032-1039 (Pubitemid 350180558)
-
(2007)
Drug Discovery Today
, vol.12
, Issue.23-24
, pp. 1032-1039
-
-
Siegal, G.1
Ab, E.2
Schultz, J.3
-
79
-
-
13244266921
-
Lead- and drug-like compounds: The rule-of-five revolution
-
DOI 10.1016/j.ddtec.2004.11.007, PII S1740674904000551
-
Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1(4): 337-341 (Pubitemid 40186335)
-
(2004)
Drug Discovery Today: Technologies
, vol.1
, Issue.4
, pp. 337-341
-
-
Lipinski, C.A.1
-
80
-
-
30844456535
-
SOFAST-HMQC experiments for recording two-dimensional deteronuclear correlation spectra of proteins within a few seconds
-
DOI 10.1007/s10858-005-4425-x
-
Schanda P, Kupce E, Brutscher B (2005) SOFAST-HMQC experiments for recording twodimensional heteronuclear correlation spectra of proteins within a few seconds. J Biomol NMR 33(4): 199-211 (Pubitemid 43118574)
-
(2005)
Journal of Biomolecular NMR
, vol.33
, Issue.4
, pp. 199-211
-
-
Schanda, P.1
Kupce, E.2
Brutscher, B.3
-
81
-
-
30844452411
-
Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR
-
DOI 10.1016/j.jmr.2005.10.007, PII S1090780705003459
-
Schanda P, Brutscher B (2006) Hadamard frequency-encoded SOFAST-HMQC for ultrafast two-dimensional protein NMR. J Magn Reson 178(2): 334-339 (Pubitemid 43107941)
-
(2006)
Journal of Magnetic Resonance
, vol.178
, Issue.2
, pp. 334-339
-
-
Schanda, P.1
Brutscher, B.2
-
82
-
-
0029338320
-
Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation
-
Mori S et al (1995) Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J Magn Reson B 108(1): 94-98
-
(1995)
J Magn Reson B
, vol.108
, Issue.1
, pp. 94-98
-
-
Mori, S.1
-
84
-
-
70350370859
-
Docking and virtual screening using distributed grid technology
-
Garcia-Sosa AT, Sild S, Maran U (2009) Docking and virtual screening using distributed grid technology. QSAR Comb Sci 28: 815-821
-
(2009)
QSAR Comb Sci
, vol.28
, pp. 815-821
-
-
Garcia-Sosa, A.T.1
Sild, S.2
Maran, U.3
-
88
-
-
33845461523
-
Current molecular docking tools and comparisons thereof
-
Wandzik I (2006) Current molecular docking tools and comparisons thereof. MATCH 55 (2): 271-278 (Pubitemid 44891298)
-
(2006)
Match
, vol.55
, Issue.2
, pp. 271-278
-
-
Wandzik, I.1
-
90
-
-
73349121324
-
Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK)
-
Viji SN, Prasad PA, Gautham N (2009) Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK). J Chem Inf Model 49(12): 2687-2694
-
(2009)
J Chem Inf Model
, vol.49
, Issue.12
, pp. 2687-2694
-
-
Viji, S.N.1
Prasad, P.A.2
Gautham, N.3
-
91
-
-
68149156015
-
E-novo: An automated workflow for efficient structure-based lead optimization
-
Pearce BC et al (2009) E-novo: an automated workflow for efficient structure-based lead optimization. J Chem Inf Model 49(7): 1797-1809
-
(2009)
J Chem Inf Model
, vol.49
, Issue.7
, pp. 1797-1809
-
-
Pearce, B.C.1
-
92
-
-
0027985242
-
Rational automatic search method for stable docking models of protein and ligand
-
DOI 10.1006/jmbi.1994.1656
-
Mizutani MY, Tomioka N, Itai A (1994) Rational automatic search method for stable docking models of protein and ligand. J Mol Biol 243(2): 310-326 (Pubitemid 24331984)
-
(1994)
Journal of Molecular Biology
, vol.243
, Issue.2
, pp. 310-326
-
-
Mizutani, M.Y.1
Tomioka, N.2
Itai, A.3
-
93
-
-
66149105428
-
Beyond the virtual screening paradigm: Structure-based searching for new lead compounds
-
Schlosser J, Rarey M (2009) Beyond the virtual screening paradigm: structure-based searching for new lead compounds. J Chem Inf Model 49(4): 800-809
-
(2009)
J Chem Inf Model
, vol.49
, Issue.4
, pp. 800-809
-
-
Schlosser, J.1
Rarey, M.2
-
94
-
-
0347296066
-
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
-
DOI 10.1016/S1093-3263(02)00204-8, PII S1093326302002048
-
Bostrom J, Greenwood JR, Gottfries J (2003) Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 21(5): 449-462 (Pubitemid 36120775)
-
(2003)
Journal of Molecular Graphics and Modelling
, vol.21
, Issue.5
, pp. 449-462
-
-
Bostrom, J.1
Greenwood, J.R.2
Gottfries, J.3
-
95
-
-
0028412035
-
FLOG: A system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure
-
