-
1
-
-
39049094335
-
Virtual screening and its integration with modern drug design technologies
-
Guido RV, Oliva G, Andricopulo AD. Virtual screening and its integration with modern drug design technologies. Curr Med Chem 2008;15(1):37-46
-
(2008)
Curr Med Chem
, vol.15
, Issue.1
, pp. 37-46
-
-
Guido, R.V.1
Oliva, G.2
Andricopulo, A.D.3
-
2
-
-
0037107887
-
Structure-based virtual screening: An overview
-
Lyne PD. Structure-based virtual screening: an overview. Drug Discov Today 2002;7(20):1047-1055
-
(2002)
Drug Discov Today
, vol.7
, Issue.20
, pp. 1047-1055
-
-
Lyne, P.D.1
-
3
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
Schneider G, Fechner U. Computer-based de novo design of drug-like molecules. Nat Rev 2005;4(8):649-663
-
(2005)
Nat Rev
, vol.4
, Issue.8
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
4
-
-
71749086377
-
G protein-coupled receptors: Target-based in silico screening
-
Senderowitz H, Marantz Y. G protein-coupled receptors: target-based in silico screening. Curr Pharm Des 2009;15(35):4049-4068
-
(2009)
Curr Pharm des
, vol.15
, Issue.35
, pp. 4049-4068
-
-
Senderowitz, H.1
Marantz, Y.2
-
5
-
-
11144323163
-
Virtual screening of chemical libraries
-
Shoichet BK. Virtual screening of chemical libraries. Nature 2004;432(7019):862-865
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 862-865
-
-
Shoichet, B.K.1
-
6
-
-
0035966871
-
Detailed analysis of scoring functions for virtual screening
-
Stahl M, Rarey M. Detailed analysis of scoring functions for virtual screening. J Med Chem 2001;44(7):1035-1042
-
(2001)
J Med Chem
, vol.44
, Issue.7
, pp. 1035-1042
-
-
Stahl, M.1
Rarey, M.2
-
9
-
-
0030039619
-
The art and practice of structure-based drug design: A molecular modeling perspective
-
Bohacek RS, McMartin C, Guida WC. The art and practice of structure-based drug design: a molecular modeling perspective. Medicinal research reviews 1996;16(1):3-50
-
(1996)
Medicinal Research Reviews
, vol.16
, Issue.1
, pp. 3-50
-
-
Bohacek, R.S.1
McMartin, C.2
Guida, W.C.3
-
11
-
-
34548200847
-
Structure-based drug design: Docking and scoring
-
Kroemer RT. Structure-based drug design: docking and scoring. Curr Protein Pept Sci 2007;8(4):312-328
-
(2007)
Curr Protein Pept Sci
, vol.8
, Issue.4
, pp. 312-328
-
-
Kroemer, R.T.1
-
12
-
-
0034351495
-
Effectiveness of retrieval in similarity searches of chemical databases: A review of performance measures
-
Edgar SJ, Holliday JD, Willett P. Effectiveness of retrieval in similarity searches of chemical databases: a review of performance measures. J Mol Graph Model 2000;18(4-5):343-357
-
(2000)
J Mol Graph Model
, vol.18
, Issue.4-5
, pp. 343-357
-
-
Edgar, S.J.1
Holliday, J.D.2
Willett, P.3
-
13
-
-
33745123321
-
Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery
-
Pozzan A. Molecular descriptors and methods for ligand based virtual high throughput screening in drug discovery. Curr Pharm Des 2006;12(17):2099-2110
-
(2006)
Curr Pharm des
, vol.12
, Issue.17
, pp. 2099-2110
-
-
Pozzan, A.1
-
14
-
-
33845868822
-
PHASE: A new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results
-
Dixon SL, Smondyrev AM, Knoll EH, et al. PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results. J Comput Aided Mol Des 2006;20(10-11):647-671
-
(2006)
J Comput Aided Mol des
, vol.20
, Issue.10-11
, pp. 647-671
-
-
Dixon, S.L.1
Smondyrev, A.M.2
Knoll, E.H.3
-
15
-
-
21344473451
-
The impact of pharmacophore modeling in drug design
-
Guner OF. The impact of pharmacophore modeling in drug design. IDrugs 2005;8(7):567-572
-
(2005)
IDrugs
, vol.8
, Issue.7
, pp. 567-572
-
-
Guner, O.F.1
-
16
-
-
37649009919
-
Molecule-pharmacophore superpositioning and pattern matching in computational drug design
-
Wolber G, Seidel T, Bendix F, Langer T. Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug discovery today 2008;13(1-2):23-29
-
(2008)
Drug Discovery Today
, vol.13
, Issue.1-2
