-
1
-
-
0008446030
-
The Tall Office Building Artistically Considered
-
Sullivan, H.L. (1896) The Tall Office Building Artistically Considered. Lippincott's Monthly Magazine, issue 57, pp. 403-409.
-
(1896)
Lippincott's Monthly Magazine
, vol.57
, pp. 403-409
-
-
Sullivan, H.L.1
-
5
-
-
0035108245
-
Biocomplexity: adaptive behavior in complex stochastic dynamical systems
-
Freeman, W.J., Kozma, R., and Werbos, P.J. (2001) Biocomplexity: adaptive behavior in complex stochastic dynamical systems. Biosystems, 59, 109-123.
-
(2001)
Biosystems
, vol.59
, pp. 109-123
-
-
Freeman, W.J.1
Kozma, R.2
Werbos, P.J.3
-
7
-
-
0004106780
-
-
University of Chicago Press, Chicago
-
Tillich, P. (1951) Systematic Theology I, University of Chicago Press, Chicago.
-
(1951)
Systematic Theology I
-
-
Tillich, P.1
-
9
-
-
0026459988
-
Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase
-
King, R.D., Muggleton, S., Lewis, R.A., and Sternberg, M.J. (1992) Drug design by machine learning: the use of inductive logic programming to model the structure-activity relationships of trimethoprim analogues binding to dihydrofolate reductase. Proc. Natl. Acad. Sci. U.S.A., 89, 11322-11326.
-
(1992)
Proc. Natl. Acad. Sci. U.S.A.
, vol.89
, pp. 11322-11326
-
-
King, R.D.1
Muggleton, S.2
Lewis, R.A.3
Sternberg, M.J.4
-
10
-
-
0015222647
-
The interpretation of protein structures: estimation of static accessibility
-
Lee, B. and Richards, F.M. (1971) The interpretation of protein structures: estimation of static accessibility. J. Mol. Biol., 55, 379-400.
-
(1971)
J. Mol. Biol.
, vol.55
, pp. 379-400
-
-
Lee, B.1
Richards, F.M.2
-
11
-
-
0021107965
-
Solventaccessible surfaces of proteins and nucleic acids
-
Connolly, M.L. (1983) Solventaccessible surfaces of proteins and nucleic acids. Science, 221, 709-713.
-
(1983)
Science
, vol.221
, pp. 709-713
-
-
Connolly, M.L.1
-
12
-
-
78650643212
-
Ultrafast shape recognition: method and applications
-
Ballester, P.J. (2011) Ultrafast shape recognition: method and applications. Future Med. Chem., 3, 65-78.
-
(2011)
Future Med. Chem.
, vol.3
, pp. 65-78
-
-
Ballester, P.J.1
-
13
-
-
77950876424
-
Molecular shape technologies in drug discovery: methods and applications
-
Ebalunode, J.O. and Zheng, W. (2010) Molecular shape technologies in drug discovery: methods and applications. Curr. Top. Med. Chem., 10, 669-679.
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 669-679
-
-
Ebalunode, J.O.1
Zheng, W.2
-
14
-
-
0023751431
-
Comparative molecular field analysis (CoMFA). 1 Effect of shape on binding of steroids to carrier proteins
-
Cramer, R. III, Patterson, D., and Bunce, J. (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 110, 5959-5967.
-
(1988)
J. Am. Chem. Soc.
, vol.110
, pp. 5959-5967
-
-
Cramer, R.1
Patterson, D.2
Bunce, J.3
-
15
-
-
0028396152
-
Distance/distance matrices
-
Randic, M., Kleiner, A., and Alba, L.D. (1994) Distance/distance matrices. J. Chem. Inf. Comput. Sci., 34, 277-286.
-
(1994)
J. Chem. Inf. Comput. Sci.
, vol.34
, pp. 277-286
-
-
Randic, M.1
Kleiner, A.2
Alba, L.D.3
-
16
-
-
0001765377
-
Infrared spectra simulation of substituted benzene derivatives on the basis of a 3D structure representation
-
Schuur, J. and Gasteiger, J. (1997) Infrared spectra simulation of substituted benzene derivatives on the basis of a 3D structure representation. Anal. Chem., 69, 2398-2405.
-
(1997)
Anal. Chem.
, vol.69
, pp. 2398-2405
-
-
Schuur, J.1
Gasteiger, J.2
-
17
-
-
0031231724
-
The utilization of reduced dimensional representations of molecular structure for rapid molecular similarity calculations
-
Robinson, D., Barlow, T., and Richards, G. (1997) The utilization of reduced dimensional representations of molecular structure for rapid molecular similarity calculations. J. Chem. Inf. Comput. Sci., 37, 943-950.
-
(1997)
J. Chem. Inf. Comput. Sci.
, vol.37
, pp. 943-950
-
-
Robinson, D.1
Barlow, T.2
Richards, G.3
-
18
-
-
0001219854
-
Deriving the 3D structure of organic molecules from their infrared spectra
-
Hemmer, M., Steinhauer, V., and Gasteiger, J. (1999) Deriving the 3D structure of organic molecules from their infrared spectra. Vib. Spectrosc., 19, 151-164.
-
(1999)
Vib. Spectrosc.
, vol.19
, pp. 151-164
-
-
Hemmer, M.1
Steinhauer, V.2
Gasteiger, J.3
-
19
-
-
0034065762
-
Modelling and prediction of soil sorption coefficients of non-ionic organic pesticides by molecular descriptors
-
Gramatica, P., Corradi, M., and Consonni, V. (2000) Modelling and prediction of soil sorption coefficients of non-ionic organic pesticides by molecular descriptors. Chemosphere, 41, 763-777.
-
(2000)
Chemosphere
, vol.41
, pp. 763-777
-
-
Gramatica, P.1
Corradi, M.2
Consonni, V.3
-
20
-
-
34547260921
-
Ultrafast shape recognition to search compound databases for similar molecular shapes
-
Ballester, P.J. and Richards, W.G. (2007) Ultrafast shape recognition to search compound databases for similar molecular shapes. J. Comput. Chem., 28, 1711-1723.
-
(2007)
J. Comput. Chem.
, vol.28
, pp. 1711-1723
-
-
Ballester, P.J.1
Richards, W.G.2
-
21
-
-
0001109246
-
A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape
-
Grant, A., Gallardo, A., and Pickup, B. (1996) A fast method of molecular shape comparison: a simple application of a Gaussian description of molecular shape. J. Comput. Chem., 17, 1653-1666.
-
(1996)
J. Comput. Chem.
, vol.17
, pp. 1653-1666
-
-
Grant, A.1
Gallardo, A.2
Pickup, B.3
-
22
-
-
0034625096
-
Molecular fields in quantitative structurepermeation relationships: the VolSurf approach
-
Cruciani, G., Crivori, P., Carrupt, P.A., and Testa, B. (2000) Molecular fields in quantitative structurepermeation relationships: the VolSurf approach. J. Mol. Struct., 503, 17-30.
-
(2000)
J. Mol. Struct.
, vol.503
, pp. 17-30
-
-
Cruciani, G.1
Crivori, P.2
Carrupt, P.A.3
Testa, B.4
-
23
-
-
0036589142
-
Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 2 Application of the novel 3D molecular descriptors to QSAR/QSPR studies
-
Consonni, V., Todeschini, R., Pavan, M., and Gramatica, P. (2002) Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 2. Application of the novel 3D molecular descriptors to QSAR/QSPR studies. J. Chem. Inf. Comput. Sci., 42, 693-705.
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, pp. 693-705
-
-
Consonni, V.1
Todeschini, R.2
Pavan, M.3
Gramatica, P.4
-
24
-
-
0002016068
-
''Shrink-wrap'' surfaces: a new method for incorporating shape into pharmacophoric 3D database searching
-
Van Drie, J.H. (1997) ''Shrink-wrap'' surfaces: a new method for incorporating shape into pharmacophoric 3D database searching. J. Chem. Inf. Comput. Sci., 37, 38-42.
-
(1997)
J. Chem. Inf. Comput. Sci.
, vol.37
, pp. 38-42
-
-
Van Drie, J.H.1
-
25
-
-
0000720929
-
Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces
-
Ritchie, D. and Kemp, G. (1999) Fast computation, rotation, and comparison of low resolution spherical harmonic molecular surfaces. J. Comput. Chem., 20, 383-395.
-
(1999)
J. Comput. Chem.
, vol.20
, pp. 383-395
-
-
Ritchie, D.1
Kemp, G.2
-
26
-
-
19544389524
-
Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons
-
Morris, R.J., Najmanovich, R.J., Kahraman, A., and Thornton, J.M. (2005) Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons. Bioinformatics, 21, 2347-2355.
-
(2005)
Bioinformatics
, vol.21
, pp. 2347-2355
-
-
Morris, R.J.1
Najmanovich, R.J.2
Kahraman, A.3
Thornton, J.M.4
-
27
-
-
79958831732
-
Using spherical harmonic surface property representations for ligand-based virtual screening
-
Ṕerez-Nueno, V.I., Venkatraman, V., Mavridis, L., Clark, T., and Ritchie, D.W. (2011) Using spherical harmonic surface property representations for ligand-based virtual screening. Mol. Inf., 30, 151-159.
-
(2011)
Mol. Inf.
, vol.30
, pp. 151-159
-
-
Ṕerez-Nueno, V.I.1
Venkatraman, V.2
Mavridis, L.3
Clark, T.4
Ritchie, D.W.5
-
28
-
-
44949151490
-
Parafrag-an approach for surface-based similarity comparison of molecular fragments
-
Jakobi, A.J., Mauser, H., and Clark, T. (2008) Parafrag-an approach for surface-based similarity comparison of molecular fragments. J. Mol. Model., 14, 547-558.
-
(2008)
J. Mol. Model.
, vol.14
, pp. 547-558
-
-
Jakobi, A.J.1
Mauser, H.2
Clark, T.3
-
31
-
-
79952117852
-
The ups and downs of structure-activity landscapes
-
Guha, R. (2011) The ups and downs of structure-activity landscapes. Methods Mol. Biol., 672, 101-117.
-
(2011)
Methods Mol. Biol.
, vol.672
, pp. 101-117
-
-
Guha, R.1
-
32
-
-
67649341994
-
Navigating structure-activity landscapes
-
Bajorath, J., Peltason, L., Wawer, M., Guha, R., Lajiness, M.S., and Van Drie, J.H. (2009) Navigating structure-activity landscapes. Drug Discov. Today, 14, 698-705.
-
(2009)
Drug Discov. Today
, vol.14
, pp. 698-705
-
-
Bajorath, J.1
Peltason, L.2
Wawer, M.3
Guha, R.4
Lajiness, M.S.5
Van Drie, J.H.6
-
33
-
-
0004192613
-
-
NJ(Original publication: , Nauka Press, Moscow, 1967)
-
Bongard, M.M. (1970) Pattern Recognition, Hayden Book Co., Spartan Books, Rochelle Park, NJ(Original publication: , Nauka Press, Moscow, 1967).
-
(1970)
Pattern Recognition, Hayden Book Co., Spartan Books, Rochelle Park
-
-
Bongard, M.M.1
-
34
-
-
36749104367
-
-
Princeton University Press, Pronceton, NJ, Oxford
-
Miller, J.H. and Page, S.E. (2007) Complex Adaptive Systems -An Introduction to Computational Models of Social Life, Princeton University Press, Pronceton, NJ, Oxford.
-
(2007)
Complex Adaptive Systems -An Introduction to Computational Models of Social Life
-
-
Miller, J.H.1
Page, S.E.2
-
36
-
-
1042292416
-
Protein-Ligand Interactions: From Molecular Recognition to Drug Design
-
eds R. Mannhold, H. Kubinyi, and G. Folkers Wiley-VCH Verlag GmbH, Weinheim
-
Böhm, H.J. and Schneider, G. (eds) (2003) Protein-Ligand Interactions: From Molecular Recognition to Drug Design. Methods and Principles in Medicinal Chemistry, Vol. 19 (eds R. Mannhold, H. Kubinyi, and G. Folkers), Wiley-VCH Verlag GmbH, Weinheim.
-
(2003)
Methods and Principles in Medicinal Chemistry
, vol.19
-
-
Böhm, H.J.1
Schneider, G.2
-
37
-
-
0035984036
-
Hydrogen bridges in crystal engineering: interactions without borders
-
Desiraju, G.R. (2002) Hydrogen bridges in crystal engineering: interactions without borders. Acc. Chem. Res., 35, 565-573.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 565-573
-
-
Desiraju, G.R.1
-
38
-
-
60749137646
-
Toward accurate relative energy predictions of the bioactive conformation of drugs
-
Butler, K.T., Luque, F.J., and Barril, X. (2009) Toward accurate relative energy predictions of the bioactive conformation of drugs. J. Comput. Chem., 30, 601-610.
-
(2009)
J. Comput. Chem.
, vol.30
, pp. 601-610
-
-
Butler, K.T.1
Luque, F.J.2
Barril, X.3
-
39
-
-
84857566644
-
A robust force field based method for calculating conformational energies of charged drug-like molecules
-
Poehlsgaard, J., Harpsøe, K., Jørgensen, F.S., and Olsen, L. (2012) A robust force field based method for calculating conformational energies of charged drug-like molecules. J. Chem. Inf. Model., 52, 409-419.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 409-419
-
-
Poehlsgaard, J.1
Harpsøe, K.2
Jørgensen, F.S.3
Olsen, L.4
-
40
-
-
34250839505
-
Conformational sampling of bioactive molecules: a comparative study
-
Agrafiotis, D.K., Gibbs, A.C., Zhu, F., Izrailev, S., and Martin, E. (2007) Conformational sampling of bioactive molecules: a comparative study. J. Chem. Inf. Model., 47, 1067-1086.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1067-1086
-
-
Agrafiotis, D.K.1
Gibbs, A.C.2
Zhu, F.3
Izrailev, S.4
Martin, E.5
-
41
-
-
70450215513
-
Conformational sampling and energetics of drug-like molecules
-
Foloppe, N. and Chen, I.J. (2009) Conformational sampling and energetics of drug-like molecules. Curr. Med. Chem., 16, 3381-3413.