Miller MD et al (1994) FLOG: a system to select quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 8(2): 153-174
-
(1994)
J Comput Aided Mol des
, vol.8
, Issue.2
, pp. 153-174
-
-
Miller, M.D.1
-
96
-
-
70350501158
-
Conformational sampling for large-scale virtual screening: Accuracy versus ensemble size
-
Griewel A et al (2009) Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. J Chem Inf Model 49(10): 2303-2311
-
(2009)
J Chem Inf Model
, vol.49
, Issue.10
, pp. 2303-2311
-
-
Griewel, A.1
-
97
-
-
84859887466
-
Multiple-start monte carlo docking of flexible ligands
-
Boston
-
Hart TN, Read RJ (1994) Multiple-start Monte Carlo docking of flexible ligands. Birkhaeuser, Boston
-
(1994)
Birkhaeuser
-
-
Hart, T.N.1
Read, R.J.2
-
98
-
-
77953189302
-
A new Lamarckian genetic algorithm for flexible ligand-receptor docking
-
Fuhrmann J et al (2010) A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J Comput Chem 31(9): 1911-1918
-
(2010)
J Comput Chem
, vol.31
, Issue.9
, pp. 1911-1918
-
-
Fuhrmann, J.1
-
99
-
-
9544251421
-
A combination of numeric genetic algorithm and tabu search can be applied to molecular docking
-
Cao T, Li T (2004) A combination of numeric genetic algorithm and tabu search can be applied to molecular docking. Comput Biol Chem 28(4): 303-312
-
(2004)
Comput Biol Chem
, vol.28
, Issue.4
, pp. 303-312
-
-
Cao, T.1
Li, T.2
-
100
-
-
77957899529
-
Advances and challenges in protein-ligand docking
-
Huang S-Y, Zou X (2010) Advances and challenges in protein-ligand docking. Int J Mol Sci 11: 3016-3034
-
(2010)
Int J Mol Sci
, vol.11
, pp. 3016-3034
-
-
Huang, S.-Y.1
Zou, X.2
-
101
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
-
Huang S-Y, Grinter SZ, Zou X (2010) Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys Chem Chem Phys 12(40): 12899-12908
-
(2010)
Phys Chem Chem Phys
, vol.12
, Issue.40
, pp. 12899-12908
-
-
Huang, S.-Y.1
Grinter, S.Z.2
Zou, X.3
-
102
-
-
77955800755
-
Mean-force scoring functions for protein-ligand binding
-
Huang S-Y, Zou X (2010) Mean-force scoring functions for protein-ligand binding. Annu Rep Comput Chem 6: 281-296
-
(2010)
Annu Rep Comput Chem
, vol.6
, pp. 281-296
-
-
Huang, S.-Y.1
Zou, X.2
-
103
-
-
0032551404
-
Piperacillin/tazobactam versus cefepime as initial empirical antimicrobial therapy in febrile neutropenic patients: A prospective randomized pilot study
-
Bohme A et al (1998) Piperacillin/tazobactam versus cefepime as initial empirical antimicrobial therapy in febrile neutropenic patients: a prospective randomized pilot study. Eur J Med Res 3(7): 324-330
-
(1998)
Eur J Med Res
, vol.3
, Issue.7
, pp. 324-330
-
-
Bohme, A.1
-
104
-
-
0031226772
-
Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge MD et al (1997) Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 11(5): 425-445 (Pubitemid 127505895)
-
(1997)
Journal of Computer-Aided Molecular Design
, vol.11
, Issue.5
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
105
-
-
0035011980
-
Protein ligand docking based on empirical method for binding affinity estimation
-
DOI 10.1023/A:1011188704521
-
Tao P, Lai L (2001) Protein ligand docking based on empirical method for binding affinity estimation. J Comput Aided Mol Des 15(5): 429-446 (Pubitemid 32454469)
-
(2001)
Journal of Computer-Aided Molecular Design
, vol.15
, Issue.5
, pp. 429-446
-
-
Tao, P.1
Lai, L.2
-
106
-
-
0036022960
-
Further development and validation of empirical scoring functions for structure-based binding affinity prediction
-
DOI 10.1023/A:1016357811882
-
Wang R, Lai L, Wang S (2002) Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 16(1): 11-26 (Pubitemid 34855041)
-
(2002)
Journal of Computer-Aided Molecular Design
, vol.16
, Issue.1
, pp. 11-26
-
-
Wang, R.1
Lai, L.2
Wang, S.3
-
107
-
-
0033545622
-
A general and fast scoring function for protein-ligand interactions: A simplified potential approach
-
DOI 10.1021/jm980536j
-
Muegge I, Martin YC (1999) A general and fast scoring function for protein-ligand interactions: a simplified potential approach. J Med Chem 42(5): 791-804 (Pubitemid 29136170)
-
(1999)
Journal of Medicinal Chemistry
, vol.42
, Issue.5
, pp. 791-804
-
-