, pp. 23-29
-
-
Wolber, G.1
Seidel, T.2
Bendix, F.3
Langer, T.4
-
18
-
-
36949022890
-
Predictive QSAR modeling workflow, model applicability domains, and virtual screening
-
Tropsha A, Golbraikh A. Predictive QSAR modeling workflow, model applicability domains, and virtual screening. Curr Pharm Des 2007;13(34):3494-3504
-
(2007)
Curr Pharm des
, vol.13
, Issue.34
, pp. 3494-3504
-
-
Tropsha, A.1
Golbraikh, A.2
-
19
-
-
23944454816
-
Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein-and ligand-based virtual screening protocols
-
Evers A, Hessler G, Matter H, Klabunde T. Virtual screening of biogenic amine-binding G-protein coupled receptors: comparative evaluation of protein-and ligand-based virtual screening protocols. J Med Chem 2005;48(17):5448-5465
-
(2005)
J Med Chem
, vol.48
, Issue.17
, pp. 5448-5465
-
-
Evers, A.1
Hessler, G.2
Matter, H.3
Klabunde, T.4
-
20
-
-
33846212271
-
Comparison of shape-matching and docking as virtual screening tools
-
Hawkins PC, Skillman AG, Nicholls A. Comparison of shape-matching and docking as virtual screening tools. J Med Chem 2007;50(1):74-82
-
(2007)
J Med Chem
, vol.50
, Issue.1
, pp. 74-82
-
-
Hawkins, P.C.1
Skillman, A.G.2
Nicholls, A.3
-
21
-
-
34547673017
-
Comparison of topological, shape, and docking methods in virtual screening
-
McGaughey GB, Sheridan RP, Bayly CI, et al. Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 2007;47(4):1504-1519
-
(2007)
J Chem Inf Model
, vol.47
, Issue.4
, pp. 1504-1519
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
-
22
-
-
42149089443
-
Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking
-
Perez-Nueno VI, Ritchie DW, Rabal O, et al. Comparison of ligand-based and receptor-based virtual screening of HIV entry inhibitors for the CXCR4 and CCR5 receptors using 3D ligand shape matching and ligand-receptor docking. J Chem Inf Model 2008;48(3):509-533
-
(2008)
J Chem Inf Model
, vol.48
, Issue.3
, pp. 509-533
-
-
Perez-Nueno, V.I.1
Ritchie, D.W.2
Rabal, O.3
-
23
-
-
54849439948
-
Integrating structure-and ligand-based virtual screening: Comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets
-
Tan L, Geppert H, Sisay MT, et al. Integrating structure-and ligand-based virtual screening: comparison of individual, parallel, and fused molecular docking and similarity search calculations on multiple targets. ChemMedChem 2008;3(10):1566-1571
-
(2008)
ChemMedChem
, vol.3
, Issue.10
, pp. 1566-1571
-
-
Tan, L.1
Geppert, H.2
Sisay, M.T.3
-
24
-
-
74849085203
-
Comparison of structure-and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors
-
Kruger DM, Evers A. Comparison of structure-and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. ChemMedChem 2009;5(1):148-158
-
(2009)
ChemMedChem
, vol.5
, Issue.1
, pp. 148-158
-
-
Kruger, D.M.1
Evers, A.2
-
26
-
-
0001858251
-
Application of a theory of enzyme specificity to protein synthesis
-
Koshland DE. Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 1958;44(2):98-104
-
(1958)
Proc Natl Acad Sci USA
, vol.44
, Issue.2
, pp. 98-104
-
-
Koshland, D.E.1
-
27
-
-
2342586724
-
Conformational analysis of drug-like molecules bound to proteins: An extensive study of ligand reorganization upon binding
-
Perola E, Charifson PS. Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. J Med Chem 2004;47(10):2499-2510
-
(2004)
J Med Chem
, vol.47
, Issue.10
, pp. 2499-2510
-
-
Perola, E.1
Charifson, P.S.2
-
28
-
-
72949085818
-
Bioactive conformational biasing: A new method for focusing conformational ensembles on bioactive-like conformers
-
Musafia B, Senderowitz H. Bioactive conformational biasing: a new method for focusing conformational ensembles on bioactive-like conformers. J Chem Inf Model 2009;49(11):2469-2480
-
(2009)
J Chem Inf Model
, vol.49
, Issue.11
, pp. 2469-2480
-
-
Musafia, B.1
Senderowitz, H.2
-
29
-
-
0042229161
-
Simultaneous determination of bioactive conformations and alignment rules by multi-way PLS modeling