-
(2009)
Curr. Med. Chem.
, vol.16
, pp. 3381-3413
-
-
Foloppe, N.1
Chen, I.J.2
-
42
-
-
84864400966
-
Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding
-
Biela, A., Betz, M., Heine, A., and Klebe, G. (2012) Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding. ChemMedChem, 7, 1423-1434.
-
(2012)
ChemMedChem
, vol.7
, pp. 1423-1434
-
-
Biela, A.1
Betz, M.2
Heine, A.3
Klebe, G.4
-
43
-
-
84876847879
-
Do medicinal chemists learn from activity cliffs? A systematic evaluation of cliff progression in evolving compound data sets
-
Dimova, D., Heikamp, K., Stumpfe, D., and Bajorath, J. (2013) Do medicinal chemists learn from activity cliffs? A systematic evaluation of cliff progression in evolving compound data sets. J. Med. Chem., 56, 3339-3345.
-
(2013)
J. Med. Chem.
, vol.56
, pp. 3339-3345
-
-
Dimova, D.1
Heikamp, K.2
Stumpfe, D.3
Bajorath, J.4
-
44
-
-
0033954256
-
The protein data bank
-
Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N., and Bourne, P.E. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
-
(2000)
Nucleic Acids Res.
, vol.28
, pp. 235-242
-
-
Berman, H.M.1
Westbrook, J.2
Feng, Z.3
Gilliland, G.4
Bhat, T.N.5
Weissig, H.6
Shindyalov, I.N.7
Bourne, P.E.8
-
45
-
-
0033578333
-
Binding of buried structural water increases the flexibility of proteins
-
Fischer, S. and Verma, C.S. (1999) Binding of buried structural water increases the flexibility of proteins. Proc. Natl. Acad. Sci. U.S.A, 96, 9613-9615.
-
(1999)
Proc. Natl. Acad. Sci. U.S.A
, vol.96
, pp. 9613-9615
-
-
Fischer, S.1
Verma, C.S.2
-
46
-
-
77953631827
-
A medicinal chemist's guide to molecular interactions
-
Bissantz, C., Kuhn, B., and Stahl, M. (2010) A medicinal chemist's guide to molecular interactions. J. Med. Chem., 53, 5061-5084.
-
(2010)
J. Med. Chem.
, vol.53
, pp. 5061-5084
-
-
Bissantz, C.1
Kuhn, B.2
Stahl, M.3
-
47
-
-
84860359784
-
Finding the sweet spot: the role of nature and nurture in medicinal chemistry
-
Hann, M.M. and Keserü, G.M. (2012) Finding the sweet spot: the role of nature and nurture in medicinal chemistry. Nat. Rev. Drug Discov., 11, 355-365.
-
(2012)
Nat. Rev. Drug Discov.
, vol.11
, pp. 355-365
-
-
Hann, M.M.1
Keserü, G.M.2
-
48
-
-
77957237209
-
Enthalpic efficiency of ligand binding
-
Ferenczy, G.G. and Keserü, G.M. (2010) Enthalpic efficiency of ligand binding. J. Chem. Inf. Model., 50, 1536-1541.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1536-1541
-
-
Ferenczy, G.G.1
Keserü, G.M.2
-
49
-
-
52049123291
-
Do enthalpy and entropy distinguish first in class from best in class?
-
Freire, E. (2008) Do enthalpy and entropy distinguish first in class from best in class? Drug Discov. Today, 13, 869-874.
-
(2008)
Drug Discov. Today
, vol.13
, pp. 869-874
-
-
Freire, E.1
-
50
-
-
1942453243
-
Ligand efficiency: a useful metric for lead selection
-
Hopkins, A.L., Groom, C.R., and Alex, A. (2004) Ligand efficiency: a useful metric for lead selection. Drug Discov. Today, 9, 430-431.
-
(2004)
Drug Discov. Today
, vol.9
, pp. 430-431
-
-
Hopkins, A.L.1
Groom, C.R.2
Alex, A.3
-
51
-
-
61649109015
-
The influence of lead discovery strategies on the properties of drug candidates
-
Keserü, G.M. and Makara, G.M. (2009) The influence of lead discovery strategies on the properties of drug candidates. Nat. Rev. Drug Discov., 8, 203-212.
-
(2009)
Nat. Rev. Drug Discov.
, vol.8
, pp. 203-212
-
-
Keserü, G.M.1
Makara, G.M.2
-
52
-
-
0037394124
-
Designing screens: how to make your hits a hit
-
Walters, W.P. and Namchuk, M. (2003) Designing screens: how to make your hits a hit. Nat. Rev. Drug Discov., 2, 259-266.
-
(2003)
Nat. Rev. Drug Discov.
, vol.2
, pp. 259-266
-
-
Walters, W.P.1
Namchuk, M.2
-
53
-
-
84856782646
-
Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery
-
Reutlinger, M. and Schneider, G. (2012) Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery. J. Mol. Graph. Model., 34, 108-117.
-
(2012)
J. Mol. Graph. Model.
, vol.34
, pp. 108-117
-
-
Reutlinger, M.1
Schneider, G.2
-
54
-
-
0000325341
-
Philos.
-
Pearson, K. (1901) Philos. Mag., 2, 559-572.
-
(1901)
Mag.
, vol.2
, pp. 559-572
-
-
Pearson, K.1
-
55
-
-
0022888694
-
On the use of some multivariate statistical methods in pharmacological research
-
St°ahle, L. and Wold, S. (1986) On the use of some multivariate statistical methods in pharmacological research. J. Pharmacol. Methods, 16, 91-110.
-
(1986)
J. Pharmacol. Methods
, vol.16
, pp. 91-110
-
-
St°ahle, L.1
Wold, S.2
-
56
-
-
0020068152
-
Self-organized formation of topologically correct feature maps
-
Kohonen, T. (1982) Self-organized formation of topologically correct feature maps. Biol. Cybern., 43, 59-69.
-
(1982)
Biol. Cybern.
, vol.43
, pp. 59-69
-
-
Kohonen, T.1
-
58
-
-
0037365305
-
A geodesic framework for analyzing molecular similarities
-
Agrafiotis, D.K. and Xu, H. (2003) A geodesic framework for analyzing molecular similarities. J. Chem. Inf. Comput. Sci., 43, 475-484.
-
(2003)
J. Chem. Inf. Comput. Sci.
, vol.43
, pp. 475-484
-
-
Agrafiotis, D.K.1
Xu, H.2
-
59
-
-
82455205704
-
Neighborhood-preserving visualization of adaptive structure-activity landscapes: application to drug discovery
-
Reutlinger, M., Guba, W., Martin, R.E., Alanine, A.I., Hoffmann, T., Klenner, A., Hiss, J.A., Schneider, P., and Schneider, G. (2011) Neighborhood-preserving visualization of adaptive structure-activity landscapes: application to drug discovery. Angew. Chem. Int. Ed., 50, 11633-11636.
-
(2011)
Angew. Chem. Int. Ed.
, vol.50
, pp. 11633-11636
-
-
Reutlinger, M.1
Guba, W.2
Martin, R.E.3
Alanine, A.I.4
Hoffmann, T.5
Klenner, A.6
Hiss, J.A.7
Schneider, P.8
Schneider, G.9
-
60
-
-
0029114410
-
Molecular biology of somatostatin receptors
-
Reisine, T. and Bell, G.I. (1995) Molecular biology of somatostatin receptors. Endocrinol. Rev., 16, 427-442.
-
(1995)
Endocrinol. Rev.
, vol.16
, pp. 427-442
-
-
Reisine, T.1
Bell, G.I.2
-
61
-
-
37049020280
-
Discovery of the first nonpeptidic, small-molecule, highly selective somatostatin receptor subtype 5 antagonists: a chemogenomics approach
-
Martin, R.E., Green, L.G., Guba, W., Kratochwil, N., and Christm, A. (2007) Discovery of the first nonpeptidic, small-molecule, highly selective somatostatin receptor subtype 5 antagonists: a chemogenomics approach. J. Med. Chem., 50, 6291-6294.
-
(2007)
J. Med. Chem.
, vol.50
, pp. 6291-6294
-
-
Martin, R.E.1
Green, L.G.2
Guba, W.3
Kratochwil, N.4
Christm, A.5
-
62
-
-
0026619394
-
Looking at proteins: representations, folding, packing, and design
-
Richardson, J.S., Richardson, D.C., Tweedy, N.B., Gernert, K.M., Quinn, T.P., Hecht, M.H., Erickson, B.W., Yan, Y., Mc Clain, R.D., and Donlan, M.E. (1992) Looking at proteins: representations, folding, packing, and design. Biophys. J., 63, 1185-1209.
-
(1992)
Biophys. J.
, vol.63
, pp. 1185-1209
-
-
Richardson, J.S.1
Richardson, D.C.2
Tweedy, N.B.3
Gernert, K.M.4
Quinn, T.P.5
Hecht, M.H.6
Erickson, B.W.7
Yan, Y.8
Mc Clain, R.D.9
Donlan, M.E.10
-
63
-
-
84866686849
-
Machine learning techniques and drug design
-
Gertrudes, J.C., Maltarollo, V.G., Silva, R.A., Oliveira, P.R., Hońorio, K.M., and da Silva, A.B. (2012) Machine learning techniques and drug design. Curr. Med. Chem., 19, 4289-4297.
-
(2012)
Curr. Med. Chem.
, vol.19
, pp. 4289-4297
-
-
Gertrudes, J.C.1
Maltarollo, V.G.2
Silva, R.A.3
Oliveira, P.R.4
Hońorio, K.M.5
da Silva, A.B.6
-
64
-
-
33947245022
-
Evaluation of machinelearning methods for ligand-based virtual screening
-
Chen, B., Harrison, R.F., Papadatos, G., Willett, P., Wood, D.J., Lewell, X.Q., Greenidge, P., and Stiefl, N. (2007) Evaluation of machinelearning methods for ligand-based virtual screening. J. Comput. Aided Mol. Des., 21, 53-62.
-
(2007)
J. Comput. Aided Mol. Des.
, vol.21
, pp. 53-62
-
-
Chen, B.1
Harrison, R.F.2
Papadatos, G.3
Willett, P.4
Wood, D.J.5
Lewell, X.Q.6
Greenidge, P.7
Stiefl, N.8
-
65
-
-
66249086244
-
Machine learning in virtual screening
-
Melville, J.L., Burke, E.K., and Hirst, J.D. (2009) Machine learning in virtual screening. Comb. Chem. High Throughput Screening, 12, 332-343.
-
(2009)
Comb. Chem. High Throughput Screening
, vol.12
, pp. 332-343
-
-
Melville, J.L.1
Burke, E.K.2
Hirst, J.D.3
-
67
-
-
0033931867
-
Assessing the accuracy of prediction algorithms for classification: an overview
-
Baldi, P., Brunak, S., Chauvin, Y., Andersen, C.A.F., and Nielsen, H. (2000) Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics, 16, 412-424.
-
(2000)
Bioinformatics
, vol.16
, pp. 412-424
-
-
Baldi, P.1
Brunak, S.2
Chauvin, Y.3
Andersen, C.A.F.4
Nielsen, H.5
-
68
-
-
0016772212
-
Comparison of the predicted and observed secondary structure of T4 phage lysozyme
-
Matthews, B.W. (1975) Comparison of the predicted and observed secondary structure of T4 phage lysozyme. Biochim. Biophys. Acta, 405, 442-451.
-
(1975)
Biochim. Biophys. Acta
, vol.405
, pp. 442-451
-
-
Matthews, B.W.1
-
70
-
-
34247272948
-
Evaluating virtual screening methods: good and bad metrics for the ''early recognition'' problem
-
Truchon, J.F. and Bayly, C.I. (2007) Evaluating virtual screening methods: good and bad metrics for the ''early recognition'' problem. J. Chem. Inf. Model., 47, 488-508.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 488-508
-
-
Truchon, J.F.1
Bayly, C.I.2
-
71
-
-
79952118088
-
What do we know? Simple statistical techniques that help
-
Nicholls, A. (2011) What do we know? Simple statistical techniques that help. Methods Mol. Biol., 672, 531-581.
-
(2011)
Methods Mol. Biol.
, vol.672
, pp. 531-581
-
-
Nicholls, A.1
-
72
-
-
78951489458
-
Systematic generation of chemical structures for rational drug design based on QSAR models
-
Funatsu, K., Miyao, T., and Arakawa, M. (2011) Systematic generation of chemical structures for rational drug design based on QSAR models. Curr. Comput. Aided Drug Des., 7, 1-9.
-
(2011)
Curr. Comput. Aided Drug Des.
, vol.7
, pp. 1-9
-
-
Funatsu, K.1
Miyao, T.2
Arakawa, M.3
-
73
-
-
37349048522
-
On some aspects of validation of predictive quantitative structure-activity relationship models
-
Roy, K. (2007) On some aspects of validation of predictive quantitative structure-activity relationship models. Expert Opin. Drug Discov., 2, 1567-1577.
-
(2007)
Expert Opin. Drug Discov.
