-
1
-
-
0037008160
-
Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
-
Gohlke H., Klebe G. Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors. Angew Chem Int Ed Engl. 41:2002;2644-2676
-
(2002)
Angew Chem Int Ed Engl
, vol.41
, pp. 2644-2676
-
-
Gohlke, H.1
Klebe, G.2
-
3
-
-
1642540577
-
Evaluation of docking performance: Comparative data on docking algorithms
-
A thorough evaluation of several docking programs with respect to their ability to reproduce experimentally observed poses and rank them, showing that the 'best' pose is usually not the highest ranking one.
-
Kontoyianni M., McClellan L.M., Sokol G.S. Evaluation of docking performance: comparative data on docking algorithms. J Med Chem. 47:2004;558-565 A thorough evaluation of several docking programs with respect to their ability to reproduce experimentally observed poses and rank them, showing that the 'best' pose is usually not the highest ranking one.
-
(2004)
J Med Chem
, vol.47
, pp. 558-565
-
-
Kontoyianni, M.1
McClellan, L.M.2
Sokol, G.S.3
-
4
-
-
36148994401
-
Recent advances in virtual ligand screening
-
Blake J.F., Laird E.R. Recent advances in virtual ligand screening. Annu Rep Med Chem. 38:2003;305-314
-
(2003)
Annu Rep Med Chem
, vol.38
, pp. 305-314
-
-
Blake, J.F.1
Laird, E.R.2
-
5
-
-
0037107887
-
Structure-based virtual screening: An overview
-
Lyne P.D. Structure-based virtual screening: an overview. Drug Discov Today. 7:2002;1047-1055
-
(2002)
Drug Discov Today
, vol.7
, pp. 1047-1055
-
-
Lyne, P.D.1
-
6
-
-
0038792292
-
Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking
-
Vangrevelinghe E., Zimmermann K., Schoepfer J., Portmann R., Fabbro D., Furet P. Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. J Med Chem. 46:2003;2656-2662
-
(2003)
J Med Chem
, vol.46
, pp. 2656-2662
-
-
Vangrevelinghe, E.1
Zimmermann, K.2
Schoepfer, J.3
Portmann, R.4
Fabbro, D.5
Furet, P.6
-
8
-
-
0037103119
-
Successful virtual screening for novel inhibitors of human carbonic anhydrase: Strategy and experimental confirmation
-
Gruneberg S., Stubbs M.T., Klebe G. Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J Med Chem. 45:2002;3588-3602
-
(2002)
J Med Chem
, vol.45
, pp. 3588-3602
-
-
Gruneberg, S.1
Stubbs, M.T.2
Klebe, G.3
-
9
-
-
0345269288
-
Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis
-
Brenk R., Naerum L., Gradler U., Gerber H.D., Garcia G.A., Reuter K., Stubbs M.T., Klebe G. Virtual screening for submicromolar leads of tRNA-guanine transglycosylase based on a new unexpected binding mode detected by crystal structure analysis. J Med Chem. 46:2003;1133-1143
-
(2003)
J Med Chem
, vol.46
, pp. 1133-1143
-
-
Brenk, R.1
Naerum, L.2
Gradler, U.3
Gerber, H.D.4
Garcia, G.A.5
Reuter, K.6
Stubbs, M.T.7
Klebe, G.8
-
12
-
-
2942564021
-
Pursuing the leadlikeness concept in pharmaceutical research
-
in press.
-
Hann MM, Oprea TI: Pursuing the leadlikeness concept in pharmaceutical research. Curr Opin Chem Biol 2004, 8: in press.
-
(2004)
Curr Opin Chem Biol
, pp. 8
-
-
Hann, M.M.1
Oprea, T.I.2
-
13
-
-
1642357706
-
The many roles of computation in drug discovery
-
Jorgensen W.L. The many roles of computation in drug discovery. Science. 303:2004;1813-1818
-
(2004)
Science
, vol.303
, pp. 1813-1818
-
-
Jorgensen, W.L.1
-
14
-
-
3242888975
-
Integrating virtual screening in lead discovery
-
in press.
-
Oprea TI, Matter H: Integrating virtual screening in lead discovery. Curr Opin Chem Biol 2004, 8: in press.