-
Hasegawa K, Arakawa M, Funatsu K. Simultaneous determination of bioactive conformations and alignment rules by multi-way PLS modeling. Comput Biol Chem 2003;27(3):211-216
-
(2003)
Comput Biol Chem
, vol.27
, Issue.3
, pp. 211-216
-
-
Hasegawa, K.1
Arakawa, M.2
Funatsu, K.3
-
30
-
-
34547594044
-
Frog: A FRee Online druG 3D conformation generator
-
(Web Server issue)
-
Leite TB, Gomes D, Miteva MA, et al. Frog: a FRee Online druG 3D conformation generator. Nucleic Acids Res 2007;35(Web Server issue):W568-72
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Leite, T.B.1
Gomes, D.2
Miteva, M.A.3
-
31
-
-
65549133951
-
Cyndi: A multi-objective evolution algorithm based method for bioactive molecular conformational generation
-
Liu X, Bai F, Ouyang S, et al. Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation. BMC Bioinformatics 2009;10:101
-
(2009)
BMC Bioinformatics
, vol.10
, pp. 101
-
-
Liu, X.1
Bai, F.2
Ouyang, S.3
-
32
-
-
73349120955
-
Conformational sampling with stochastic proximity embedding and self-organizing superimposition: Establishing reasonable parameters for their practical use
-
Tresadern G, Agrafiotis DK. Conformational sampling with stochastic proximity embedding and self-organizing superimposition: establishing reasonable parameters for their practical use. J Chem Inf Model 2009;49(12):2786-2800
-
(2009)
J Chem Inf Model
, vol.49
, Issue.12
, pp. 2786-2800
-
-
Tresadern, G.1
Agrafiotis, D.K.2
-
33
-
-
61349109390
-
MED-3DMC: A new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space
-
Sperandio O, Souaille M, Delfaud F, et al. MED-3DMC: a new tool to generate 3D conformation ensembles of small molecules with a Monte Carlo sampling of the conformational space. Eur J Med Chem 2009;44(4):1405-1409
-
(2009)
Eur J Med Chem
, vol.44
, Issue.4
, pp. 1405-1409
-
-
Sperandio, O.1
Souaille, M.2
Delfaud, F.3
-
34
-
-
70450215513
-
Conformational sampling and energetics of drug-like molecules
-
Foloppe N, Chen IJ. Conformational sampling and energetics of drug-like molecules. Curr Med Chem 2009;16(26):3381-3413
-
(2009)
Curr Med Chem
, vol.16
, Issue.26
, pp. 3381-3413
-
-
Foloppe, N.1
Chen, I.J.2
-
35
-
-
67349149676
-
Exploring ligand conformations in drug design
-
Mannhold R, Kubinyi H, Folkers G, editors Wiley-VCH, Weinheim
-
Bostrom J, Grant A. Exploring ligand conformations in drug design. In: Mannhold R, Kubinyi H, Folkers G, editors. Molecular drug properties, measurement and prediction. Wiley-VCH, Weinheim: 2007:183-206
-
(2007)
Molecular Drug Properties, Measurement and Prediction
, pp. 183-206
-
-
Bostrom, J.1
Grant, A.2
-
36
-
-
0001507789
-
Pharmacophoric pattern searching and receptor matching
-
Gund P. Pharmacophoric pattern searching and receptor matching. Annu Rep Med Chem 1979;14:299-308
-
(1979)
Annu Rep Med Chem
, vol.14
, pp. 299-308
-
-
Gund, P.1
-
37
-
-
0001797110
-
Rapid generation of high quality approximate 3D molecular structures
-
Pearlman RS. Rapid generation of high quality approximate 3D molecular structures. Chem Des Automot News 1987;2(1):5-7
-
(1987)
Chem des Automot News
, vol.2
, Issue.1
, pp. 5-7
-
-
Pearlman, R.S.1
-
38
-
-
31444452744
-
Automatic generation of 3D-atomic coordinates for organic molecules
-
Gasteiger J, Rudolph C, Sadowski J. Automatic generation of 3D-atomic coordinates for organic molecules. Tetrahedron Comp Methodol 1990;3:537-547
-
(1990)
Tetrahedron Comp Methodol
, vol.3
, pp. 537-547
-
-
Gasteiger, J.1
Rudolph, C.2
Sadowski, J.3
-
39
-
-
44949267284
-
An alternative method for the alignment of molecular structures: Maximizing electrostatic and steric overlap
-
Kearsley SK, Smith GM. An alternative method for the alignment of molecular structures: maximizing electrostatic and steric overlap. Tetrahedron Comp Methodol 1990;3(6):615-633
-
(1990)
Tetrahedron Comp Methodol
, vol.3
, Issue.6
, pp. 615-633
-
-
Kearsley, S.K.1