, vol.2
, pp. 1567-1577
-
-
Roy, K.1
-
74
-
-
79952117092
-
Bayesian methods in virtual screening and chemical biology
-
Bender, A. (2011) Bayesian methods in virtual screening and chemical biology. Methods Mol. Biol., 672, 175-196.
-
(2011)
Methods Mol. Biol.
, vol.672
, pp. 175-196
-
-
Bender, A.1
-
75
-
-
0003922190
-
-
John Wiley & Sons, Inc., New York
-
Duda, R., Hart, P., and Stork, D. (2001) Pattern Classification, John Wiley & Sons, Inc., New York.
-
(2001)
Pattern Classification
-
-
Duda, R.1
Hart, P.2
Stork, D.3
-
76
-
-
84870987376
-
Automated design of ligands to polypharmacological profiles
-
Besnard, J., Ruda, G.F., Setola, V., Abecassis, K., Rodriguiz, R.M., Huang, X.P., Norval, S., Sassano, M.F., Shin, A.I., Webster, L.A., Simeons, F.R., Stojanovski, L., Prat, A., Seidah, N.G., Constam, D.B., Bickerton, G.R., Read, K.D., Wetsel, W.C., Gilbert, I.H., Roth, B.L., and Hopkins, A.L. (2012) Automated design of ligands to polypharmacological profiles. Nature, 492, 215-220.
-
(2012)
Nature
, vol.492
, pp. 215-220
-
-
Besnard, J.1
Ruda, G.F.2
Setola, V.3
Abecassis, K.4
Rodriguiz, R.M.5
Huang, X.P.6
Norval, S.7
Sassano, M.F.8
Shin, A.I.9
Webster, L.A.10
Simeons, F.R.11
Stojanovski, L.12
Prat, A.13
Seidah, N.G.14
Constam, D.B.15
Bickerton, G.R.16
Read, K.D.17
Wetsel, W.C.18
Gilbert, I.H.19
Roth, B.L.20
Hopkins, A.L.21
more..
-
77
-
-
58149388697
-
Overview of artificial neural networks
-
Zou, J., Han, Y., and So, S.S. (2008) Overview of artificial neural networks. Methods Mol. Biol., 458, 15-23.
-
(2008)
Methods Mol. Biol.
, vol.458
, pp. 15-23
-
-
Zou, J.1
Han, Y.2
So, S.S.3
-
80
-
-
58149402899
-
Associative neural network
-
Tetko, I.V. (2008) Associative neural network. Methods Mol. Biol., 458, 185-202.
-
(2008)
Methods Mol. Biol.
, vol.458
, pp. 185-202
-
-
Tetko, I.V.1
-
82
-
-
0347243182
-
Nonlinear component analysis as a kernel eigenvalue problem
-
Schölkopf, B., Smola, A., and Müller, K.R. (1998) Nonlinear component analysis as a kernel eigenvalue problem. Neural Comput., 10, 1299-1319.
-
(1998)
Neural Comput.
, vol.10
, pp. 1299-1319
-
-
Schölkopf, B.1
Smola, A.2
Müller, K.R.3
-
83
-
-
0034740222
-
Drug design by machine learning: support vector machines for pharmaceutical data analysis
-
Burbidge, R., Trotter, M., Buxton, B., and Holden, S. (2001) Drug design by machine learning: support vector machines for pharmaceutical data analysis. Comput. Chem., 26, 5-14.
-
(2001)
Comput. Chem.
, vol.26
, pp. 5-14
-
-
Burbidge, R.1
Trotter, M.2
Buxton, B.3
Holden, S.4
-
84
-
-
79952116048
-
Application of support vector machine-based ranking strategies to search for target-selective compounds
-
Wassermann, A.M., Geppert, H., and Bajorath, J. (2011) Application of support vector machine-based ranking strategies to search for target-selective compounds. Methods Mol. Biol., 672, 517-530.
-
(2011)
Methods Mol. Biol.
, vol.672
, pp. 517-530
-
-
Wassermann, A.M.1
Geppert, H.2
Bajorath, J.3
-
85
-
-
34247186391
-
Accurate solubility prediction with error bars for electrolytes: a machine learning approach
-
Schwaighofer, A., Schroeter, T., Mika, S., Laub, J., Laak, A., Sülzle, D., Ganzer, U., Heinrich, N., and Müller, K.R. (2007) Accurate solubility prediction with error bars for electrolytes: a machine learning approach. J. Chem. Inf. Model., 47, 407-424.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 407-424
-
-
Schwaighofer, A.1
Schroeter, T.2
Mika, S.3
Laub, J.4
Laak, A.5
Sülzle, D.6
Ganzer, U.7
Heinrich, N.8
Müller, K.R.9
-
86
-
-
35248832636
-
Gaussian processes: a method for automatic QSAR modeling of ADME properties
-
Obrezanova, O., Csanyi, G., Gola, J.M., and Segall, M.D. (2007) Gaussian processes: a method for automatic QSAR modeling of ADME properties. J. Chem. Inf. Model., 47, 1847-1857.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 1847-1857
-
-
Obrezanova, O.1
Csanyi, G.2
Gola, J.M.3
Segall, M.D.4
-
87
-
-
67650067615
-
Bias-correction of regression models: a case study on hERG inhibition
-
Hansen, K., Rathke, F., Schroeter, T., Rast, G., Fox, T., Kriegl, J.M., and Mika, S. (2009) Bias-correction of regression models: a case study on hERG inhibition. J. Chem. Inf. Model., 49, 1486-1496.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1486-1496
-
-
Hansen, K.1
Rathke, F.2
Schroeter, T.3
Rast, G.4
Fox, T.5
Kriegl, J.M.6
Mika, S.7
-
88
-
-
66849142177
-
How wrong can we get? A review of machine learning approaches and error bars
-
Schwaighofer, A., Schroeter, T., Mika, S., and Blanchard, G. (2009) How wrong can we get? A review of machine learning approaches and error bars. Comb. Chem. High Throughput Screening, 12, 453-468.
-
(2009)
Comb. Chem. High Throughput Screening
, vol.12
, pp. 453-468
-
-
Schwaighofer, A.1
Schroeter, T.2
Mika, S.3
Blanchard, G.4
-
89
-
-
75749099299
-
From machine learning to natural product derivatives that selectively activate transcription factor PPARgamma
-
Rupp, M., Schroeter, T., Steri, R., Zettl, H., Proschak, E., Hansen, K., Rau, O., Schwarz, O., Müller-Kuhrt, L., Schubert-Zsilavecz, M., Müller, K.R., and Schneider, G. (2010) From machine learning to natural product derivatives that selectively activate transcription factor PPARgamma. ChemMedChem, 5, 191-194.
-
(2010)
ChemMedChem
, vol.5
, pp. 191-194
-
-
Rupp, M.1
Schroeter, T.2
Steri, R.3
Zettl, H.4
Proschak, E.5
Hansen, K.6
Rau, O.7
Schwarz, O.8
Müller-Kuhrt, L.9
Schubert-Zsilavecz, M.10
Müller, K.R.11
Schneider, G.12
-
91
-
-
0242467732
-
Collection of bioactive reference compounds for focused library design
-
Schneider, P. and Schneider, G. (2003) Collection of bioactive reference compounds for focused library design. QSAR Comb. Sci., 22, 713-718.
-
(2003)
QSAR Comb. Sci.
, vol.22
, pp. 713-718
-
-
Schneider, P.1
Schneider, G.2
-
92
-
-
84866355546
-
Exploring chemical space for drug discovery using the chemical universe database
-
Reymond, J.L. and Awale, M. (2012) Exploring chemical space for drug discovery using the chemical universe database. ACS Chem. Neurosci., 3, 649-657.
-
(2012)
ACS Chem. Neurosci.
, vol.3
, pp. 649-657
-
-
Reymond, J.L.1
Awale, M.2
-
93
-
-
84873036431
-
Visualization and virtual screening of the chemical universe database GDB-17
-
Ruddigkeit, L., Blum, L.C., and Reymond, J.L. (2013) Visualization and virtual screening of the chemical universe database GDB-17. J. Chem. Inf. Model., 53, 56-65.
-
(2013)
J. Chem. Inf. Model.
, vol.53
, pp. 56-65
-
-
Ruddigkeit, L.1
Blum, L.C.2
Reymond, J.L.3
-
94
-
-
0034130399
-
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
-
Schneider, G., Lee, M.L., Stahl, M., and Schneider, P. (2000) De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J. Comp. Aided Mol. Des., 14, 487-494.
-
(2000)
J. Comp. Aided Mol. Des.
, vol.14
, pp. 487-494
-
-
Schneider, G.1
Lee, M.L.2
Stahl, M.3
Schneider, P.4
-
95
-
-
0034680641
-
Virtual screening for bioactive molecules by evolutionary de novo design
-
Schneider, G., Cĺement-Chomienne, O., Hilfiger, L., Schneider, P., Kirsch, S., Böhm, H.J., and Neidhart, W. (2000) Virtual screening for bioactive molecules by evolutionary de novo design. Angew. Chem. Int. Ed., 39, 4130-4133.
-
(2000)
Angew. Chem. Int. Ed.
, vol.39
, pp. 4130-4133
-
-
Schneider, G.1
Cĺement-Chomienne, O.2
Hilfiger, L.3
Schneider, P.4
Kirsch, S.5
Böhm, H.J.6
Neidhart, W.7
-
96
-
-
33745809902
-
Hit discovery and hit-to-lead approaches
-
Keserü, G.M. and Makara, G.M. (2006) Hit discovery and hit-to-lead approaches. Drug Discov. Today, 11, 741-748.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 741-748
-
-
Keserü, G.M.1
Makara, G.M.2
-
97
-
-
33845364148
-
Fragment-based drug design: how big is too big?
-
Hajduk, P.J. (2006) Fragment-based drug design: how big is too big? J. Med. Chem., 49, 6972-6976.
-
(2006)
J. Med. Chem.
, vol.49
, pp. 6972-6976
-
-
Hajduk, P.J.1
-
98
-
-
79958840084
-
Compound design by fragment-linking
-
Ichihara, O., Barker, J., Law, R.J., and Whittaker, M. (2011) Compound design by fragment-linking. Mol. Inf., 30, 298-306.
-
(2011)
Mol. Inf.
, vol.30
, pp. 298-306
-
-
Ichihara, O.1
Barker, J.2
Law, R.J.3
Whittaker, M.4
-
99
-
-
33751076241
-
Deconstructing fragment-based inhibitor discovery
-
Babaoglu, K. and Shoichet, B.K. (2006) Deconstructing fragment-based inhibitor discovery. Nat. Chem. Biol., 2, 720-723.
-
(2006)
Nat. Chem. Biol.
, vol.2
, pp. 720-723
-
-
Babaoglu, K.1
Shoichet, B.K.2
-
100
-
-
0036821028
-
The consequences of translational and rotational entropy lost by small molecules on binding to proteins
-
Murray, C.W. and Verdonk, M.L. (2002) The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J. Comput. Aided Mol. Des., 16, 741-753.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 741-753
-
-
Murray, C.W.1
Verdonk, M.L.2
-
101
-
-
34249094150
-
Informatics and modeling challenges in fragment-based drug discovery
-
Hubbard, R.E., Chen, I., and Davis, B. (2007) Informatics and modeling challenges in fragment-based drug discovery. Curr. Opin. Drug Discov. Dev., 10, 289-297.
-
(2007)
Curr. Opin. Drug Discov. Dev.
, vol.10
, pp. 289-297
-
-
Hubbard, R.E.1
Chen, I.2
Davis, B.3
-
102
-
-
84856010975
-
Fragment deconstruction of small, potent factor Xa inhibitors: exploring the superadditivity energetics of fragment linking in protein-ligand complexes
-
Nazaŕe, M., Matter, H., Will, D.W., Wagner, M., Urmann, M., Czech, J., Schreuder, H., Bauer, A., Ritter, K., and Wehner, V. (2012) Fragment deconstruction of small, potent factor Xa inhibitors: exploring the superadditivity energetics of fragment linking in protein-ligand complexes. Angew. Chem. Int. Ed., 51, 905-911.
-
(2012)
Angew. Chem. Int. Ed.
, vol.51
, pp. 905-911
-
-
Nazaŕe, M.1
Matter, H.2
Will, D.W.3
Wagner, M.4
Urmann, M.5
Czech, J.6
Schreuder, H.7
Bauer, A.8
Ritter, K.9
Wehner, V.10
-
103
-
-
84861142957
-
DOGS: reactiondriven de novo design of bioactive compounds
-
Hartenfeller, M., Zettl, H., Walter, M., Rupp, M., Reisen, F., Proschak, E., Weggen, S., Stark, H., and Schneider, G. (2012) DOGS: reactiondriven de novo design of bioactive compounds. PLoS Comput. Biol., 8, e1002380.
-
(2012)
PLoS Comput. Biol.
, vol.8
, pp. e1002380
-
-
Hartenfeller, M.1
Zettl, H.2
Walter, M.3
Rupp, M.4
Reisen, F.5
Proschak, E.6
Weggen, S.7
Stark, H.8
Schneider, G.9
-
104
-
-
57849156863
-
Voyages to the (un)known: adaptive design of bioactive compounds
-
Schneider, G., Hartenfeller, M., Reutlinger, M., Tanrikulu, Y., Proschak, E., and Schneider, P. (2009) Voyages to the (un)known: adaptive design of bioactive compounds. Trends Biotechnol., 27, 18-26.
-
(2009)
Trends Biotechnol.