Muegge, I.1
Martin, Y.C.2
-
108
-
-
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
-
109
-
-
26444588137
-
CSD-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction
-
DOI 10.1021/jm050436v
-
Velec HF, Gohlke H, Klebe G (2005) DrugScore(CSD)-knowledge-based scoring function derived from small molecule crystal data with superior recognition rate of near-native ligand poses and better affinity prediction. J Med Chem 48(20): 6296-6303 (Pubitemid 41428984)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.20
, pp. 6296-6303
-
-
Velec, H.F.G.1
Gohlke, H.2
Klebe, G.3
-
110
-
-
61349117968
-
The importance of discerning shape in molecular pharmacology
-
Kortagere S, Krasowski MD, Ekins S (2009) The importance of discerning shape in molecular pharmacology. Trends Pharmacol Sci 30(3): 138-147
-
(2009)
Trends Pharmacol Sci
, vol.30
, Issue.3
, pp. 138-147
-
-
Kortagere, S.1
Krasowski, M.D.2
Ekins, S.3
-
112
-
-
78349285507
-
Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis
-
Stark JL et al (2010) Solution structure and function of YndB, an AHSA1 protein from Bacillus subtilis. Proteins 78(16): 3328-3340
-
(2010)
Proteins
, vol.78
, Issue.16
, pp. 3328-3340
-
-
Stark, J.L.1
-
113
-
-
4444360113
-
Fluctuation analysis and accuracy of a large-scale in silico screen
-
Merlitz H, Herges T, Wenzel W (2004) Fluctuation analysis and accuracy of a large-scale in silico screen. J Comput Chem 25(13): 1568-1575
-
(2004)
J Comput Chem
, vol.25
, Issue.13
, pp. 1568-1575
-
-
Merlitz, H.1
Herges, T.2
Wenzel, W.3
-
114
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
DOI 10.1021/jm060763i
-
Tirado-Rives J, Jorgensen WL (2006) Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J Med Chem 49(20): 5880-5884 (Pubitemid 44484934)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
115
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
DOI 10.1021/jm990352k
-
Charifson PS et al (1999) Consensus scoring: a method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J Med Chem 42(25): 5100-5109 (Pubitemid 30020261)
-
(1999)
Journal of Medicinal Chemistry
, vol.42
, Issue.25
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
116
-
-
61449163022
-
Communication breakdown: Protein dynamics and drug design
-
Peng JW (2009) Communication breakdown: protein dynamics and drug design. Structure 17(3): 319-320
-
(2009)
Structure
, vol.17
, Issue.3
, pp. 319-320
-
-
Peng, J.W.1
-
117
-
-
84934444735
-
Normal modes and essential dynamics
-
Molecular Modeling of Proteins
-
Hayward S, de Groot BL (2008) Normal modes and essential dynamics. Methods Mol Biol 443: 89-106 (Molecular Modeling of Proteins)
-
(2008)
Methods Mol Biol
, vol.443
, pp. 89-106
-
-
Hayward, S.1
De Groot, B.L.2
-
118
-
-
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 (Pubitemid 46053470)
-
(2007)
Proteins: Structure, Function and Genetics
, vol.66
, Issue.2
, pp. 399-421
-
-
Huang, S.-Y.1
Zou, X.2
-
121
-
-
40149093773
-
Rapid protein-ligand costructures using chemical shift perturbations
-
DOI 10.1021/ja0737974
-
Stark J, Powers R (2008) Rapid protein-ligand costructures using chemical shift perturbations. J Am Chem Soc 130(2): 535-545 (Pubitemid 351455567)
-
(2008)
Journal of the American Chemical Society
, vol.130
, Issue.2
, pp. 535-545
-
-
Stark, J.1
Powers, R.2
-
122
-
-
63149162777
-
Managing protein flexibility in docking and its applications
-
B-Rao C, Subramanian J, Sharma SD (2009) Managing protein flexibility in docking and its applications. Drug Discov Today 14(7-8): 394-400
-
(2009)
Drug Discov Today
, vol.14
, Issue.7-8
, pp. 394-400
-
-
B-Rao, C.1
Subramanian, J.2
Sharma, S.D.3
-
123
-
-
0026310932
-
Soft docking: Matching of molecular surface cubes
-
Jiang F, Kim SH (1991) "Soft docking": matching of molecular surface cubes. J Mol Biol 219 (1): 79-102 (Pubitemid 121003975)
-
(1991)
Journal of Molecular Biology
, vol.219
, Issue.1
, pp. 79-102
-
-
Jiang, F.1
Kim, S.-H.2
-
124
-
-
0035957528
-
FLEXE: Efficient molecular docking considering protein structure variations
-
DOI 10.1006/jmbi.2001.4551
-
Claussen H et al (2001) FlexE: efficient molecular docking considering protein structurevariations. J Mol Biol 308(2): 377-395 (Pubitemid 33043576)