Smith, G.M.2
-
40
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz ID, Blaney JM, Oatley SJ, et al. A geometric approach to macromolecule-ligand interactions. J Mol Biol 1982;161(2):269-288
-
(1982)
J Mol Biol
, vol.161
, Issue.2
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
-
41
-
-
0024725804
-
ALADDIN: An integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures
-
Van Drie JH, Weininger D, Martin YC. ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of three-dimensional molecular structures. J Comput Aided Mol Des 1989;3(3):225-251
-
(1989)
J Comput Aided Mol des
, vol.3
, Issue.3
, pp. 225-251
-
-
Van Drie, J.H.1
Weininger, D.2
Martin, Y.C.3
-
42
-
-
0028522982
-
Flexibases: A way to enhance the use of molecular docking methods
-
Kearsley SK, Underwood DJ, Sheridan RP, Miller MD. Flexibases: a way to enhance the use of molecular docking methods. J Comput Aided Mol Des 1994;8(5):565-582
-
(1994)
J Comput Aided Mol des
, vol.8
, Issue.5
, pp. 565-582
-
-
Kearsley, S.K.1
Underwood, D.J.2
Sheridan, R.P.3
Miller, M.D.4
-
43
-
-
0028412035
-
FLOG: A system to select "quasi-flexible ligands complementary to a receptor of known three-dimensional structure
-
Miller MD, Kearsley SK, Underwood DJ, Sheridan RP. FLOG: a system to select "quasi-flexible ligands complementary to a receptor of known three-dimensional structure. J Comput Aided Mol Des 1994;8(2):153-174
-
(1994)
J Comput Aided Mol des
, vol.8
, Issue.2
, pp. 153-174
-
-
Miller, M.D.1
Kearsley, S.K.2
Underwood, D.J.3
Sheridan, R.P.4
-
44
-
-
0025470173
-
Automated conformational analysis and structure generation: Algorithms for molecular perception
-
Leach AR, Dolata DP, Prout K. Automated conformational analysis and structure generation: algorithms for molecular perception. J Chem Inf Comput Sci 1990;30(3):316-324
-
(1990)
J Chem Inf Comput Sci
, vol.30
, Issue.3
, pp. 316-324
-
-
Leach, A.R.1
Dolata, D.P.2
Prout, K.3
-
45
-
-
84986437005
-
Macromodel-an integrated software system for modeling organic and bioorganic molecules using molecular mechanics
-
Mohamadi F, Richards NGJ, Guida WC, et al. Macromodel-an integrated software system for modeling organic and bioorganic molecules using molecular mechanics. J Comput Chem 1990;11(4):440-467
-
(1990)
J Comput Chem
, vol.11
, Issue.4
, pp. 440-467
-
-
Mohamadi, F.1
Ngj, R.2
Guida, W.C.3
-
46
-
-
0142236572
-
Low mode search. An efficient, automated computational method for conformational analysis: Application to cyclic and acyclic alkanes and cyclic peptides
-
Kolossvary I, Guida WC. Low mode search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides. J Am Chem Soc 1996;118(21):5011-5019
-
(1996)
J Am Chem Soc
, vol.118
, Issue.21
, pp. 5011-5019
-
-
Kolossvary, I.1
Guida, W.C.2
-
47
-
-
77956805796
-
-
ROTATE, Germany. Available from
-
ROTATE is available from Molecular Networks Erlagen, Germany. Available from: http://www. molecular-networks.com
-
Molecular Networks Erlagen
-
-
-
48
-
-
77956797957
-
-
OMEGA is available from Santa Fe, NM, USA. Available from
-
OMEGA is available from OpenEye Scientific Software Inc. Santa Fe, NM, USA. Available from: http://www. eyesopen.com
-
-
-
-
49
-
-
84884672735
-
-
is available from Accelrys, Inc. San Diego, CA, USA. Available from
-
Catalyst is available from Accelrys, Inc. San Diego, CA, USA. Available from:http://www.accelrys.com
-
Catalyst
-
-
-
51
-
-
43049146552
-
MS-DOCK: Accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening
-
Sauton N, Lagorce D, Villoutreix BO, Miteva MA. MS-DOCK: accurate multiple conformation generator and rigid docking protocol for multi-step virtual ligand screening. BMC Bioinformatics 2008;9:184
-
(2008)
BMC Bioinformatics
, vol.9
, pp. 184
-
-
Sauton, N.1
Lagorce, D.2
Villoutreix, B.O.3
Miteva, M.A.4
-
53
-
-
66149105428
-
Beyond the virtual screening paradigm: Structure-based searching for new lead compounds
-