, vol.27
, pp. 18-26
-
-
Schneider, G.1
Hartenfeller, M.2
Reutlinger, M.3
Tanrikulu, Y.4
Proschak, E.5
Schneider, P.6
-
105
-
-
78049500819
-
Concepts and applications of ''natural computing'' techniques in de novo drug and peptide design
-
Hiss, J.A., Hartenfeller, M., and Schneider, G. (2010) Concepts and applications of ''natural computing'' techniques in de novo drug and peptide design. Curr. Pharm. Des., 16, 1656-1665.
-
(2010)
Curr. Pharm. Des.
, vol.16
, pp. 1656-1665
-
-
Hiss, J.A.1
Hartenfeller, M.2
Schneider, G.3
-
106
-
-
45449111186
-
Concept of combinatorial de novo design of druglike molecules by particle swarm optimization
-
Hartenfeller, M., Proschak, E., Schüller, A., and Schneider, G. (2008) Concept of combinatorial de novo design of druglike molecules by particle swarm optimization. Chem. Biol. Drug Des., 72, 16-26.
-
(2008)
Chem. Biol. Drug Des.
, vol.72
, pp. 16-26
-
-
Hartenfeller, M.1
Proschak, E.2
Schüller, A.3
Schneider, G.4
-
107
-
-
68149124133
-
FOG: Fragment optimized growth algorithm for the de novo generation of molecules occupying druglike chemical space
-
Kutchukian, P.S., Lou, D., and Shakhnovich, E.I. (2009) FOG: Fragment optimized growth algorithm for the de novo generation of molecules occupying druglike chemical space. J. Chem. Inf. Model., 49, 1630-1642.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1630-1642
-
-
Kutchukian, P.S.1
Lou, D.2
Shakhnovich, E.I.3
-
108
-
-
0032058905
-
RECAP-retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry
-
Lewell, X.Q., Judd, D., Watson, S., and Hann, M. (1998) RECAP-retrosynthetic combinatorial analysis procedure: a powerful new technique for identifying privileged molecular fragments with useful applications in combinatorial chemistry. J. Chem. Inf. Comput. Sci., 38, 511-522.
-
(1998)
J. Chem. Inf. Comput. Sci.
, vol.38
, pp. 511-522
-
-
Lewell, X.Q.1
Judd, D.2
Watson, S.3
Hann, M.4
-
109
-
-
0032840569
-
DREAM++: flexible docking program for virtual combinatorial libraries
-
Makino, S., Ewing, T.J.A., and Kuntz, I.D. (1999) DREAM++: flexible docking program for virtual combinatorial libraries. J. Comput. Aided Mol. Des., 13, 513-532.
-
(1999)
J. Comput. Aided Mol. Des.
, vol.13
, pp. 513-532
-
-
Makino, S.1
Ewing, T.J.A.2
Kuntz, I.D.3
-
110
-
-
0037777697
-
Synopsis: synthesize and optimize system in silico
-
Vinkers, H.M., de Jonge, M.R., Daeyaert, F.F., Heeres, J., Koymans, L.M., van Lenthe, J.H., Lewi, P.J., Timmerman, H., Van Aken, K., and Janssen, P.A. (2003) Synopsis: synthesize and optimize system in silico. J. Med. Chem., 46, 2765-2773.
-
(2003)
J. Med. Chem.
, vol.46
, pp. 2765-2773
-
-
Vinkers, H.M.1
de Jonge, M.R.2
Daeyaert, F.F.3
Heeres, J.4
Koymans, L.M.5
van Lenthe, J.H.6
Lewi, P.J.7
Timmerman, H.8
Van Aken, K.9
Janssen, P.A.10
-
111
-
-
0002820943
-
SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility
-
Gillett, V.J. (1995) SPROUT, HIPPO and CAESA: tools for de novo structure generation and estimation of synthetic accessibility. Perspect. Drug Discov. Des., 3, 34-50.
-
(1995)
Perspect. Drug Discov. Des.
, vol.3
, pp. 34-50
-
-
Gillett, V.J.1
-
112
-
-
67650945012
-
Second-generation de novo design: a view from a medicinal chemist perspective
-
Zaliani, A., Boda, K., Seidel, T., Herwig, A., Schwab, C.H., Gasteiger, J., Claussen, H., Lemmen, C., Degen, J., Pärn, J., and Rarey, M. (2009) Second-generation de novo design: a view from a medicinal chemist perspective. J. Comput. Aided Mol. Des., 23, 593-602.
-
(2009)
J. Comput. Aided Mol. Des.
, vol.23
, pp. 593-602
-
-
Zaliani, A.1
Boda, K.2
Seidel, T.3
Herwig, A.4
Schwab, C.H.5
Gasteiger, J.6
Claussen, H.7
Lemmen, C.8
Degen, J.9
Pärn, J.10
Rarey, M.11
-
113
-
-
65249148540
-
Route designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation
-
Law, J., Zsoldos, Z., Simon, A., Reid, D., Liu, Y., Khew, S.Y., Johnson, A.P., Major, S., Wade, R.A., and Ando, H.Y. (2009) Route designer: a retrosynthetic analysis tool utilizing automated retrosynthetic rule generation. J. Chem. Inf. Model., 49, 593-602.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 593-602
-
-
Law, J.1
Zsoldos, Z.2
Simon, A.3
Reid, D.4
Liu, Y.5
Khew, S.Y.6
Johnson, A.P.7
Major, S.8
Wade, R.A.9
Ando, H.Y.10
-
114
-
-
0024549279
-
Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogenbonding regions at protein surfaces
-
Danziger, D.J. and Dean, P.M. (1989) Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogenbonding regions at protein surfaces. Proc. R. Soc. London, Ser. B, 236, 101-113.
-
(1989)
Proc. R. Soc. London Ser. B
, vol.236
, pp. 101-113
-
-
Danziger, D.J.1
Dean, P.M.2
-
115
-
-
0024503067
-
Automated site-directed drug design: the concept of spacer skeletons for primary structure generation
-
Lewis, R.A. and Dean, P.M. (1989) Automated site-directed drug design: the concept of spacer skeletons for primary structure generation. Proc. R. Soc. London, Ser. B, 236, 125-140.
-
(1989)
Proc. R. Soc. London Ser. B
, vol.236
, pp. 125-140
-
-
Lewis, R.A.1
Dean, P.M.2
-
116
-
-
0011803040
-
Automated structure design in 3D
-
Gillett, V.A., Johnson, A.P., Mata, P., and Sike, S. (1990) Automated structure design in 3D. Tetrahedron Comp. Methodol., 3, 681-696.
-
(1990)
Tetrahedron Comp. Methodol.
, vol.3
, pp. 681-696
-
-
Gillett, V.A.1
Johnson, A.P.2
Mata, P.3
Sike, S.4
-
117
-
-
0026694615
-
Automated site-directed drug design using molecular lattices
-
Lewis, R.A., Roe, D.C., Huang, C., Ferrin, T.E., Langridge, R., and Kuntz, I.D. (1992) Automated site-directed drug design using molecular lattices. J. Mol. Graph., 10, 66-78.
-
(1992)
J. Mol. Graph.
, vol.10
, pp. 66-78
-
-
Lewis, R.A.1
Roe, D.C.2
Huang, C.3
Ferrin, T.E.4
Langridge, R.5
Kuntz, I.D.6
-
119
-
-
0027517544
-
Confirmation of usefulness of a structure construction program based on threedimensional receptor structure for rational lead generation
-
Nishibata, Y. and Itai, A. (1993) Confirmation of usefulness of a structure construction program based on threedimensional receptor structure for rational lead generation. J. Med. Chem., 36, 2921-2928.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 2921-2928
-
-
Nishibata, Y.1
Itai, A.2
-
120
-
-
0027136267
-
The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypothesis
-
Tschinke, V. and Cohen, N.C. (1993) The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypothesis. J. Med. Chem., 36, 3863-3870.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 3863-3870
-
-
Tschinke, V.1
Cohen, N.C.2
-
121
-
-
0001391169
-
SPLICE: a program to assemble partial query solutions from three-dimensional database searches into novel ligands
-
Ho, C.M.W. and Marshall, G.R. (1993) SPLICE: a program to assemble partial query solutions from three-dimensional database searches into novel ligands. J. Comput. Aided Mol. Des., 7, 623-647.
-
(1993)
J. Comput. Aided Mol. Des.
, vol.7
, pp. 623-647
-
-
Ho, C.M.W.1
Marshall, G.R.2
-
122
-
-
0027193713
-
GroupBuild: a fragment-based method for de novo drug design
-
Rotstein, S.H. and Murcko, M.A. (1993) GroupBuild: a fragment-based method for de novo drug design. J. Med. Chem., 36, 1700-1710.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 1700-1710
-
-
Rotstein, S.H.1
Murcko, M.A.2
-
123
-
-
0348242299
-
CONCEPTS: new dynamic algorithm for de novo design suggestion
-
Pearlman, D.A. and Murcko, M.A. (1993) CONCEPTS: new dynamic algorithm for de novo design suggestion. J. Comput. Chem., 14, 1184-1193.
-
(1993)
J. Comput. Chem.
, vol.14
, pp. 1184-1193
-
-
Pearlman, D.A.1
Murcko, M.A.2
-
124
-
-
0027586682
-
SPROUT: a program for structure generation
-
Gillet, V.J., Johnson, A.P., Mata, P., Sike, S., and Williams, P. (1993) SPROUT: a program for structure generation. J. Comput. Aided Mol. Des., 7, 127-153.
-
(1993)
J. Comput. Aided Mol. Des.
, vol.7
, pp. 127-153
-
-
Gillet, V.J.1
Johnson, A.P.2
Mata, P.3
Sike, S.4
Williams, P.5
-
125
-
-
0028167547
-
SPROUT: recent developments in the de novo design of molecules
-
Gillet, V.J., Newell, W., Mata, P., Myatt, G., Sike, S., Zsoldos, Z., and Johnson, A.P. (1994) SPROUT: recent developments in the de novo design of molecules. J. Comput. Aided Mol. Des., 34, 207-217.
-
(1994)
J. Comput. Aided Mol. Des.
, vol.34
, pp. 207-217
-
-
Gillet, V.J.1
Newell, W.2
Mata, P.3
Myatt, G.4
Sike, S.5
Zsoldos, Z.6
Johnson, A.P.7
-
126
-
-
0001125111
-
SPROUT: 3D structure generation using templates
-
Mata, P., Gillet, V.J., Johnson, A.P., Lampreia, J., Myatt, G.J., Sike, S., and Stebbings, A.L. (1995) SPROUT: 3D structure generation using templates. J. Chem. Inf. Comput. Sci., 35, 479-493.
-
(1995)
J. Chem. Inf. Comput. Sci.
, vol.35
, pp. 479-493
-
-
Mata, P.1
Gillet, V.J.2
Johnson, A.P.3
Lampreia, J.4
Myatt, G.J.5
Sike, S.6
Stebbings, A.L.7
-
127
-
-
0028282687
-
HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site
-
Eisen, M.B., Wiley, D.C., Karplus, M., and Hubbard, R.E. (1994) HOOK: a program for finding novel molecular architectures that satisfy the chemical and steric requirements of a macromolecule binding site. Proteins, 19, 199-221.
-
(1994)
Proteins
, vol.19
, pp. 199-221
-
-
Eisen, M.B.1
Wiley, D.C.2
Karplus, M.3
Hubbard, R.E.4
-
128
-
-
0027219536
-
Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase
-
Caflish, A., Miranker, A., and Karplus, M. (1993) Multiple copy simultaneous search and construction of ligands in binding sites: application to inhibitors of HIV-1 aspartic proteinase. J. Med. Chem., 36, 2142-2167.
-
(1993)
J. Med. Chem.
, vol.36
, pp. 2142-2167
-
-
Caflish, A.1
Miranker, A.2
Karplus, M.3
-
129
-
-
0028036120
-
Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of a de novo design method incorporating combinatorial growth
-
Bohacek, R.S. and Mc Martin, C. (1994) Multiple highly diverse structures complementary to enzyme binding sites: results of extensive application of a de novo design method incorporating combinatorial growth. J. Am. Chem. Soc., 116, 5560-5571.
-
(1994)
J. Am. Chem. Soc.
, vol.116
, pp. 5560-5571
-
-
Bohacek, R.S.1
Mc Martin, C.2
-
130
-
-
0029285723
-
A genetic algorithm for the automated generation of molecules within constraints
-
Glen, R.C. and Payne, A.W. (1995) A genetic algorithm for the automated generation of molecules within constraints. J. Comput. Aided Mol. Des., 9, 181-202.
-
(1995)
J. Comput. Aided Mol. Des.
, vol.9
, pp. 181-202
-
-
Glen, R.C.1
Payne, A.W.2
-
131
-
-
0029320501
-
PRO LIGAND: an approach to de novo molecular design. 1 Application to the design of organic molecules
-
Clark, D.E., Frenkel, D., Levy, S.A., Li, J., Murray, C.W., Robson, B., Waszkowycz, B., and Westhead, D.R. (1995) PRO LIGAND: an approach to de novo molecular design. 1. Application to the design of organic molecules. J. Comput. Aided Mol. Des., 9, 13-32.
-
(1995)
J. Comput. Aided Mol. Des.
, vol.9
, pp. 13-32
-
-
Clark, D.E.1
Frenkel, D.2
Levy, S.A.3
Li, J.4
Murray, C.W.5
Robson, B.6
Waszkowycz, B.7
Westhead, D.R.8
-
132
-
-
0028081385
-
PRO LIGAND: an approach to de novo molecular design. 2 Design of novel molecules from molecular field analysis (MFA) models and pharmacophores
-
Waszkowycz, B., Clark, D.E., Frenkel, D., Li, J., Murray, C.W., Robson, B., and Westhead, D.R. (1994) PRO LIGAND: an approach to de novo molecular design. 2. Design of novel molecules from molecular field analysis (MFA) models and pharmacophores. J. Med. Chem., 37, 3994-4002.