-
(2004)
Curr Opin Chem Biol
, vol.8
-
-
Oprea, T.I.1
Matter, H.2
-
16
-
-
3342990667
-
-
Magnet Documentation on World Wide Web
-
Magnet Documentation on World Wide Web URL: http://www.metaphorics.com/ products/magnet/index.html.
-
-
-
-
17
-
-
0036022958
-
Flexible docking under pharmacophore type constraints
-
Development and application of pharmacophore type constraints for post-processing filters and for guiding the searching algorithm of FlexX towards biased poses.
-
Hindle S.A., Rarey M., Buning C., Lengauer T. Flexible docking under pharmacophore type constraints. J Comput Aided Mol Des. 16:2002;129-149 Development and application of pharmacophore type constraints for post-processing filters and for guiding the searching algorithm of FlexX towards biased poses.
-
(2002)
J Comput Aided Mol des
, vol.16
, pp. 129-149
-
-
Hindle, S.A.1
Rarey, M.2
Buning, C.3
Lengauer, T.4
-
18
-
-
0038185582
-
Binding site characteristics in structure-based virtual screening: Evaluation of current docking tools
-
Schulz-Gasch T., Stahl M. Binding site characteristics in structure-based virtual screening: evaluation of current docking tools. J Mol Model (Online). 9:2003;47-57
-
(2003)
J Mol Model (Online)
, vol.9
, pp. 47-57
-
-
Schulz-Gasch, T.1
Stahl, M.2
-
19
-
-
3343021675
-
-
FRED Documentation on World Wide Web
-
FRED Documentation on World Wide Web URL: http://www.eyesopen.com/ products/applications/fred.html.
-
-
-
-
20
-
-
3343021674
-
-
SEA Documentation on World Wide Web
-
SEA Documentation on World Wide Web URL: http://www.metaphorics.com/ products/magnet/sea/index.html.
-
-
-
-
21
-
-
3343004430
-
The FlexX database docking environment - Rational extraction of receptor based pharmacophores
-
Clear description of an integrated expert system for handling and analysis of IPs, with an application to extract and apply receptor-based pharmacophores.
-
Claussen H., Gastreich M., Apelt V., Greene J., Hindle S.A., Lemmen C. The FlexX database docking environment - rational extraction of receptor based pharmacophores. Curr Drug Discov Technol. 1:2004;49-60 Clear description of an integrated expert system for handling and analysis of IPs, with an application to extract and apply receptor-based pharmacophores.
-
(2004)
Curr Drug Discov Technol
, vol.1
, pp. 49-60
-
-
Claussen, H.1
Gastreich, M.2
Apelt, V.3
Greene, J.4
Hindle, S.A.5
Lemmen, C.6
-
22
-
-
0346962971
-
Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional protein-ligand binding interactions
-
Elegant implementation of fingerprinting methodology to organize, analyze and visualize IPs. Applications are described that include binding mode analysis, analysis of IPs across related targets and post-processing filters.
-
Deng Z., Chuaqui C., Singh J. Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. J Med Chem. 47:2004;337-344 Elegant implementation of fingerprinting methodology to organize, analyze and visualize IPs. Applications are described that include binding mode analysis, analysis of IPs across related targets and post-processing filters.
-
(2004)
J Med Chem
, vol.47
, pp. 337-344
-
-
Deng, Z.1
Chuaqui, C.2
Singh, J.3
-
23
-
-
0002273571
-
Virtual screening in lead discovery: A viewpoint
-
Oprea T.I. Virtual screening in lead discovery: a viewpoint. Mol. 7:2002;51-62
-
(2002)
Mol
, vol.7
, pp. 51-62
-
-
Oprea, T.I.1
-
24
-
-
0037413569
-
Surface descriptors for protein-ligand affinity prediction
-
Zamora I., Oprea T., Cruciani G., Pastor M., Ungell A.L. Surface descriptors for protein-ligand affinity prediction. J Med Chem. 46:2003;25-33
-
(2003)
J Med Chem
, vol.46
, pp. 25-33
-
-
Zamora, I.1
Oprea, T.2
Cruciani, G.3
Pastor, M.4
Ungell, A.L.5
-
25
-
-
0029000922
-
Prediction of drug binding affinities by comparative binding energy analysis
-
Ortiz A.R., Pisabarro M.T., Gago F., Wade R.C. Prediction of drug binding affinities by comparative binding energy analysis. J Med Chem. 38:1995;2681-2691
-
(1995)
J Med Chem
, vol.38
, pp. 2681-2691
-
-
Ortiz, A.R.1
Pisabarro, M.T.2
Gago, F.3
Wade, R.C.4
-
26
-
-
0035866695
-
Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes
-
Use of experimental affinities, 3D structures of target-ligand complexes and statistical methods to determine which residues contribute most to the variance in affinities, to predict affinities of novel structures, and to guide structure-based design.