Schlosser J, Rarey M. Beyond the virtual screening paradigm: structure-based searching for new lead compounds. J Chem Inf Model 2009;49(4):800-809
-
(2009)
J Chem Inf Model
, vol.49
, Issue.4
, pp. 800-809
-
-
Schlosser, J.1
Rarey, M.2
-
54
-
-
70350340728
-
The role of dynamic conformational ensembles in biomolecular recognition
-
Boehr DD, Nussinov R, Wright PE. The role of dynamic conformational ensembles in biomolecular recognition. Nat Chem Biol 2009;5(11):789-796
-
(2009)
Nat Chem Biol
, vol.5
, Issue.11
, pp. 789-796
-
-
Boehr, D.D.1
Nussinov, R.2
Wright, P.E.3
-
55
-
-
64049102289
-
Binding of small-molecule ligands to proteins: "What you see" is not always "what you get"
-
Mobley DL, Dill KA. Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure 2009;17(4):489-498
-
(2009)
Structure
, vol.17
, Issue.4
, pp. 489-498
-
-
Mobley, D.L.1
Dill, K.A.2
-
56
-
-
33746626424
-
Representation of target-bound drugs by computed conformers: Implications for conformational libraries
-
Gunther S, Senger C, Michalsky E, et al. Representation of target-bound drugs by computed conformers: implications for conformational libraries. BMC Bioinformatics 2006;7:293
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 293
-
-
Gunther, S.1
Senger, C.2
Michalsky, E.3
-
57
-
-
67650097333
-
Novel method for the evaluation of 3D conformation generators
-
Takagi T, Amano M, Tomimoto M. Novel method for the evaluation of 3D conformation generators. J Chem Inf Model 2009;49(6):1377-1388
-
(2009)
J Chem Inf Model
, vol.49
, Issue.6
, pp. 1377-1388
-
-
Takagi, T.1
Amano, M.2
Tomimoto, M.3
-
58
-
-
70350501158
-
Conformational sampling for large-scale virtual screening: Accuracy versus ensemble size
-
Griewel A, Kayser O, Schlosser J, Rarey M. Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. J Chem Inf Model 2009;49(10):2303-2311
-
(2009)
J Chem Inf Model
, vol.49
, Issue.10
, pp. 2303-2311
-
-
Griewel, A.1
Kayser, O.2
Schlosser, J.3
Rarey, M.4
-
59
-
-
0029025224
-
Conformational changes of small molecules binding to proteins
-
Nicklaus MC, Wang S, Driscoll JS, Milne GW. Conformational changes of small molecules binding to proteins. Bioorg Med Chem 1995;3(4):411-428
-
(1995)
Bioorg Med Chem
, vol.3
, Issue.4
, pp. 411-428
-
-
Nicklaus, M.C.1
Wang, S.2
Driscoll, J.S.3
Milne, G.W.4
-
60
-
-
11344267679
-
Receptor rigidity and ligand mobility in trypsin-ligand complexes
-
Guvench O, Price DJ, Brooks CL, III. Receptor rigidity and ligand mobility in trypsin-ligand complexes. Proteins 2005;58(2):407-417
-
(2005)
Proteins
, vol.58
, Issue.2
, pp. 407-417
-
-
Guvench, O.1
Price, D.J.2
Brooks Iii, C.L.3
-
61
-
-
0032112610
-
Conformational energy penalties of protein-bound ligands
-
Bostrom J, Norrby PO, Liljefors T. Conformational energy penalties of protein-bound ligands. J Comput Aided Mol Des 1998;12(4):383-396
-
(1998)
J Comput Aided Mol des
, vol.12
, Issue.4
, pp. 383-396
-
-
Bostrom, J.1
Norrby, P.O.2
Liljefors, T.3
-
62
-
-
60749137646
-
Toward accurate relative energy predictions of the bioactive conformation of drugs
-
Butler KT, Luque FJ, Barril X. Toward accurate relative energy predictions of the bioactive conformation of drugs. J Comput Chem 2009;30(4):601-610
-
(2009)
J Comput Chem
, vol.30
, Issue.4
, pp. 601-610
-
-
Butler, K.T.1
Luque, F.J.2
Barril, X.3
-
63
-
-
77956840975
-
-
is available from Chemical Computing Group, Montreal, Quebec, Canada
-
MOE is available from Chemical Computing Group, Montreal, Quebec, Canada. Available from: http://www. chemcomp.com
-
MOE
-
-
-
64
-
-
0035555863
-
Reproducing the conformations of protein-bound ligands: A critical evaluation of several popular conformational searching tools
-
Bostrom J. Reproducing the conformations of protein-bound ligands: a critical evaluation of several popular conformational searching tools. J Comput Aided Mol Des 2001;15(12):1137-1152
-
(2001)
J Comput Aided Mol des
, vol.15
, Issue.12