-
(1994)
J. Med. Chem.
, vol.37
, pp. 3994-4002
-
-
Waszkowycz, B.1
Clark, D.E.2
Frenkel, D.3
Li, J.4
Murray, C.W.5
Robson, B.6
Westhead, D.R.7
-
133
-
-
0029281478
-
PRO LIGAND: an approach to de novo molecular design. 3 A genetic algorithm for structure refinement
-
Westhead, D.R., Clark, D.E., Frenkel, D., Li, J., Murray, C.W., Robson, B., and Waszkowycz, B. (1995) PRO LIGAND: an approach to de novo molecular design. 3. A genetic algorithm for structure refinement. J. Comput. Aided Mol. Des., 9, 139-148.
-
(1995)
J. Comput. Aided Mol. Des.
, vol.9
, pp. 139-148
-
-
Westhead, D.R.1
Clark, D.E.2
Frenkel, D.3
Li, J.4
Murray, C.W.5
Robson, B.6
Waszkowycz, B.7
-
134
-
-
0029320501
-
PRO LIGAND: an approach de novo molecular design. 4 Application to the design of peptides
-
Frenkel, D., Clark, D.E., Li, J., Murray, C.W., Robson, B., Waszkowycz, B., and Westhead, D.R. (1995) PRO LIGAND: an approach de novo molecular design. 4. Application to the design of peptides. J. Comput. Aided Mol. Des., 9, 213-225.
-
(1995)
J. Comput. Aided Mol. Des.
, vol.9
, pp. 213-225
-
-
Frenkel, D.1
Clark, D.E.2
Li, J.3
Murray, C.W.4
Robson, B.5
Waszkowycz, B.6
Westhead, D.R.7
-
135
-
-
0345522652
-
PRO LIGAND: an approach to de novo molecular design. 5 Tools for the analysis of generated structures
-
Clark, D.E. and Murray, C.W. (1995) PRO LIGAND: an approach to de novo molecular design. 5. Tools for the analysis of generated structures. J. Chem. Inf. Comput. Sci., 35, 914-923.
-
(1995)
J. Chem. Inf. Comput. Sci.
, vol.35
, pp. 914-923
-
-
Clark, D.E.1
Murray, C.W.2
-
136
-
-
0029385233
-
PRO LIGAND: an approach to de novo molecular design Flexible fitting in the design of peptides
-
Murray, C.W., Clark, D.E., and Byrne, D.G. (1995) PRO LIGAND: an approach to de novo molecular design. Flexible fitting in the design of peptides. J. Comput. Aided Mol. Des., 9, 381-395.
-
(1995)
J. Comput. Aided Mol. Des.
, vol.9
, pp. 381-395
-
-
Murray, C.W.1
Clark, D.E.2
Byrne, D.G.3
-
137
-
-
0000934205
-
SMoG de novo design method based on simple, fast, and accurate free energy estimates. 1 Methodology and supporting evidence
-
De Witte, R.S. and Shakhnovich, E.I. (1996) SMoG de novo design method based on simple, fast, and accurate free energy estimates. 1. Methodology and supporting evidence. J. Am. Chem. Soc., 118, 11733-11744.
-
(1996)
J. Am. Chem. Soc.
, vol.118
, pp. 11733-11744
-
-
De Witte, R.S.1
Shakhnovich, E.I.2
-
138
-
-
0037142298
-
SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions
-
Ishchenko, A.V. and Shakhnovich, E.I. (2002) SMall Molecule Growth 2001 (SMoG2001): an improved knowledge-based scoring function for protein-ligand interactions. J. Med. Chem., 45, 2770-2780.
-
(2002)
J. Med. Chem.
, vol.45
, pp. 2770-2780
-
-
Ishchenko, A.V.1
Shakhnovich, E.I.2
-
139
-
-
0037022302
-
Combinatorial computational method gives new picomolar ligands for a known enzyme
-
Grzybowski, B.A., Ishchenko, A.V., Kim, C.Y., Topalov, G., Chapman, R., Christianson, D.W., Whitesides, G.M., and Shakhnovich, E.I. (2002) Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc. Natl. Acad. Sci. U.S.A., 99, 1270-1273.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 1270-1273
-
-
Grzybowski, B.A.1
Ishchenko, A.V.2
Kim, C.Y.3
Topalov, G.4
Chapman, R.5
Christianson, D.W.6
Whitesides, G.M.7
Shakhnovich, E.I.8
-
140
-
-
0029965861
-
CONCERTS: dynamic connection of fragments as an approach to de novo ligand design
-
Pearlman, D.A. and Murcko, M.A. (1996) CONCERTS: dynamic connection of fragments as an approach to de novo ligand design. J. Med. Chem., 39, 1651-1663.
-
(1996)
J. Med. Chem.
, vol.39
, pp. 1651-1663
-
-
Pearlman, D.A.1
Murcko, M.A.2
-
141
-
-
0030277958
-
RASSE: a new method for structurebased drug design
-
Luo, Z., Wang, R., and Lai, L. (1996) RASSE: a new method for structurebased drug design. J. Chem. Inf. Comput. Sci., 36, 1187-1194.
-
(1996)
J. Chem. Inf. Comput. Sci.
, vol.36
, pp. 1187-1194
-
-
Luo, Z.1
Wang, R.2
Lai, L.3
-
142
-
-
0031087525
-
PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1 Technology
-
Murray, C.W., Clark, D.E., Auton, T.R., Firth, M.A., Li, J., Sykes, R.A., Waszkowycz, B., Westhead, D.R., and Young, S.C. (1997) PRO_SELECT: combining structure-based drug design and combinatorial chemistry for rapid lead discovery. 1. Technology. J. Comput. Aided Mol. Des., 11, 193-207.
-
(1997)
J. Comput. Aided Mol. Des.
, vol.11
, pp. 193-207
-
-
Murray, C.W.1
Clark, D.E.2
Auton, T.R.3
Firth, M.A.4
Li, J.5
Sykes, R.A.6
Waszkowycz, B.7
Westhead, D.R.8
Young, S.C.9
-
143
-
-
0031226772
-
Empirical scoring functions: I The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
-
Eldridge, M.D., Murray, C.W., Auton, T.R., Paolini, G.V., and Mee, R.P. (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, 425-445.
-
(1997)
J. Comput. Aided Mol. Des.
, vol.11
, pp. 425-445
-
-
Eldridge, M.D.1
Murray, C.W.2
Auton, T.R.3
Paolini, G.V.4
Mee, R.P.5
-
144
-
-
0031088353
-
Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
-
Todorov, N.P. and Dean, P.M. (1997) Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design. J. Comput. Aided Mol. Des., 11, 175-192.
-
(1997)
J. Comput. Aided Mol. Des.
, vol.11
, pp. 175-192
-
-
Todorov, N.P.1
Dean, P.M.2
-
145
-
-
0032111471
-
A branch-and-bound method for optimal atom-type assignment in de novo ligand design
-
Todorov, N.P. and Dean, P.M. (1998) A branch-and-bound method for optimal atom-type assignment in de novo ligand design. J. Comput. Aided Mol. Des., 12, 335-350.
-
(1998)
J. Comput. Aided Mol. Des.
, vol.12
, pp. 335-350
-
-
Todorov, N.P.1
Dean, P.M.2
-
146
-
-
3242688618
-
A validation study on the practical use of automated de novo design
-
Stahl, M., Todorov, N.P., James, T., Mauser, H., Böhm, H.J., and Dean, P.M. (2002) A validation study on the practical use of automated de novo design. J. Comput. Aided Mol. Des., 16, 459-478.
-
(2002)
J. Comput. Aided Mol. Des.
, vol.16
, pp. 459-478
-
-
Stahl, M.1
Todorov, N.P.2
James, T.3
Mauser, H.4
Böhm, H.J.5
Dean, P.M.6
-
147
-
-
0011137935
-
Molecular evolution: a hierarchical representation for chemical topology its automated manipulation
-
Nachbar, R.B. (1998) Molecular evolution: a hierarchical representation for chemical topology and its automated manipulation. Proceedings of the 3rd Annual Genetic Programming Conference, pp. 246-253;
-
(1998)
Proceedings of the 3rd Annual Genetic Programming Conference
, pp. 246-253
-
-
Nachbar, R.B.1
-
148
-
-
0003913260
-
Molecular evolution: automated manipulation of hierarchical chemical topology and its application to average molecular structures
-
Nachbar, R.B. (2000) Molecular evolution: automated manipulation of hierarchical chemical topology and its application to average molecular structures. Genet. Program. Evolv. Mach., 1, 57-94.
-
(2000)
Genet. Program. Evolv. Mach.
, vol.1
, pp. 57-94
-
-
Nachbar, R.B.1
-
149
-
-
0032675130
-
Automatic molecular design using evolutionary algorithms
-
Globus, A., Lawton, J., and Wipke, W.T. (1999) Automatic molecular design using evolutionary algorithms. Nanotechnology, 10, 290-299.
-
(1999)
Nanotechnology
, vol.10
, pp. 290-299
-
-
Globus, A.1
Lawton, J.2
Wipke, W.T.3
-
150
-
-
0032769150
-
Structure-based ligand design by dynamically assembling molecular building blocks at binding site
-
Liu, H., Duan, Z., Luo, Q., and Shi, Y. (1999) Structure-based ligand design by dynamically assembling molecular building blocks at binding site. Proteins, 36, 462-470.
-
(1999)
Proteins
, vol.36
, pp. 462-470
-
-
Liu, H.1
Duan, Z.2
Luo, Q.3
Shi, Y.4
-
151
-
-
0035003876
-
Design of selective inhibitors of cyclooxygenase-2 dynamic assembly of molecular building blocks
-
Zhu, J., Yu, H., Fan, H., Liu, H., and Shi, Y. (2001) Design of selective inhibitors of cyclooxygenase-2 dynamic assembly of molecular building blocks. J. Comput. Aided Mol. Des., 15, 447-463.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 447-463
-
-
Zhu, J.1
Yu, H.2
Fan, H.3
Liu, H.4
Shi, Y.5
-
152
-
-
0034085674
-
A genetic algorithm for the automated generation of small organic molecules: drug design using an evolutionary algorithm
-
Douguet, D., Thoreau, E., and Grassy, G. (2000) A genetic algorithm for the automated generation of small organic molecules: drug design using an evolutionary algorithm. J. Comput. Aided Mol. Des., 14, 449-466.
-
(2000)
J. Comput. Aided Mol. Des.
, vol.14
, pp. 449-466
-
-
Douguet, D.1
Thoreau, E.2
Grassy, G.3
-
153
-
-
0000217414
-
LigBuilder: a multi-purpose program for structure-based drug design
-
Wang, R., Gao, Y., and Lai, L. (2000) LigBuilder: a multi-purpose program for structure-based drug design. J. Mol. Model., 6, 498-516.
-
(2000)
J. Mol. Model.
, vol.6
, pp. 498-516
-
-
Wang, R.1
Gao, Y.2
Lai, L.3
-
154
-
-
0035731507
-
Structure-based ligand design for flexible proteins: application of new F-DycoBlock
-
Zhu, J., Fan, H., Liu, H., and Shi, Y. (2001) Structure-based ligand design for flexible proteins: application of new F-DycoBlock. J. Comput. Aided Mol. Des., 15, 979-996.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 979-996
-
-
Zhu, J.1
Fan, H.2
Liu, H.3
Shi, Y.4
-
155
-
-
0035570105
-
A genetic algorithm for structure-based de novo design
-
Pegg, S.C.H., Haresco, J.J., and Kuntz, I.D. (2001) A genetic algorithm for structure-based de novo design. J. Comput. Aided Mol. Des., 15, 911-933.
-
(2001)
J. Comput. Aided Mol. Des.
, vol.15
, pp. 911-933
-
-
Pegg, S.C.H.1
Haresco, J.J.2
Kuntz, I.D.3
-
156
-
-
1542608322
-
Development and testing of a de novo drug-design algorithm
-
Pellegrini, E. and Field, M.J. (2003) Development and testing of a de novo drug-design algorithm. J. Comput. Aided Mol. Des., 17, 621-641.
-
(2003)
J. Comput. Aided Mol. Des.
, vol.17
, pp. 621-641
-
-
Pellegrini, E.1
Field, M.J.2
-
157
-
-
2942700379
-
A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules
-
Brown, N., Mc Kay, B., Gilardoni, F., and Gasteiger, J. (2004) A graph-based genetic algorithm and its application to the multiobjective evolution of median molecules. J. Chem. Inf. Comput. Sci., 44, 1079-1087.
-
(2004)
J. Chem. Inf. Comput. Sci.
, vol.44
, pp. 1079-1087
-
-
Brown, N.1
Mc Kay, B.2
Gilardoni, F.3
Gasteiger, J.4
-
158
-
-
2442647742
-
BREED: generating novel inhibitors through hybridization of known ligands Application to CDK2 P38, and HIV protease
-
Pierce, A.C., Rao, G., and Bemis, G.W. (2004) BREED: generating novel inhibitors through hybridization of known ligands. Application to CDK2, P38, and HIV protease. J. Med. Chem., 47, 2768-2775.