-
(2001)
Journal of Molecular Biology
, vol.308
, Issue.2
, pp. 377-395
-
-
Claussen, H.1
Buning, C.2
Rarey, M.3
Lengauer, T.4
-
125
-
-
27144484954
-
Receptor flexibility in de novo ligand design and docking
-
DOI 10.1021/jm050196j
-
Alberts IL, Todorov NP, Dean PM (2005) Receptor flexibility in de novo ligand design and docking. J Med Chem 48(21): 6585-6596 (Pubitemid 41504716)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.21
, pp. 6585-6596
-
-
Alberts, I.L.1
Todorov, N.P.2
Dean, P.M.3
-
126
-
-
21244479779
-
Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
-
DOI 10.1021/jm048972v
-
Barril X, Morley SD (2005) Unveiling the full potential of flexible receptor docking using multiple crystallographic structures. J Med Chem 48(13): 4432-4443 (Pubitemid 40884945)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.13
, pp. 4432-4443
-
-
Barril, X.1
Morley, S.D.2
-
127
-
-
33745199815
-
Virtual ligand screening: Strategies, perspectives and limitations
-
Klebe G (2006) Virtual ligand screening: strategies, perspectives and limitations. Drug Discov Today 11(13-14): 580-594
-
(2006)
Drug Discov Today
, vol.11
, Issue.13-14
, pp. 580-594
-
-
Klebe, G.1
-
128
-
-
0036007208
-
Virtual screening and fast automated docking methods
-
Schneider G, Bohm HJ (2002) Virtual screening and fast automated docking methods. Drug Discov Today 7(1): 64-70
-
(2002)
Drug Discov Today
, vol.7
, Issue.1
, pp. 64-70
-
-
Schneider, G.1
Bohm, H.J.2
-
130
-
-
1642540577
-
Evaluation of docking performance: Comparative data on docking algorithms
-
DOI 10.1021/jm0302997
-
Kontoyianni M, McClellan LM, Sokol GS (2004) Evaluation of docking performance: comparative data on docking algorithms. J Med Chem 47(3): 558-565 (Pubitemid 38129714)
-
(2004)
Journal of Medicinal Chemistry
, vol.47
, Issue.3
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
131
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection - What can we learn from earlier mistakes?
-
DOI 10.1007/s10822-007-9163-6
-
Kirchmair J et al (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-what can we learn from earlier mistakes? J Comput Aided Mol Des 22(3-4): 213-228 (Pubitemid 351447959)
-
(2008)
Journal of Computer-Aided Molecular Design
, vol.22
, Issue.3-4
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
132
-
-
26944443036
-
A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication
-
DOI 10.1021/ci0500177
-
Bender A, Glen RC (2005) A discussion of measures of enrichment in virtual screening: comparing the information content of descriptors with increasing levels of sophistication. J Chem Inf Model 45(5): 1369-1375 (Pubitemid 41478810)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.5
, pp. 1369-1375
-
-
Bender, A.1
Glen, R.C.2
-
133
-
-
34247272948
-
Evaluating virtual screening methods: Good and bad metrics for the early recognition problem
-
DOI 10.1021/ci600426e
-
Truchon J-F, Bayly CI (2007) Evaluating virtual screening methods: good and bad metrics for the "early recognition" problem. J Chem Inf Model 47(2): 488-508 (Pubitemid 46615951)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 488-508
-
-
Truchon, J.-F.1
Bayly, C.I.2
-
136
-
-
33646517064
-
Drug discovery: Selecting the optimal approach
-
Sams-Dodd F (2006) Drug discovery: selecting the optimal approach. Drug Discov Today 11(9-10): 465-472
-
(2006)
Drug Discov Today
, vol.11
, Issue.9-10
, pp. 465-472
-
-
Sams-Dodd, F.1
-
137
-
-
34247194965
-
Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: Assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery
-
DOI 10.1021/ci600423u
-
Fink T, Reymond JL (2007) Virtual exploration of the chemical universe up to 11 atoms of C, N, O, F: assembly of 26.4 million structures (110.9 million stereoisomers) and analysis for new ring systems, stereochemistry, physicochemical properties, compound classes, and drug discovery. J Chem Inf Model 47(2): 342-353 (Pubitemid 46615939)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 342-353
-
-
Fink, T.1
Raymond, J.-L.2
-
138
-
-
0032872173
-
How many leads from HTS?