, pp. 1137-1152
-
-
Bostrom, J.1
-
65
-
-
0029320502
-
Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: Comparison of predicted and experimental conformations of inhibitors of three enzymes
-
McMartin C, Bohacek RS. Flexible matching of test ligands to a 3D pharmacophore using a molecular superposition force field: comparison of predicted and experimental conformations of inhibitors of three enzymes. J Comput Aided Mol Des 1995;9(3):237-250
-
(1995)
J Comput Aided Mol des
, vol.9
, Issue.3
, pp. 237-250
-
-
McMartin, C.1
Bohacek, R.S.2
-
66
-
-
0031181346
-
QXP: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C, Bohacek RS. QXP: powerful, rapid computer algorithms for structure-based drug design. J Comput Aided Mol Des 1997;11(4):333-344
-
(1997)
J Comput Aided Mol des
, vol.11
, Issue.4
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
67
-
-
0347296066
-
Assessing the performance of OMEGA with respect to retrieving bioactive conformations
-
Bostrom J, Greenwood JR, Gottfries J. Assessing the performance of OMEGA with respect to retrieving bioactive conformations. J Mol Graph Model 2003;21(5):449-462
-
(2003)
J Mol Graph Model
, vol.21
, Issue.5
, pp. 449-462
-
-
Bostrom, J.1
Greenwood, J.R.2
Gottfries, J.3
-
68
-
-
0027955787
-
Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins
-
Abagyan R, Totrov M. Biased probability Monte Carlo conformational searches and electrostatic calculations for peptides and proteins. J Mol Biol 1994;235(3):983-1002
-
(1994)
J Mol Biol
, vol.235
, Issue.3
, pp. 983-1002
-
-
Abagyan, R.1
Totrov, M.2
-
69
-
-
54249090791
-
Conformational sampling of drug like molecules with MOE and catalyst: Implications for pharmacophore modeling and virtual screening
-
Chen IJ, Foloppe N. Conformational sampling of drug like molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening. J Chem Inf Model 2008;48(9):1773-1791
-
(2008)
J Chem Inf Model
, vol.48
, Issue.9
, pp. 1773-1791
-
-
Chen, I.J.1
Foloppe, N.2
-
70
-
-
50249126705
-
A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers
-
Dorfman RJ, Smith KM, Masek BB, Clark RD. A knowledge-based approach to generating diverse but energetically representative ensembles of ligand conformers. J Comput Aided Mol Des 2008;22(9):681-691
-
(2008)
J Comput Aided Mol des
, vol.22
, Issue.9
, pp. 681-691
-
-
Dorfman, R.J.1
Smith, K.M.2
Masek, B.B.3
Clark, R.D.4
-
71
-
-
77952750760
-
Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: Comparison to programs MOE and catalyst
-
Chen IJ, Foloppe N. Drug-like bioactive structures and conformational coverage with the LigPrep/ConfGen suite: comparison to programs MOE and catalyst. J Chem Inf Model 2010;50(5):822-839
-
J Chem Inf Model 2010
, vol.50
, Issue.5
, pp. 822-839
-
-
Chen, I.J.1
Foloppe, N.2
-
72
-
-
18344382014
-
Comparative analysis of protein-bound ligand conformations with respect to catalysts conformational space subsampling algorithms
-
Kirchmair J, Laggner C, Wolber G, Langer T. Comparative analysis of protein-bound ligand conformations with respect to catalysts conformational space subsampling algorithms. J Chem Inf Model 2005;45(2):422-430
-
(2005)
J Chem Inf Model
, vol.45
, Issue.2
, pp. 422-430
-
-
Kirchmair, J.1
Laggner, C.2
Wolber, G.3
Langer, T.4
-
73
-
-
35248863951
-
CAESAR: A new conformer generation algorithm based on recursive build up and local rotational symmetry consideration
-
Li J, Ehlers T, Sutter J, et al. CAESAR: a new conformer generation algorithm based on recursive build up and local rotational symmetry consideration. J Chem Inf Model 2007;47(5):1923-1932
-
(2007)
J Chem Inf Model
, vol.47
, Issue.5
, pp. 1923-1932
-
-
Li, J.1
Ehlers, T.2
Sutter, J.3
-
74
-
-
37249065124
-
Generating conformer ensembles using a multiobjective genetic algorithm
-
Vainio MJ, Johnson MS. Generating conformer ensembles using a multiobjective genetic algorithm. J Chem Inf Model 2007;47(6):2462-2474