-
(2004)
J. Med. Chem.
, vol.47
, pp. 2768-2775
-
-
Pierce, A.C.1
Rao, G.2
Bemis, G.W.3
-
159
-
-
20344378493
-
A very large diversity space of synthetically accessible compounds for use with drug design programs
-
Nikitin, S., Zaitseva, N., Demina, O., Solovieva, V., Mazin, E., Mikhalev, S., Smolov, M., Rubinov, A., Vlasov, P., Lepikhin, D., Khachko, D., Fokin, V., Queen, C., and Zosimov, V. (2005) A very large diversity space of synthetically accessible compounds for use with drug design programs. J. Comput. Aided Mol. Des., 19, 47-63.
-
(2005)
J. Comput. Aided Mol. Des.
, vol.19
, pp. 47-63
-
-
Nikitin, S.1
Zaitseva, N.2
Demina, O.3
Solovieva, V.4
Mazin, E.5
Mikhalev, S.6
Smolov, M.7
Rubinov, A.8
Vlasov, P.9
Lepikhin, D.10
Khachko, D.11
Fokin, V.12
Queen, C.13
Zosimov, V.14
-
160
-
-
17144419244
-
LEA3D: a computer-aided ligand design for structure-based drug design
-
Douguet, D., Munier-Lehmann, H., Labesse, G., and Pochet, S. (2005) LEA3D: a computer-aided ligand design for structure-based drug design. J. Med. Chem., 48, 2457-2468.
-
(2005)
J. Med. Chem.
, vol.48
, pp. 2457-2468
-
-
Douguet, D.1
Munier-Lehmann, H.2
Labesse, G.3
Pochet, S.4
-
161
-
-
33646265985
-
Flux (1): a virtual synthesis scheme for fragment-based de novo design
-
Fechner, U. and Schneider, G. (2006) Flux (1): a virtual synthesis scheme for fragment-based de novo design. J. Chem. Inf. Model., 46, 699-707.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, pp. 699-707
-
-
Fechner, U.1
Schneider, G.2
-
162
-
-
34247191329
-
Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design
-
Fechner, U. and Schneider, G. (2007) Flux (2): comparison of molecular mutation and crossover operators for ligand-based de novo design. J. Chem. Inf. Model., 47, 656-667.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, pp. 656-667
-
-
Fechner, U.1
Schneider, G.2
-
163
-
-
33748652464
-
FlexNovo: structure-based searching in large fragment spaces
-
Degen, J. and Rarey, M. (2006) FlexNovo: structure-based searching in large fragment spaces. ChemMedChem, 1, 854-868.
-
(2006)
ChemMedChem
, vol.1
, pp. 854-868
-
-
Degen, J.1
Rarey, M.2
-
164
-
-
38049014405
-
The use of ligand-based de novo design for scaffold hopping and sidechain optimization: two case studies
-
Feher, M., Gao, Y., Baber, C., Shirley, W.A., and Saunders, J. (2008) The use of ligand-based de novo design for scaffold hopping and sidechain optimization: two case studies. Bioorg. Med. Chem., 16, 422-427.
-
(2008)
Bioorg. Med. Chem.
, vol.16
, pp. 422-427
-
-
Feher, M.1
Gao, Y.2
Baber, C.3
Shirley, W.A.4
Saunders, J.5
-
165
-
-
42149174453
-
Fragment-based de novo ligand design by multiobjective evolutionary optimization
-
Dey, F. and Caflisch, A. (2008) Fragment-based de novo ligand design by multiobjective evolutionary optimization. J. Chem. Inf. Model., 48, 679-690.
-
(2008)
J. Chem. Inf. Model.
, vol.48
, pp. 679-690
-
-
Dey, F.1
Caflisch, A.2
-
166
-
-
58549112609
-
From molecular shape to potent bioactive agents II: fragment-based de novo design
-
Proschak, E., Sander, K., Zettl, H., Tanrikulu, Y., Rau, O., Schneider, P., Schubert-Zsilavecz, M., Stark, H., and Schneider, G. (2009) From molecular shape to potent bioactive agents II: fragment-based de novo design. ChemMedChem, 4, 45-48.
-
(2009)
ChemMedChem
, vol.4
, pp. 45-48
-
-
Proschak, E.1
Sander, K.2
Zettl, H.3
Tanrikulu, Y.4
Rau, O.5
Schneider, P.6
Schubert-Zsilavecz, M.7
Stark, H.8
Schneider, G.9
-
167
-
-
58549110666
-
From molecular shape to potent bioactive agents I: bioisosteric replacement of molecular fragments
-
Proschak, E., Zettl, H., Tanrikulu, Y., Weisel, M., Kriegl, J.M., Rau, O., Schubert-Zsilavecz, M., and Schneider, G. (2009) From molecular shape to potent bioactive agents I: bioisosteric replacement of molecular fragments. ChemMedChem, 4, 41-44.
-
(2009)
ChemMedChem
, vol.4
, pp. 41-44
-
-
Proschak, E.1
Zettl, H.2
Tanrikulu, Y.3
Weisel, M.4
Kriegl, J.M.5
Rau, O.6
Schubert-Zsilavecz, M.7
Schneider, G.8
-
168
-
-
66149089880
-
A novel in silico approach to drug discovery via computational intelligence
-
Hecht, D. and Fogel, G.B. (2009) A novel in silico approach to drug discovery via computational intelligence. J. Chem. Inf. Model., 49, 1105-1121.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1105-1121
-
-
Hecht, D.1
Fogel, G.B.2
-
169
-
-
65249116422
-
Computational fragment-based approach at PDB scale by protein local similarity
-
Moriaud, F., Doppelt-Azeroual, O., Martin, L., Oguievetskaia, K., Koch, K., Vorotyntsev, A., Adcock, S.A., and Delfaud, F. (2009) Computational fragment-based approach at PDB scale by protein local similarity. J. Chem. Inf. Model., 49, 280-294.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 280-294
-
-
Moriaud, F.1
Doppelt-Azeroual, O.2
Martin, L.3
Oguievetskaia, K.4
Koch, K.5
Vorotyntsev, A.6
Adcock, S.A.7
Delfaud, F.8
-
170
-
-
65249111062
-
De novo drug design using multiobjective evolutionary graphs
-
Nicolaou, C.A., Apostolakis, J., and Pattichis, C.S. (2009) De novo drug design using multiobjective evolutionary graphs. J. Chem. Inf. Model., 49, 295-307.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 295-307
-
-
Nicolaou, C.A.1
Apostolakis, J.2
Pattichis, C.S.3
-
171
-
-
66249100884
-
Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design
-
Nisius, B. and Rester, U. (2009) Fragment shuffling: an automated workflow for three-dimensional fragment-based ligand design. J. Chem. Inf. Model., 49, 1211-1222.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1211-1222
-
-
Nisius, B.1
Rester, U.2
-
172
-
-
58849145223
-
AutoGrow: a novel algorithm for protein inhibitor design
-
Durrant, J.D., Amaro, R.E., and Mc Cammon, J.A. (2009) AutoGrow: a novel algorithm for protein inhibitor design. Chem. Biol. Drug Des., 73, 168-178.
-
(2009)
Chem. Biol. Drug Des.
, vol.73
, pp. 168-178
-
-
Durrant, J.D.1
Amaro, R.E.2
Mc Cammon, J.A.3
-
173
-
-
78049416427
-
NovoFLAP: a ligand-based de novo design approach for the generation of medicinally relevant ideas
-
Damewood, J.R., Lerman, C.L., and Masek, B.B. (2010) NovoFLAP: a ligand-based de novo design approach for the generation of medicinally relevant ideas. J. Chem. Inf. Model., 50, 1296-1303.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1296-1303
-
-
Damewood, J.R.1
Lerman, C.L.2
Masek, B.B.3
-
174
-
-
77952097547
-
PhDD: a new pharmacophorebased de novo design method of drug-like molecules combined with assessment of synthetic accessibility
-
Huang, Q., Li, L.L., and Yang, S.J. (2010) PhDD: a new pharmacophorebased de novo design method of drug-like molecules combined with assessment of synthetic accessibility. J. Mol. Graph. Model., 28, 775-787.
-
(2010)
J. Mol. Graph. Model.
, vol.28
, pp. 775-787
-
-
Huang, Q.1
Li, L.L.2
Yang, S.J.3
-
175
-
-
77957227802
-
GARLig: a fully automated tool for subset selection of large fragment spaces via a selfadaptive genetic algorithm
-
Pfeffer, P., Fober, T., Hüllermeier, E., and Klebe, G. (2010) GARLig: a fully automated tool for subset selection of large fragment spaces via a selfadaptive genetic algorithm. J. Chem. Inf. Model., 50, 1644-1659.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1644-1659
-
-
Pfeffer, P.1
Fober, T.2
Hüllermeier, E.3
Klebe, G.4
-
176
-
-
78049448019
-
Generative models for chemical structures
-
White, D. and Wilson, R.C. (2010) Generative models for chemical structures. J. Chem. Inf. Model., 50, 1257-1274.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, pp. 1257-1274
-
-
White, D.1
Wilson, R.C.2
-
177
-
-
84855191711
-
De novo design by pharmacophore-based searches in fragment spaces
-
Lippert, T., Schulz-Gasch, T., Roche, O., Guba, W., and Rarey, M. (2011) De novo design by pharmacophore-based searches in fragment spaces. J. Comput. Aided Mol. Des., 25, 931-945.
-
(2011)
J. Comput. Aided Mol. Des.
, vol.25
, pp. 931-945
-
-
Lippert, T.1
Schulz-Gasch, T.2
Roche, O.3
Guba, W.4
Rarey, M.5
-
178
-
-
79957623774
-
EvoMD: an algorithm for evolutionary molecular design
-
Wong, S.S., Luo, W., and Chan, K.C. (2011) EvoMD: an algorithm for evolutionary molecular design. IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 987-1003.
-
(2011)
IEEE/ACM Trans. Comput. Biol. Bioinform.
, vol.8
, pp. 987-1003
-
-
Wong, S.S.1
Luo, W.2
Chan, K.C.3
-
179
-
-
80052576062
-
De novo design, synthesis and biological evaluation of 1,4-dihydroquinolin-4-ones and 1,2,3,4-tetrahydroquinazolin-4-ones as potent kinesin spindle protein (KSP) inhibitors
-
Jiang, C., Yang, L., Wu, W.T., Guo, Q.L., and You, Q.D. (2011) De novo design, synthesis and biological evaluation of 1,4-dihydroquinolin-4-ones and 1,2,3,4-tetrahydroquinazolin-4-ones as potent kinesin spindle protein (KSP) inhibitors. Bioorg. Med. Chem., 19, 5612-5627.
-
(2011)
Bioorg. Med. Chem.
, vol.19
, pp. 5612-5627
-
-
Jiang, C.1
Yang, L.2
Wu, W.T.3
Guo, Q.L.4
You, Q.D.5
-
180
-
-
84878095568
-
De novo design of protein kinase inhibitors by in silico identification of hinge regionbinding fragments
-
Urich, R., Wishart, G., Kiczun, M., Richters, A., Tidten-Luksch, N., Rauh, D., Sherborne, B., Wyatt, P.G., and Brenk, R. (2013) De novo design of protein kinase inhibitors by in silico identification of hinge regionbinding fragments. ACS Chem. Biol., 8, 1044-1052.
-
(2013)
ACS Chem. Biol.
, vol.8
, pp. 1044-1052
-
-
Urich, R.1
Wishart, G.2
Kiczun, M.3
Richters, A.4
Tidten-Luksch, N.5
Rauh, D.6
Sherborne, B.7
Wyatt, P.G.8
Brenk, R.9
-
181
-
-
80053593946
-
Enabling future drug discovery by de novo design
-
Hartenfeller, M. and Schneider, G. (2011) Enabling future drug discovery by de novo design. WIREs Comput. Mol. Sci., 1, 742-759.
-
(2011)
WIREs Comput. Mol. Sci.
, vol.1
, pp. 742-759
-
-
Hartenfeller, M.1
Schneider, G.2
-
182
-
-
8844263008
-
Docking and scoring in virtual screening for drug discovery: methods and applications
-
Kitchen, D.B., Decornez, H., Furr, J.R., and Bajorath, J. (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat. Rev. Drug Discov., 3, 935-949.
-
(2004)
Nat. Rev. Drug Discov.
, vol.3
, pp. 935-949
-
-
Kitchen, D.B.1
Decornez, H.2
Furr, J.R.3
Bajorath, J.4
-
183
-
-
35348868045
-
A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations
-
Wang, B., Westerhoff, L.M., and Merz, K.M. Jr., (2007) A critical assessment of the performance of protein-ligand scoring functions based on NMR chemical shift perturbations. J. Med. Chem., 50, 5128-5134.
-
(2007)
J. Med. Chem.
, vol.50
, pp. 5128-5134
-
-
Wang, B.1
Westerhoff, L.M.2
Merz, K.M.Jr.3
-
184
-
-
33749449880
-
Docking and scoring-theoretically easy, practically impossible?
-
Coupez, B. and Lewis, R.A. (2006) Docking and scoring-theoretically easy, practically impossible? Curr. Med. Chem., 13, 2995-3003.
-
(2006)
Curr. Med. Chem.
, vol.13
, pp. 2995-3003
-
-
Coupez, B.1
Lewis, R.A.2
-
185
-
-
78650194463
-
Rigorous free energy calculations in structure-based drug design
-
Michel, J., Foloppe, N., and Essex, J.W. (2010) Rigorous free energy calculations in structure-based drug design. Mol. Inf., 29, 570-578.
-
(2010)
Mol. Inf.