-
Lahana R (1999) How many leads from HTS? Drug Discov Today 4(10): 447-448
-
(1999)
Drug Discov Today
, vol.4
, Issue.10
, pp. 447-448
-
-
Lahana, R.1
-
139
-
-
43049089747
-
Identification of promiscuous small molecule activators in high-throughput enzyme activation screens
-
DOI 10.1021/jm701583b
-
Goode DR et al (2008) Identification of promiscuous small molecule activators in highthroughput enzyme activation screens. J Med Chem 51(8): 2346-2349 (Pubitemid 351628495)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.8
, pp. 2346-2349
-
-
Goode, D.R.1
Totten, R.K.2
Heeres, J.T.3
Hergenrother, P.J.4
-
140
-
-
33747254345
-
Identification of chemically diverse Chk1 inhibitors by receptor-based virtual screening
-
Foloppe N et al (2006) Identification of chemically diverse Chk1 inhibitors by receptor-based virtual screening. Bioorg Med Chem 14(14): 4792-4802
-
(2006)
Bioorg Med Chem
, vol.14
, Issue.14
, pp. 4792-4802
-
-
Foloppe, N.1
-
141
-
-
34250349894
-
Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping
-
DOI 10.1016/j.bmcl.2007.04.110, PII S0960894X07005550
-
Richardson CM et al (2007) Discovery of a potent CDK2 inhibitor with a novel binding mode, using virtual screening and initial, structure-guided lead scoping. Bioorg Med Chem Lett 17(14): 3880-3885 (Pubitemid 46920948)
-
(2007)
Bioorganic and Medicinal Chemistry Letters
, vol.17
, Issue.14
, pp. 3880-3885
-
-
Richardson, C.M.1
Nunns, C.L.2
Williamson, D.S.3
Parratt, M.J.4
Dokurno, P.5
Howes, R.6
Borgognoni, J.7
Drysdale, M.J.8
Finch, H.9
Hubbard, R.E.10
Jackson, P.S.11
Kierstan, P.12
Lentzen, G.13
Moore, J.D.14
Murray, J.B.15
Simmonite, H.16
Surgenor, A.E.17
Torrance, C.J.18
-
142
-
-
11144352156
-
NMR-based techniques in the hit identification and optimisation processes
-
DOI 10.1517/14728222.8.6.597
-
Pellecchia M et al (2004) NMR-based techniques in the hit identification and optimization processes. Expert Opin Ther Targets 8(6): 597-611 (Pubitemid 40028369)
-
(2004)
Expert Opinion on Therapeutic Targets
, vol.8
, Issue.6
, pp. 597-611
-
-
Pellecchia, M.1
Becattini, B.2
Crowell, K.J.3
Fattorusso, R.4
Forino, M.5
Fragai, M.6
Jung, D.7
Mustelin, T.8
Tautz, L.9
-
143
-
-
77955042462
-
From complete genome sequence to 'complete' understanding?
-
Galperin MY, Koonin EV (2010) From complete genome sequence to 'complete' understanding? Trends Biotechnol 28(8): 398-406
-
(2010)
Trends Biotechnol
, vol.28
, Issue.8
, pp. 398-406
-
-
Galperin, M.Y.1
Koonin, E.V.2
-
144
-
-
0037107026
-
High-throughput cell-based assays in yeast
-
DOI 10.1016/S1359-6446(02)02409-1, PII S1359644602024091
-
Tucker CL (2002) High-throughput cell-based assays in yeast. Drug Discov Today 7(18 Suppl): S125-S130 (Pubitemid 35286906)
-
(2002)
Drug Discovery Today
, vol.7
, Issue.18
-
-
Tucker, C.L.1
-
145
-
-
22844441447
-
Gene knockdown by large circular antisense for high-throughput functional genomics
-
Lee YH et al (2005) Gene knockdown by large circular antisense for high-throughput functional genomics. Nat Biotechnol 23(5): 591-599
-
(2005)
Nat Biotechnol
, vol.23
, Issue.5
, pp. 591-599
-
-
Lee, Y.H.1
-
147
-
-
1342263835
-
High-throughput protein analysis integrating bioinformatics and experimental assays
-
del Val C et al (2004) High-throughput protein analysis integrating bioinformatics and experimental assays. Nucleic Acids Res 32(2): 742-748
-
(2004)
Nucleic Acids Res
, vol.32
, Issue.2
, pp. 742-748
-
-
Del Val, C.1
-
148
-
-
33749506205
-
Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening
-
DOI 10.2174/138920306778559386
-
Laurie AT, Jackson RM (2006) Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. Curr Protein Pept Sci 7(5): 395-406 (Pubitemid 44524489)