-
(2007)
J Chem Inf Model
, vol.47
, Issue.6
, pp. 2462-2474
-
-
Vainio, M.J.1
Johnson, M.S.2
-
75
-
-
34547653846
-
Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space
-
Borodina YV, Bolton E, Fontaine F, Bryant SH. Assessment of conformational ensemble sizes necessary for specific resolutions of coverage of conformational space. J Chem Inf Model 2007;47(4):1428-1437
-
(2007)
J Chem Inf Model
, vol.47
, Issue.4
, pp. 1428-1437
-
-
Borodina, Y.V.1
Bolton, E.2
Fontaine, F.3
Bryant, S.H.4
-
76
-
-
0029277503
-
Analysis of conformational coverage. 1. Validation and estimation of coverage
-
Smellie A, Kahn SD, Teig SL. Analysis of conformational coverage. 1. Validation and estimation of coverage. J Chem Inf Comput Sci 1995;35(2):285-294
-
(1995)
J Chem Inf Comput Sci
, vol.35
, Issue.2
, pp. 285-294
-
-
Smellie, A.1
Kahn, S.D.2
Teig, S.L.3
-
77
-
-
0029276206
-
Analysis of conformational coverage. 2. applications of conformational models
-
Smellie A, Kahn SD, Teig SL. Analysis of conformational coverage. 2. applications of conformational models. J Chem Inf Comput Sci 1995;35(2):295-304
-
(1995)
J Chem Inf Comput Sci
, vol.35
, Issue.2
, pp. 295-304
-
-
Smellie, A.1
Kahn, S.D.2
Teig, S.L.3
-
78
-
-
0006298689
-
Correlation of structure and function in enzyme action
-
Koshland DE Jr. Correlation of structure and function in enzyme action. Science 1963;142:1533-1541
-
(1963)
Science
, vol.142
, pp. 1533-1541
-
-
Koshland Jr., D.E.1
-
79
-
-
2342614067
-
Conformation changes at the active site during enzyme Action
-
Koshland DE Jr. Conformation changes at the active site during enzyme Action. Fed Proc 1964;23:719-726
-
(1964)
Fed Proc
, vol.23
, pp. 719-726
-
-
Koshland Jr., D.E.1
-
80
-
-
0000558316
-
Evidence for conformation changes induced by substrates of phosphoglucomutase
-
Yankeelov JA Jr, Koshland DE Jr. Evidence for conformation changes induced by substrates of phosphoglucomutase. J Biol Chem 1965;240:1593-1602
-
(1965)
J Biol Chem
, vol.240
, pp. 1593-1602
-
-
Yankeelov Jr., J.A.1
Koshland Jr., D.E.2
-
81
-
-
40749129010
-
Preference of small molecules for local minimum conformations when binding to proteins
-
Wang Q, Pang YP. Preference of small molecules for local minimum conformations when binding to proteins. PLoS One 2007;2(9):e820
-
(2007)
PLoS One
, vol.2
, Issue.9
-
-
Wang, Q.1
Pang, Y.P.2
-
82
-
-
0032197018
-
Do active site conformations of small ligands correspond to low free-energy solution structures?
-
Vieth M, Hirst JD, Brooks CL III. Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput Aided Mol Des 1998;12(6):563-572
-
(1998)
J Comput Aided Mol des
, vol.12
, Issue.6
, pp. 563-572
-
-
Vieth, M.1
Hirst, J.D.2
Brooks Iii, C.L.3
-
83
-
-
33749242759
-
Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding
-
Tirado-Rives J, Jorgensen WL. Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding. J Med Chem 2006;49(20):5880-5884
-
(2006)
J Med Chem
, vol.49
, Issue.20
, pp. 5880-5884
-
-
Tirado-Rives, J.1
Jorgensen, W.L.2
-
84
-
-
77955658562
-
Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble
-
Yongye AB, Bender A, Martinez-Mayorga K. Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble. J Comput Aided Mol Des 2010;24(8):675-686
-
J Comput Aided Mol des 2010
, vol.24
, Issue.8
, pp. 675-686
-
-
Yongye, A.B.1
Bender, A.2
Martinez-Mayorga, K.3
-
85
-
-
31344462177
-
Conformational diversity of ligands bound to proteins
-
Stockwell GR, Thornton JM. Conformational diversity of ligands bound to proteins. J Mol Biol 2006;356(4):928-944
-
(2006)
J Mol Biol
, vol.356
, Issue.4
, pp. 928-944
-
-
Stockwell, G.R.1
Thornton, J.M.2
-
86
-
-
11144239572
-
Targacept active conformation search: A new method for predicting the conformation of a ligand bound to its protein target
-
Klucik J, Xiao YD, Hammond PS, et al. Targacept active conformation search: a new method for predicting the conformation of a ligand bound to its protein target. J Med Chem 2004;47(27):6831-6839