, vol.29
, pp. 570-578
-
-
Michel, J.1
Foloppe, N.2
Essex, J.W.3
-
186
-
-
0036007208
-
Virtual screening and fast automated docking methods
-
Schneider, G. and Böhm, H.J. (2002) Virtual screening and fast automated docking methods. Drug Discov. Today, 7, 64-70.
-
(2002)
Drug Discov. Today
, vol.7
, pp. 64-70
-
-
Schneider, G.1
Böhm, H.J.2
-
187
-
-
0035312864
-
Statistical potentials and scoring functions applied to protein-ligand binding
-
Gohlke, H. and Klebe, G. (2001) Statistical potentials and scoring functions applied to protein-ligand binding. Curr. Opin. Struct. Biol., 11, 231-235.
-
(2001)
Curr. Opin. Struct. Biol.
, vol.11
, pp. 231-235
-
-
Gohlke, H.1
Klebe, G.2
-
188
-
-
0036001094
-
From knowledge-based potentials to combinatorial lead design in silico
-
Grzybowski, B.A., Ishchenko, A.V., Shimada, J., and Shakhnovich, E.I. (2002) From knowledge-based potentials to combinatorial lead design in silico. Acc. Chem. Res., 35, 261-269.
-
(2002)
Acc. Chem. Res.
, vol.35
, pp. 261-269
-
-
Grzybowski, B.A.1
Ishchenko, A.V.2
Shimada, J.3
Shakhnovich, E.I.4
-
189
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
Schneider, G. and Fechner, U. (2005) Computer-based de novo design of drug-like molecules. Nat. Rev. Drug Discov., 4, 649-663.
-
(2005)
Nat. Rev. Drug Discov.
, vol.4
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
190
-
-
36949018707
-
Chemical genomics: a challenge for de novo drug design
-
Dean, P.M. (2007) Chemical genomics: a challenge for de novo drug design. Mol. Biotechnol., 37, 237-245.
-
(2007)
Mol. Biotechnol.
, vol.37
, pp. 237-245
-
-
Dean, P.M.1
-
191
-
-
42449095567
-
Recent developments in de novo design and scaffold hopping
-
Mauser, H. and Guba, W. (2008) Recent developments in de novo design and scaffold hopping. Curr. Opin. Drug Discov. Dev., 11, 365-374.
-
(2008)
Curr. Opin. Drug Discov. Dev.
, vol.11
, pp. 365-374
-
-
Mauser, H.1
Guba, W.2
-
192
-
-
67649225348
-
Efficient drug lead discovery and optimization
-
Jorgensen, W.L. (2009) Efficient drug lead discovery and optimization. Acc. Chem. Res., 42, 724-733.
-
(2009)
Acc. Chem. Res.
, vol.42
, pp. 724-733
-
-
Jorgensen, W.L.1
-
193
-
-
79952221121
-
The quest for novel chemical matter and the contribution of computer-aided de novo design
-
Pirard, B. (2011) The quest for novel chemical matter and the contribution of computer-aided de novo design. Expert Opin. Drug Discov., 6, 225-231.
-
(2011)
Expert Opin. Drug Discov.
, vol.6
, pp. 225-231
-
-
Pirard, B.1
-
194
-
-
79952118858
-
Some trends in chem(o)informatics
-
Warr, W.A. (2011) Some trends in chem(o)informatics. Methods Mol. Biol., 672, 1-37.
-
(2011)
Methods Mol. Biol.
, vol.672
, pp. 1-37
-
-
Warr, W.A.1
-
195
-
-
77954787493
-
De novo design: balancing novelty and confined chemical space
-
Kutchukian, P.S. and Shakhnovich, E.I. (2010) De novo design: balancing novelty and confined chemical space. Expert Opin. Drug Discov., 5, 789-812.
-
(2010)
Expert Opin. Drug Discov.
, vol.5
, pp. 789-812
-
-
Kutchukian, P.S.1
Shakhnovich, E.I.2
-
196
-
-
77958566813
-
In silico fragment-based drug design
-
Konteatis, Z.D. (2010) In silico fragment-based drug design. Expert Opin. Drug Discov., 5, 1047-1065.
-
(2010)
Expert Opin. Drug Discov.
, vol.5
, pp. 1047-1065
-
-
Konteatis, Z.D.1
-
198
-
-
84876079596
-
Fragment informatics and computational fragment-based drug design: an overview and update
-
Sheng, C. and Zhang, W. (2013) Fragment informatics and computational fragment-based drug design: an overview and update. Med. Res. Rev., 33, 554-598.
-
(2013)
Med. Res. Rev.
, vol.33
, pp. 554-598
-
-
Sheng, C.1
Zhang, W.2
-
199
-
-
84866460237
-
Multi-objective optimization methods in de novo drug design
-
Nicolaou, C.A., Kannas, C., and Loizidou, E. (2012) Multi-objective optimization methods in de novo drug design. Mini Rev. Med. Chem., 12, 979-987.
-
(2012)
Mini Rev. Med. Chem.
, vol.12
, pp. 979-987
-
-
Nicolaou, C.A.1
Kannas, C.2
Loizidou, E.3
-
200
-
-
0017184784
-
Compounds designed to fit a site of known structure in human haemoglobin
-
Beddell, C.R., Goodford, P.J., Norrington, F.E., Wilkinson, S., and Wootton, R. (1976) Compounds designed to fit a site of known structure in human haemoglobin. Br. J. Pharmacol., 57, 201-209.
-
(1976)
Br. J. Pharmacol.
, vol.57
, pp. 201-209
-
-
Beddell, C.R.1
Goodford, P.J.2
Norrington, F.E.3
Wilkinson, S.4
Wootton, R.5
-
201
-
-
0018409314
-
Species differences in the binding of compounds designed to fit a site of known structure in adult human haemoglobin
-
Beddell, C.R., Goodford, P.J., Stammers, D.K., and Wootton, R. (1979) Species differences in the binding of compounds designed to fit a site of known structure in adult human haemoglobin. Br. J. Pharmacol., 65, 535-543.
-
(1979)
Br. J. Pharmacol.
, vol.65
, pp. 535-543
-
-
Beddell, C.R.1
Goodford, P.J.2
Stammers, D.K.3
Wootton, R.4
-
202
-
-
0007907064
-
Computer searching of a molecular structure file for pharmacophoric patterns
-
Gund, P., Wipke, W.T., and Langridge, R. (1974) Computer searching of a molecular structure file for pharmacophoric patterns. Comput. Chem. Res. Educ. Technol., 3, 5-21.
-
(1974)
Comput. Chem. Res. Educ. Technol.
, vol.3
, pp. 5-21
-
-
Gund, P.1
Wipke, W.T.2
Langridge, R.3
-
203
-
-
85050542952
-
-
eds K. Lipkowitz and D. Boyd), Wiley-VCH Verlag GmbH, Weinheim
-
Martin, Y.C., Bures, M.G., and Willett, P. (1990) in Reviews in Computational Chemistry, Vol. 1 (eds K. Lipkowitz and D. Boyd), Wiley-VCH Verlag GmbH, Weinheim, pp. 213-263.
-
(1990)
Reviews in Computational Chemistry
, vol.1
, pp. 213-263
-
-
Martin, Y.C.1
Bures, M.G.2
Willett, P.3
-
204
-
-
0023436445
-
Designing novel nicotinic agonists by searching a database of molecular shapes
-
Sheridan, R.P. and Venkataraghavan, R. (1987) Designing novel nicotinic agonists by searching a database of molecular shapes. J. Comput. Aided Mol. Des., 1, 243-256.
-
(1987)
J. Comput. Aided Mol. Des.
, vol.1
, pp. 243-256
-
-
Sheridan, R.P.1
Venkataraghavan, R.2
-
205
-
-
0024501968
-
Automated site-directed drug design: the formation of molecular templates in primary structure generation
-
Lewis, R.A. and Dean, P.M. (1989) Automated site-directed drug design: the formation of molecular templates in primary structure generation. Proc. R. Soc. London, Ser. B, 236, 141-162.
-
(1989)
Proc. R. Soc. London Ser. B
, vol.236
, pp. 141-162
-
-
Lewis, R.A.1
Dean, P.M.2
-
206
-
-
0024725804
-
ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of threedimensional molecular structures
-
Van Drie, J.H., Weininger, D., and Martin, Y.C. (1989) ALADDIN: an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric, and substructure searching of threedimensional molecular structures. J. Comput. Aided Mol. Des., 3, 225-240.
-
(1989)
J. Comput. Aided Mol. Des.
, vol.3
, pp. 225-240
-
-
Van Drie, J.H.1
Weininger, D.2
Martin, Y.C.3
-
207
-
-
0012257335
-
Molecular Recognition in Chemical and Biological Problems
-
ed. S.M. Roberts London
-
Bartlett, P.A., Shea, G.T., Telfer, S.J., and Waterman, S. (1989) in Molecular Recognition in Chemical and Biological Problems, Vol. 78 (ed. S.M. Roberts), Royal Society of Chemistry, London, pp. 182-196.
-
(1989)
Royal Society of Chemistry
, vol.78
, pp. 182-196
-
-
Bartlett, P.A.1
Shea, G.T.2
Telfer, S.J.3
Waterman, S.4
-
208
-
-
0028380643
-
CAVEAT: a program to facilitate the design of organic molecules
-
Lauri, G. and Bartlett, P.A. (1994) CAVEAT: a program to facilitate the design of organic molecules. J. Comput. Aided Mol. Des., 8, 51-66.
-
(1994)
J. Comput. Aided Mol. Des.
, vol.8
, pp. 51-66
-
-
Lauri, G.1
Bartlett, P.A.2
-
209
-
-
0000212997
-
GENOA: a computer program for structure elucidation utilizing overlapping and alternative substructures
-
Carhart, R.E., Smith, D.H., Gray, N.A.B., Nourse, J.G., and Djerassi, C. (1981) GENOA: a computer program for structure elucidation utilizing overlapping and alternative substructures. J. Org. Chem., 46, 1708-1718.
-
(1981)
J. Org. Chem.
, vol.46
, pp. 1708-1718
-
-
Carhart, R.E.1
Smith, D.H.2
Gray, N.A.B.3
Nourse, J.G.4
Djerassi, C.5
-
210
-
-
5644272823
-
-
ed. J.C. Dearden, Elsevier, Amsterdam
-
Wise, M., Cramer, R.D., Smith, D., and Exman, I. (1983) in Quantitative Approaches to Drug Design (ed. J.C. Dearden), Elsevier, Amsterdam, pp. 145-146.
-
(1983)
Quantitative Approaches to Drug Design
, pp. 145-146
-
-
Wise, M.1
Cramer, R.D.2
Smith, D.3
Exman, I.4
-
211
-
-
0021871375
-
A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
-
Goodford, P.J. (1995) A computational procedure for determining energetically favorable binding sites on biologically important macromolecules. J. Med. Chem., 28, 849-857.
-
(1995)
J. Med. Chem.
, vol.28
, pp. 849-857
-
-
Goodford, P.J.1
-
212
-
-
0025916872
-
Functionality maps of binding sites: a multiple copy simultaneous search method
-
Miranker, A. and Karplus, M. (1991) Functionality maps of binding sites: a multiple copy simultaneous search method. Proteins, 11, 29-34.
-
(1991)
Proteins
, vol.11
, pp. 29-34
-
-
Miranker, A.1
Karplus, M.2
-
213
-
-
0020491251
-
A geometric approach to macromoleculeligand interactions
-
Kuntz, I.D., Blaney, J.M., Oatley, S.J., Langridge, R., and Ferrin, T.E. (1982) A geometric approach to macromoleculeligand interactions. J. Mol. Biol., 161, 269-288.
-
(1982)
J. Mol. Biol.
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
214
-
-
0028866563
-
Update on computer-aided drug design
-
Jackson, R.C. (1995) Update on computer-aided drug design. Curr. Opin. Biotechnol., 6, 646-651.
-
(1995)
Curr. Opin. Biotechnol.
, vol.6
, pp. 646-651
-
-
Jackson, R.C.1
-
215
-
-
0030220147
-
Current computational tools for de novo ligand design
-
Böhm, H.J. (1996) Current computational tools for de novo ligand design. Curr. Opin. Biotechnol., 7, 433-436.
-
(1996)
Curr. Opin. Biotechnol.
, vol.7
, pp. 433-436
-
-
Böhm, H.J.1
-
216
-
-
0031197206
-
Modern computational chemistry and drug discovery: structure generating programs
-
Bohacek, R.S. and Mc Martin, C. (1997) Modern computational chemistry and drug discovery: structure generating programs. Curr. Opin. Chem. Biol., 1, 157-161.
-
(1997)
Curr. Opin. Chem. Biol.
, vol.1
, pp. 157-161
-
-
Bohacek, R.S.1
Mc Martin, C.2
-
217
-
-
0030960230
-
Structurebased drug design: computational advances
-
Marrone, T.J., Briggs, J.M., and Mc Cammon, J.A. (1997) Structurebased drug design: computational advances. Annu. Rev. Pharmacol. Toxicol., 37, 71-90.
-
(1997)
Annu. Rev. Pharmacol. Toxicol.
, vol.37
, pp. 71-90
-
-
Marrone, T.J.1
Briggs, J.M.2
Mc Cammon, J.A.3
-
218
-
-
0002716825
-
Combinatorial and computational approaches in structurebased drug design
-
Kubinyi, H. (1998) Combinatorial and computational approaches in structurebased drug design. Curr. Opin. Drug Discov. Dev., 1, 16-27.
-
(1998)
Curr. Opin. Drug Discov. Dev.