-
(2006)
Current Protein and Peptide Science
, vol.7
, Issue.5
, pp. 395-406
-
-
Laurie, A.T.R.1
Jackson, R.M.2
-
149
-
-
33646351764
-
Structural biology and bioinformatics in drug design: Opportunities and challenges for target identification and lead discovery
-
DOI 10.1098/rstb.2005.1800
-
Blundell TL et al (2006) Structural biology and bioinformatics in drug design: opportunities and challenges for target identification and lead discovery. Philos Trans R Soc Lond B Biol Sci 361(1467): 413-423 (Pubitemid 44870098)
-
(2006)
Philosophical Transactions of the Royal Society B: Biological Sciences
, vol.361
, Issue.1467
, pp. 413-423
-
-
Blundell, T.L.1
Sibanda, B.L.2
Montalvao, R.W.3
Brewerton, S.4
Chelliah, V.5
Worth, C.L.6
Harmer, N.J.7
Davies, O.8
Burke, D.9
-
150
-
-
33646839120
-
Characterization of protein-ligand interaction sites using experimental and computational methods
-
Vajda S, Guarnieri F (2006) Characterization of protein-ligand interaction sites using experimental and computational methods. Curr Opin Drug Discov Devel 9(3): 354-362 (Pubitemid 43774164)
-
(2006)
Current Opinion in Drug Discovery and Development
, vol.9
, Issue.3
, pp. 354-362
-
-
Vajda, S.1
Guarnieri, F.2
-
151
-
-
33746586581
-
Design and characterization of a functional library for NMR screening against novel protein targets
-
DOI 10.2174/138620706777935342
-
Mercier KA, Germer K, Powers R (2006) Design and characterization of a functional library for NMR screening against novel protein targets. Comb Chem High Throughput Screen 9(7): 515-534 (Pubitemid 44156709)
-
(2006)
Combinatorial Chemistry and High Throughput Screening
, vol.9
, Issue.7
, pp. 515-534
-
-
Mercier, K.A.1
Germer, K.2
Powers, R.3
-
152
-
-
65549146338
-
A multi-step NMR screen for the identification and evaluation of chemical leads for drug discovery
-
Mercier KA, Shortridge MD, Powers R (2009) A multi-step NMR screen for the identification and evaluation of chemical leads for drug discovery. Comb Chem High Throughput Screen 12(3): 285-295
-
(2009)
Comb Chem High Throughput Screen
, vol.12
, Issue.3
, pp. 285-295
-
-
Mercier, K.A.1
Shortridge, M.D.2
Powers, R.3
-
153
-
-
33748271948
-
Comparison of protein active site structures for functional annotation of proteins and drug design
-
DOI 10.1002/prot.21092
-
Powers R et al (2006) Comparison of protein active site structures for functional annotation of proteins and drug design. Proteins 65(1): 124-135 (Pubitemid 44320622)
-
(2006)
Proteins: Structure, Function and Genetics
, vol.65
, Issue.1
, pp. 124-135
-
-
Powers, R.1
Copeland, J.C.2
Germer, K.3
Mercier, K.A.4
Ramanatlian, V.5
Revesz, P.6
-
155
-
-
61449176941
-
Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170)
-
Mercier KA et al (2009) Structure and function of Pseudomonas aeruginosa protein PA1324 (21-170). Protein Sci 18(3): 606-618
-
(2009)
Protein Sci
, vol.18
, Issue.3
, pp. 606-618
-
-
Mercier, K.A.1
-
156
-
-
77949324326
-
Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins
-
Shortridge MD, Powers R (2009) Structural and functional similarity between the bacterial type III secretion system needle protein PrgI and the eukaryotic apoptosis Bcl-2 proteins. PLoS One 4(10): e7442
-
(2009)
PLoS One
, vol.4
, Issue.10
-
-
Shortridge, M.D.1
Powers, R.2
-
157
-
-
0033636878
-
Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations
-
McCoy MA, Wyss DF (2000) Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations. J Biomol NMR 18(3): 189-198
-
(2000)
J Biomol NMR
, vol.18
, Issue.3
, pp. 189-198
-
-
McCoy, M.A.1
Wyss, D.F.2
-
158
-
-
26944493033
-
How much NMR data is required to determine a protein-ligand complex structure?