-
(2004)
J Med Chem
, vol.47
, Issue.27
, pp. 6831-6839
-
-
Klucik, J.1
Xiao, Y.D.2
Hammond, P.S.3
-
87
-
-
54249157493
-
Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns
-
Auer J, Bajorath J. Distinguishing between bioactive and modeled compound conformations through mining of emerging chemical patterns. J Chem Inf Model 2008;48(9):1747-1753
-
(2008)
J Chem Inf Model
, vol.48
, Issue.9
, pp. 1747-1753
-
-
Auer, J.1
Bajorath, J.2
-
88
-
-
25444449536
-
SuperLigands - A database of ligand structures derived from the protein data bank
-
Michalsky E, Dunkel M, Goede A, Preissner R. SuperLigands-a database of ligand structures derived from the protein data bank. BMC Bioinformatics 2005;6:122
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 122
-
-
Michalsky, E.1
Dunkel, M.2
Goede, A.3
Preissner, R.4
-
89
-
-
33751234960
-
A distance geometry heuristic for expanding the range of geometries sampled during conformational search
-
Izrailev S, Zhu F, Agrafiotis DK. A distance geometry heuristic for expanding the range of geometries sampled during conformational search. J Comput Chem 2006;27(16):1962-1969
-
(2006)
J Comput Chem
, vol.27
, Issue.16
, pp. 1962-1969
-
-
Izrailev, S.1
Zhu, F.2
Agrafiotis, D.K.3
-
91
-
-
34250839505
-
Conformational sampling of bioactive molecules: A comparative study
-
Agrafiotis DK, Gibbs AC, Zhu F, et al. Conformational sampling of bioactive molecules: a comparative study. J Chem Inf Model 2007;47(3):1067-1086
-
(2007)
J Chem Inf Model
, vol.47
, Issue.3
, pp. 1067-1086
-
-
Agrafiotis, D.K.1
Gibbs, A.C.2
Zhu, F.3
-
93
-
-
33845786627
-
MIMUMBA revisited: Torsion angle rules for conformer generation derived from X-ray structures
-
Sadowski J, Bostrom J. MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures. J Chem Inf Model 2006;46(6):2305-2309
-
(2006)
J Chem Inf Model
, vol.46
, Issue.6
, pp. 2305-2309
-
-
Sadowski, J.1
Bostrom, J.2
-
94
-
-
0001752768
-
The Cambridge Structural Database: A quarter of a million crystal structures and rising
-
Allen FH. The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr B 2002;58(Pt 3 Pt 1):380-388
-
(2002)
Acta Crystallogr B
, vol.58
, Issue.PART 3
, pp. 380-388
-
-
Allen, F.H.1
-
95
-
-
37249023634
-
Torsion angle preference and energetics of small-molecule ligands bound to proteins
-
Hao MH, Haq O, Muegge I. Torsion angle preference and energetics of small-molecule ligands bound to proteins. J Chem Inf Model 2007;47(6):2242-2252
-
(2007)
J Chem Inf Model
, vol.47
, Issue.6
, pp. 2242-2252
-
-
Hao, M.H.1
Haq, O.2
Muegge, I.3
-
96
-
-
39449105474
-
Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis
-
Brameld KA, Kuhn B, Reuter DC, Stahl M. Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis. J Chem Inf Model 2008;48(1):1-24
-
(2008)
J Chem Inf Model
, vol.48
, Issue.1
, pp. 1-24
-
-
Brameld, K.A.1
Kuhn, B.2
Reuter, D.C.3
Stahl, M.4
-
97
-
-
35248839997
-
Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms
-
Diago LA, Morell P, Aguilera L, Moreno E. Setting up a large set of protein-ligand PDB complexes for the development and validation of knowledge-based docking algorithms. BMC Bioinformatics 2007;8:310
-
(2007)
BMC Bioinformatics
, vol.8
, pp. 310
-
-
Diago, L.A.1
Morell, P.2
Aguilera, L.3
Moreno, E.4
-
98
-
-
33750991346
-
Benchmarking sets for molecular docking
-
Huang N, Shoichet BK, Irwin JJ. Benchmarking sets for molecular docking. J Med Chem 2006;49(23):6789-6801
-
(2006)
J Med Chem
, vol.49
, Issue.23
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
99
-
-
77951987154
-
ConfGen: A conformational search method for efficient generation of bioactive conformers
-
Watts KS, Dalal P, Murphy RB, et al. ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 2010;50(4):534-546
-
J Chem Inf Model 2010
, vol.50
, Issue.4
, pp. 534-546
-
-
Watts, K.S.1
Dalal, P.2
Murphy, R.B.3
|