-
Wang T., Wade R.C. Comparative binding energy (COMBINE) analysis of influenza neuraminidase-inhibitor complexes. J Med Chem. 44:2001;961-971 Use of experimental affinities, 3D structures of target-ligand complexes and statistical methods to determine which residues contribute most to the variance in affinities, to predict affinities of novel structures, and to guide structure-based design.
-
(2001)
J Med Chem
, vol.44
, pp. 961-971
-
-
Wang, T.1
Wade, R.C.2
-
27
-
-
0842304437
-
Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors
-
Murcia M., Ortiz A.R. Virtual screening with flexible docking and COMBINE-based models. Application to a series of factor Xa inhibitors. J Med Chem. 47:2004;805-820
-
(2004)
J Med Chem
, vol.47
, pp. 805-820
-
-
Murcia, M.1
Ortiz, A.R.2
-
28
-
-
0037068492
-
DrugScore meets CoMFA: Adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein
-
Gohlke H., Klebe G. DrugScore meets CoMFA: adaptation of fields for molecular comparison (AFMoC) or how to tailor knowledge-based pair-potentials to a particular protein. J Med Chem. 45:2002;4153-4170
-
(2002)
J Med Chem
, vol.45
, pp. 4153-4170
-
-
Gohlke, H.1
Klebe, G.2
-
29
-
-
0028155689
-
A new method for predicting binding affinity in computer-aided drug design
-
Aqvist J., Medina C., Samuelsson J.E. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:1994;385-391
-
(1994)
Protein Eng
, vol.7
, pp. 385-391
-
-
Aqvist, J.1
Medina, C.2
Samuelsson, J.E.3
-
31
-
-
0035950792
-
New linear interaction method for binding affinity calculations using a continuum solvent model
-
Zhou R., Friesner R.A., Ghosh A., Rizzo R.C., Jorgensen W.L., Levy R.M. New linear interaction method for binding affinity calculations using a continuum solvent model. J Phys Chem B. 105:2001;10388-10397
-
(2001)
J Phys Chem B
, vol.105
, pp. 10388-10397
-
-
Zhou, R.1
Friesner, R.A.2
Ghosh, A.3
Rizzo, R.C.4
Jorgensen, W.L.5
Levy, R.M.6
-
32
-
-
0038704856
-
Calculation of the binding affinity of beta-secretase inhibitors using the linear interaction energy method
-
Tounge B.A., Reynolds C.H. Calculation of the binding affinity of beta-secretase inhibitors using the linear interaction energy method. J Med Chem. 46:2003;2074-2082
-
(2003)
J Med Chem
, vol.46
, pp. 2074-2082
-
-
Tounge, B.A.1
Reynolds, C.H.2
-
33
-
-
0035811458
-
A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities
-
Terp G.E., Johansen B.N., Christensen I.T., Jorgensen F.S. A new concept for multidimensional selection of ligand conformations (MultiSelect) and multidimensional scoring (MultiScore) of protein-ligand binding affinities. J Med Chem. 44:2001;2333-2343
-
(2001)
J Med Chem
, vol.44
, pp. 2333-2343
-
-
Terp, G.E.1
Johansen, B.N.2
Christensen, I.T.3
Jorgensen, F.S.4
-
34
-
-
0346996357
-
Improving structure-based virtual screening by multivariate analysis of scoring data
-
Training classifiers to distinguish known actives from inactives by applying multivariate statistical methods to multidimensional scoring data from SVS of the training set, and using the classifiers in a subsequent SVS of a test set.