-
DOI 10.1002/cbic.200500092
-
Schieborr U et al (2005) How much NMR data is required to determine a protein-ligand complex structure? Chembiochem 6(10): 1891-1898 (Pubitemid 41475282)
-
(2005)
ChemBioChem
, vol.6
, Issue.10
, pp. 1891-1898
-
-
Schieborr, U.1
Vogtherr, M.2
Eishorst, B.3
Betz, M.4
Grimme, S.5
Pescatore, B.6
Langer, T.7
Saxena, K.8
Schwalbe, H.9
-
159
-
-
35348868045
-
A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations
-
DOI 10.1021/jm070484a
-
Wang B, Westerhoff LM, Merz KM Jr (2007) A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J Med Chem 50(21): 5128-5134 (Pubitemid 47585710)
-
(2007)
Journal of Medicinal Chemistry
, vol.50
, Issue.21
, pp. 5128-5134
-
-
Wang, B.1
Westerhoff, L.M.2
Merz Jr., K.M.3
-
160
-
-
70350508200
-
Steering protein-ligand docking with quantitative NMR chemical shift perturbations
-
Gonzalez-Ruiz D, Gohlke H (2009) Steering protein-ligand docking with quantitative NMR chemical shift perturbations. J Chem Inf Model 49(10): 2260-2271
-
(2009)
J Chem Inf Model
, vol.49
, Issue.10
, pp. 2260-2271
-
-
Gonzalez-Ruiz, D.1
Gohlke, H.2
-
161
-
-
0035544152
-
Automated prediction of 15N, 13CÎ, 13CÎ and 13C0 chemical shifts in proteins using a density functional database
-
Xu X-P, Case DA (2001) Automated prediction of 15N, 13CÎ, 13CÎ and 13C0 chemical shifts in proteins using a density functional database. J Biomol NMR 21(4): 321-333
-
(2001)
J Biomol NMR
, vol.21
, Issue.4
, pp. 321-333
-
-
Xu, X.-P.1
Case, D.A.2
-
162
-
-
0028907436
-
Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities
-
Nilges M (1995) Calculation of protein structures with ambiguous distance restraints. Automated assignment of ambiguous NOE crosspeaks and disulphide connectivities. J Mol Biol 245(5): 645-660
-
(1995)
J Mol Biol
, vol.245
, Issue.5
, pp. 645-660
-
-
Nilges, M.1
-
163
-
-
0035425696
-
Sampling of conformation space in torsion angle dynamics calculations
-
DOI 10.1016/S0010-4655(01)00204-1, PII S0010465501002041
-
Guntert P, Wuthrich K (2001) Sampling of conformation space in torsion angle dynamics calculations. Comput Phys Commun 138(2): 155-169 (Pubitemid 32691052)
-
(2001)
Computer Physics Communications
, vol.138
, Issue.2
, pp. 155-169
-
-
Guntert, P.1
Wuthrich, K.2
-
164
-
-
0033668689
-
Predicting binding modes, binding affinities and "hot spots" for protein-ligand complexes using a knowledge-based scoring function
-
Gohlke H, Hendlich M, Klebe G (2000) Predicting binding modes, binding affinities and "hot spots" for protein-ligand complexes using a knowledge-based scoring function. Perspect Drug Discov Des 20: 115-144
-
(2000)
Perspect Drug Discov des
, vol.20
, pp. 115-144
-
-
Gohlke, H.1
Hendlich, M.2
Klebe, G.3
-
165
-
-
0000865993
-
A new analysis of proton chemical shifts in proteins
-
Osapay K, Case DA (1991) A new analysis of proton chemical shifts in proteins. J Am Chem Soc 113(25): 9436-9444
-
(1991)
J Am Chem Soc
, vol.113
, Issue.25
, pp. 9436-9444
-
-
Osapay, K.1
Case, D.A.2
-
166
-
-
68849103899
-
Discovery of inhibitors of lupin diadenosine 50 5000-P(1), P 4)- tetraphosphate hydrolase by virtual screening
-
Branson KM et al (2009) Discovery of inhibitors of lupin diadenosine 50,5000-P(1), P(4)- tetraphosphate hydrolase by virtual screening. Biochemistry 48(32): 7614-7620
-
(2009)
Biochemistry
, vol.48
, Issue.32
, pp. 7614-7620
-
-
Branson, K.M.1
-
167
-
-
42949169980
-
Identification of Plasmodium falciparum spermidine synthase active site binders through structure-based virtual screening
-
DOI 10.1021/jm7016144
-
JacobssonMet al (2008) Identification of Plasmodium falciparum spermidine synthase active site binders through structure-based virtual screening. J Med Chem 51(9): 2777-2786 (Pubitemid 351620799)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.9
, pp. 2777-2786
-
-
Jacobsson, M.1
Garedal, M.2
Schultz, J.3
Karlen, A.4
-
168
-
-
67650128335
-
Identification of compounds exhibiting inhibitory activity toward the Pseudomonas tolaasii toxin tolaasin i using in silico docking calculations NMR binding assays, and in vitro hemolytic activity assays
-
Lee Y et al (2009) Identification of compounds exhibiting inhibitory activity toward the Pseudomonas tolaasii toxin tolaasin I using in silico docking calculations, NMR binding assays, and in vitro hemolytic activity assays. Bioorg Med Chem Lett 19(15): 4321-4324
-
(2009)
Bioorg Med Chem Lett
, vol.19
, Issue.15
, pp. 4321-4324
-
-
Lee, Y.1
-
169
-
-
77952813636
-
Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure-based drug design
-
Veldkamp CT et al (2010) Targeting SDF-1/CXCL12 with a ligand that prevents activation of CXCR4 through structure-based drug design. J Am Chem Soc 132(21): 7242-7243
-
(2010)
J Am Chem Soc
, vol.132
, Issue.21
, pp. 7242-7243
-
-
Veldkamp, C.T.1
-
170
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
DOI 10.1021/ci049714+
-
Irwin JJ, Shoichet BK (2005) ZINC-a free database of commercially available compounds for virtual screening. J Chem Inf Model 45(1): 177-182 (Pubitemid 40736970)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
171
-
-
23844444239
-
Heirarchical docking of databases of multiple ligand conformations
-
DOI 10.2174/1568026054637683
-
Lorber DM, Shoichet BK (2005) Hierarchical docking of databases of multiple ligand conformations. Curr Top Med Chem 5(8): 739-749 (Pubitemid 41179714)
-
(2005)
Current Topics in Medicinal Chemistry
, vol.5
, Issue.8
, pp. 739-749
-
-
Lorber, D.M.1
Shoichet, B.K.2
-
173
-
-
43049088827
-
Ligand binding efficiency: Trends, physical basis, and implications
-
DOI 10.1021/jm701255b
-
Reynolds CH, Tounge BA, Bembenek SD (2008) Ligand binding efficiency: trends, physical basis, and implications. J Med Chem 51(8): 2432-2438 (Pubitemid 351628504)
-
(2008)
Journal of Medicinal Chemistry
, vol.51
, Issue.8
, pp. 2432-2438
-
-
Reynolds, C.H.1
Tounge, B.A.2
Bembenek, S.D.3
-
174
-
-
77954737814
-
Discovery of fragment molecules that bind the human peroxiredoxin 5 active site
-
Barelier S et al (2010) Discovery of fragment molecules that bind the human peroxiredoxin 5 active site. PLoS One 5(3): e9744
-
(2010)
PLoS One
, vol.5
, Issue.3
-
-
Barelier, S.1
-
175
-
-
0035943382
-
Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 A resolution
-
Declercq JP et al (2001) Crystal structure of human peroxiredoxin 5, a novel type of mammalian peroxiredoxin at 1.5 A resolution. J Mol Biol 311(4): 751-759
-
(2001)
J Mol Biol
, vol.311
, Issue.4
, pp. 751-759
-
-
Declercq, J.P.1
-
176
-
-
17144373303
-
Druggability indices for protein targets derived from NMr-based screening data
-
DOI 10.1021/jm049131r
-
Hajduk PJ, Huth JR, Fesik SW (2005) Druggability indices for protein targets derived from NMR-based screening data. J Med Chem 48(7): 2518-2525 (Pubitemid 40516441)
-
(2005)
Journal of Medicinal Chemistry
, vol.48
, Issue.7
, pp. 2518-2525
-
-
Hajduk, P.J.1
Huth, J.R.2
Fesik, S.W.3
-
177
-
-
29144483936
-
Predicting protein druggability
-
DOI 10.1016/S1359-6446(05)03624-X, PII S135964460503624X
-
Hajduk PJ, Huth JR, Tse C (2005) Predicting protein druggability. Drug Discov Today 10(23-24): 1675-1682 (Pubitemid 41817616)
-
(2005)
Drug Discovery Today
, vol.10
, Issue.23-24
, pp. 1675-1682
-
-
Hajduk, P.J.1
Huth, J.R.2
Tse, C.3
-
178
-
-
0034923647
-
Nuclear magnetic resonance-based approaches for lead generation in drug discovery
-
Peng JW et al (2001) Nuclear magnetic resonance-based approaches for lead generation in drug discovery. Methods Enzymol 338: 202-230
-
(2001)
Methods Enzymol
, vol.338
, pp. 202-230
-
-
Peng, J.W.1
-
179
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris GM et al (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J Comput Chem 19(14): 1639-1662 (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
-
180
-
-
0026584349
-
Solution studies of staphylococcal nuclease H124L. 2. 1H, 13C, and 15N chemical shift assignments for the unligated enzyme and analysis of chemical shift changes that accompany formation of the nuclease-thymidine 30,50-bisphosphatecalcium ternary complex
-
Wang JF et al (1992) Solution studies of staphylococcal nuclease H124L. 2. 1H, 13C, and 15N chemical shift assignments for the unligated enzyme and analysis of chemical shift changes that accompany formation of the nuclease-thymidine 30,50-bisphosphatecalcium ternary complex. Biochemistry 31(3): 921-936
-
(1992)
Biochemistry
, vol.31
, Issue.3
, pp. 921-936
-
-
Wang, J.F.1
-
181
-
-
0025186881
-
2+ ternary complex
-
2+ ternary complex. Biochemistry 29(1): 102-113
-
(1990)
Biochemistry
, vol.29
, Issue.1
, pp. 102-113
-
-
Wang, J.F.1
|