-
Jacobsson M., Liden P., Stjernschantz E., Bostrom H., Norinder U. Improving structure-based virtual screening by multivariate analysis of scoring data. J Med Chem. 46:2003;5781-5789 Training classifiers to distinguish known actives from inactives by applying multivariate statistical methods to multidimensional scoring data from SVS of the training set, and using the classifiers in a subsequent SVS of a test set.
-
(2003)
J Med Chem
, vol.46
, pp. 5781-5789
-
-
Jacobsson, M.1
Liden, P.2
Stjernschantz, E.3
Bostrom, H.4
Norinder, U.5
-
35
-
-
0036510961
-
Identification and mapping of small-molecule binding sites in proteins: Computational tools for structure-based drug design
-
Sotriffer C., Klebe G. Identification and mapping of small-molecule binding sites in proteins: computational tools for structure-based drug design. Farmaco. 57:2002;243-251
-
(2002)
Farmaco
, vol.57
, pp. 243-251
-
-
Sotriffer, C.1
Klebe, G.2
-
36
-
-
0034284367
-
Similarity-driven flexible ligand docking
-
Fradera X., Knegtel R.M., Mestres J. Similarity-driven flexible ligand docking. Proteins. 40:2000;623-636
-
(2000)
Proteins
, vol.40
, pp. 623-636
-
-
Fradera, X.1
Knegtel, R.M.2
Mestres, J.3
-
37
-
-
3343002717
-
-
DockIt Documentation on World Wide Web
-
DockIt Documentation on World Wide Web URL: http://www.metaphorics.com/ products/dockit.html.
-
-
-
-
38
-
-
3343021676
-
-
GOLD Documentation on World Wide Web
-
GOLD Documentation on World Wide Web URL: http://www.ccdc.cam.ac.uk/ products/life_sciences/gold/.
-
-
-
-
40
-
-
0027385177
-
Matching chemistry and shape in molecular docking
-
Shoichet B.K., Kuntz I.D. Matching chemistry and shape in molecular docking. Protein Eng. 6:1993;723-732
-
(1993)
Protein Eng
, vol.6
, pp. 723-732
-
-
Shoichet, B.K.1
Kuntz, I.D.2
-
41
-
-
0028452628
-
A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors
-
DesJarlais R.L., Dixon J.S. A shape- and chemistry-based docking method and its use in the design of HIV-1 protease inhibitors. J Comput Aided Mol Des. 8:1994;231-242
-
(1994)
J Comput Aided Mol des
, vol.8
, pp. 231-242
-
-
Desjarlais, R.L.1
Dixon, J.S.2
-
42
-
-
12444278563
-
Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: Mapping a pharmacophore for success
-
Good A.C., Cheney D.L., Sitkoff D.F., Tokarski J.S., Stouch T.R., Bassolino D.A., Krystek S.R., Li Y., Mason J.S., Perkins T.D. Analysis and optimization of structure-based virtual screening protocols. 2. Examination of docked ligand orientation sampling methodology: mapping a pharmacophore for success. J Mol Graph Model. 22:2003;31-40
-
(2003)
J Mol Graph Model
, vol.22
, pp. 31-40
-
-
Good, A.C.1
Cheney, D.L.2
Sitkoff, D.F.3
Tokarski, J.S.4
Stouch, T.R.5
Bassolino, D.A.6
Krystek, S.R.7
Li, Y.8
Mason, J.S.9
Perkins, T.D.10
-
43
-
-
0033674405
-
Virtual screening with solvation and ligand-induced complementarity
-
Schnecke V., Kuhn L.A. Virtual screening with solvation and ligand-induced complementarity. Perspect Drug Discov Des. 20:2000;171-190
-
(2000)
Perspect Drug Discov des
, vol.20
, pp. 171-190
-
-
Schnecke, V.1
Kuhn, L.A.2
-
44
-
-
0038174853
-
Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening
-
Zavodszky M.I., Sanschagrin P.C., Korde R.S., Kuhn L.A. Distilling the essential features of a protein surface for improving protein-ligand docking, scoring, and virtual screening. J Comput Aided Mol Des. 16:2002;883-902
-
(2002)
J Comput Aided Mol des
, vol.16
, pp. 883-902
-
-
Zavodszky, M.I.1
Sanschagrin, P.C.2
Korde, R.S.3
Kuhn, L.A.4
|