, vol.1
, pp. 16-27
-
-
Kubinyi, H.1
-
219
-
-
0026345685
-
Computer design of bioactive molecules: a method for receptorbased de novo ligand design
-
Moon, J.B. and Howe, W.J. (1991) Computer design of bioactive molecules: a method for receptorbased de novo ligand design. Proteins, 11, 314-328.
-
(1991)
Proteins
, vol.11
, pp. 314-328
-
-
Moon, J.B.1
Howe, W.J.2
-
220
-
-
0026813925
-
The computer program LUDI: a new method for the de novo design of enzyme inhibitors
-
Böhm, H.J. (1992) The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J. Comput. Aided Mol. Des., 6, 61-78.
-
(1992)
J. Comput. Aided Mol. Des.
, vol.6
, pp. 61-78
-
-
Böhm, H.J.1
-
221
-
-
0027027467
-
LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads
-
Böhm, H.J. (1992) LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads. J. Comput. Aided Mol. Des., 6, 593-606.
-
(1992)
J. Comput. Aided Mol. Des.
, vol.6
, pp. 593-606
-
-
Böhm, H.J.1
-
222
-
-
70450203818
-
The medicinal chemistry of peptides
-
Nestor, J.J. Jr., (2009) The medicinal chemistry of peptides. Curr. Med. Chem., 16, 4399-4418.
-
(2009)
Curr. Med. Chem.
, vol.16
, pp. 4399-4418
-
-
Nestor, J.J.Jr.1
-
223
-
-
79954780449
-
Computational design of peptide ligands
-
Vanhee, P., van der Sloot, A.M., Verschueren, E., Serrano, L., Rousseau, F., and Schymkowitz, J. (2011) Computational design of peptide ligands. Trends Biotechnol., 29, 231-239.
-
(2011)
Trends Biotechnol.
, vol.29
, pp. 231-239
-
-
Vanhee, P.1
van der Sloot, A.M.2
Verschueren, E.3
Serrano, L.4
Rousseau, F.5
Schymkowitz, J.6
-
224
-
-
84874945035
-
Approaches for enhancing oral bioavailability of peptides and proteins
-
Renukuntla, J., Vadlapudi, A.D., Patel, A., Boddu, S.H., and Mitra, A.K. (2013) Approaches for enhancing oral bioavailability of peptides and proteins. Int. J. Pharm., 447, 75-93.
-
(2013)
Int. J. Pharm.
, vol.447
, pp. 75-93
-
-
Renukuntla, J.1
Vadlapudi, A.D.2
Patel, A.3
Boddu, S.H.4
Mitra, A.K.5
-
225
-
-
65549144355
-
Discovery of a novel HCV helicase inhibitor by a de novo drug design approach
-
Kandil, S., Biondaro, S., Vlachakis, D., Cummins, A.C., Coluccia, A., Berry, C., Leyssen, P., Neyts, J., and Brancale, A. (2009) Discovery of a novel HCV helicase inhibitor by a de novo drug design approach. Bioorg. Med. Chem. Lett., 19, 2935-2937.
-
(2009)
Bioorg. Med. Chem. Lett.
, vol.19
, pp. 2935-2937
-
-
Kandil, S.1
Biondaro, S.2
Vlachakis, D.3
Cummins, A.C.4
Coluccia, A.5
Berry, C.6
Leyssen, P.7
Neyts, J.8
Brancale, A.9
-
226
-
-
8544222806
-
Identification of novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel synthesis
-
Rogers-Evans, M., Alanine, A., Bleicher, K., Kube, D., and Schneider, G. (2004) Identification of novel cannabinoid receptor ligands via evolutionary de novo design and rapid parallel synthesis. QSAR Comb. Sci., 26, 426-430.
-
(2004)
QSAR Comb. Sci.
, vol.26
, pp. 426-430
-
-
Rogers-Evans, M.1
Alanine, A.2
Bleicher, K.3
Kube, D.4
Schneider, G.5
-
227
-
-
0033523672
-
'Scaffoldhopping' by topological pharmacophore search: a contribution to virtual screening
-
Schneider, G., Neidhart, W., Giller, T., and Schmid, G. (1999) 'Scaffoldhopping' by topological pharmacophore search: a contribution to virtual screening. Angew. Chem. Int. Ed., 38, 2894-2896.
-
(1999)
Angew. Chem. Int. Ed.
, vol.38
, pp. 2894-2896
-
-
Schneider, G.1
Neidhart, W.2
Giller, T.3
Schmid, G.4
-
228
-
-
41849138619
-
Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity
-
Alig, L., Alsenz, J., Andjelkovic, M., Bendels, S., Benardeau, A., Bleicher, K., Bourson, A., David-Pierson, P., Guba, W., Hildbrand, S., Kube, D., Lübbers, T., Mayweg, A.V., Narquizian, R., Neidhart, W., Nettekoven, M., Plancher, J.M., Rocha, C., Rogers-Evans, M., Röver, S., Schneider, G., Taylor, S., and Waldmeier, P. (2008) Benzodioxoles: novel cannabinoid-1 receptor inverse agonists for the treatment of obesity. J. Med. Chem., 51, 2115-2127.
-
(2008)
J. Med. Chem.
, vol.51
, pp. 2115-2127
-
-
Alig, L.1
Alsenz, J.2
Andjelkovic, M.3
Bendels, S.4
Benardeau, A.5
Bleicher, K.6
Bourson, A.7
David-Pierson, P.8
Guba, W.9
Hildbrand, S.10
Kube, D.11
Lübbers, T.12
Mayweg, A.V.13
Narquizian, R.14
Neidhart, W.15
Nettekoven, M.16
Plancher, J.M.17
Rocha, C.18
Rogers-Evans, M.19
Röver, S.20
Schneider, G.21
Taylor, S.22
Waldmeier, P.23
more..
-
229
-
-
79960977184
-
Large-scale integrated super-computing platform for next generation virtual drug discovery
-
Mitchell, W. and Matsumoto, S. (2011) Large-scale integrated super-computing platform for next generation virtual drug discovery. Curr. Opin. Chem. Biol., 15, 553-559.
-
(2011)
Curr. Opin. Chem. Biol.
, vol.15
, pp. 553-559
-
-
Mitchell, W.1
Matsumoto, S.2
-
230
-
-
84867458442
-
Structure-based de novo design of Eya2 phosphatase inhibitors
-
Park, H., Ryu, S.E., and Kim, S.J. (2012) Structure-based de novo design of Eya2 phosphatase inhibitors. J. Mol. Graph. Model., 38, 382-388.
-
(2012)
J. Mol. Graph. Model.
, vol.38
, pp. 382-388
-
-
Park, H.1
Ryu, S.E.2
Kim, S.J.3
-
231
-
-
84855708686
-
Structure-based de novo design and biochemical evaluation of novel BRAF kinase inhibitors
-
Park, H., Jeong, Y., and Hong, S. (2012) Structure-based de novo design and biochemical evaluation of novel BRAF kinase inhibitors. Bioorg. Med. Chem. Lett., 22, 1027-1030.
-
(2012)
Bioorg. Med. Chem. Lett.
, vol.22
, pp. 1027-1030
-
-
Park, H.1
Jeong, Y.2
Hong, S.3
-
232
-
-
84865517667
-
Structure-based design technology contour and its application to the design of renin inhibitors
-
Ishchenko, A., Liu, Z., Lindblom, P., Wu, G., Jim, K.C., Gregg, R.D., Claremon, D.A., and Singh, S.B. (2012) Structure-based design technology contour and its application to the design of renin inhibitors. J. Chem. Inf. Model., 52, 2089-2097.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 2089-2097
-
-
Ishchenko, A.1
Liu, Z.2
Lindblom, P.3
Wu, G.4
Jim, K.C.5
Gregg, R.D.6
Claremon, D.A.7
Singh, S.B.8
-
233
-
-
84864202186
-
Multi-objective evolutionary design of adenosine receptor ligands
-
van der Horst, E., Marqúes-Gallego, P., Mulder-Krieger, T., van Veldhoven, J., Kruisselbrink, J., Aleman, A., Emmerich, M.T., Brussee, J., Bender, A., and Ijzerman, A.P. (2012) Multi-objective evolutionary design of adenosine receptor ligands. J. Chem. Inf. Model., 52, 1713-1721.
-
(2012)
J. Chem. Inf. Model.
, vol.52
, pp. 1713-1721
-
-
van der Horst, E.1
Marqúes-Gallego, P.2
Mulder-Krieger, T.3
van Veldhoven, J.4
Kruisselbrink, J.5
Aleman, A.6
Emmerich, M.T.7
Brussee, J.8
Bender, A.9
Ijzerman, A.P.10
-
234
-
-
79961166537
-
Finding promiscuous old drugs for new uses
-
Ekins, S. and Williams, A.J. (2011) Finding promiscuous old drugs for new uses. Pharm. Res., 28, 1785-1791.
-
(2011)
Pharm. Res.
, vol.28
, pp. 1785-1791
-
-
Ekins, S.1
Williams, A.J.2
-
235
-
-
72049100230
-
Identification and validation of a potent type II inhibitor of inactive polo-like kinase 1
-
Keppner, S., Proschak, E., Schneider, G., and Spänkuch, B. (2009) Identification and validation of a potent type II inhibitor of inactive polo-like kinase 1. ChemMedChem, 4, 1806-1809.
-
(2009)
ChemMedChem
, vol.4
, pp. 1806-1809
-
-
Keppner, S.1
Proschak, E.2
Schneider, G.3
Spänkuch, B.4
-
236
-
-
79953672431
-
Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors
-
Schneider, G., Geppert, T., Hartenfeller, M., Reisen, F., Klenner, A., Reutlinger, M., Hähnke, V., Hiss, J.A., Zettl, H., Keppner, S., Spänkuch, S., and Schneider, P. (2011) Reaction-driven de novo design, synthesis and testing of potential type II kinase inhibitors. Future Med. Chem., 3, 415-424.
-
(2011)
Future Med. Chem.
, vol.3
, pp. 415-424
-
-
Schneider, G.1
Geppert, T.2
Hartenfeller, M.3
Reisen, F.4
Klenner, A.5
Reutlinger, M.6
Hähnke, V.7
Hiss, J.A.8
Zettl, H.9
Keppner, S.10
Spänkuch, S.11
Schneider, P.12
-
237
-
-
84876480311
-
Drugs by numbers: reaction-driven de novo design of potent and selective anticancer leads
-
Spänkuch, B., Keppner, S., Lange, L., Rodrigues, T., Zettl, H., Koch, C.P., Reutlinger, M., Hartenfeller, M., Schneider, P., and Schneider, G. (2013) Drugs by numbers: reaction-driven de novo design of potent and selective anticancer leads. Angew. Chem. Int. Ed., 52, 4676-4681.
-
(2013)
Angew. Chem. Int. Ed.
, vol.52
, pp. 4676-4681
-
-
Spänkuch, B.1
Keppner, S.2
Lange, L.3
Rodrigues, T.4
Zettl, H.5
Koch, C.P.6
Reutlinger, M.7
Hartenfeller, M.8
Schneider, P.9
Schneider, G.10
-
238
-
-
84876736732
-
De novo design and optimization of Aurora A kinase inhibitors
-
Rodrigues, T., Roudnicky, F., Koch, C.P., Kudoh, T., Reker, D., Detmar, M., and Schneider, G. (2013) De novo design and optimization of Aurora A kinase inhibitors. Chem. Sci., 4, 1229-1233.
-
(2013)
Chem. Sci.
, vol.4
, pp. 1229-1233
-
-
Rodrigues, T.1
Roudnicky, F.2
Koch, C.P.3
Kudoh, T.4
Reker, D.5
Detmar, M.6
Schneider, G.7
-
239
-
-
77949345618
-
Computational approaches for fragment-based and de novo design
-
Loving, K., Alberts, I., and Sherman, W. (2010) Computational approaches for fragment-based and de novo design. Curr. Top. Med. Chem., 10, 14-32.
-
(2010)
Curr. Top. Med. Chem.
, vol.10
, pp. 14-32
-
-
Loving, K.1
Alberts, I.2
Sherman, W.3
-
240
-
-
77952732009
-
Bioisosteric replacement and scaffold hopping in lead generation and optimization
-
Langdon, S.R., Ertl, P., and Brown, N. (2010) Bioisosteric replacement and scaffold hopping in lead generation and optimization. Mol. Inf., 29, 366-385.
-
(2010)
Mol. Inf.
, vol.29
, pp. 366-385
-
-
Langdon, S.R.1
Ertl, P.2
Brown, N.3
-
241
-
-
0035145264
-
High-throughput chemistry and structure-based design: survival of the smartest
-
Bailey, D. and Brown, D. (2001) High-throughput chemistry and structure-based design: survival of the smartest. Drug Discov. Today, 6, 57-59.
-
(2001)
Drug Discov. Today
, vol.6
, pp. 57-59
-
-
Bailey, D.1
Brown, D.2
-
242
-
-
0038387389
-
Hit and lead generation: beyond high-throughput screening
-
Bleicher, K.H., Böhm, H.J., Müller, K., and Alanine, A.I. (2003) Hit and lead generation: beyond high-throughput screening. Nat. Rev. Drug Discov., 2, 369-378.
-
(2003)
Nat. Rev. Drug Discov.
, vol.2
, pp. 369-378
-
-
Bleicher, K.H.1
Böhm, H.J.2
Müller, K.3
Alanine, A.I.4
-
243
-
-
77950503976
-
Virtual screening: an endless staircase?
-
Schneider, G. (2010) Virtual screening: an endless staircase? Nat. Rev. Drug Discov., 9, 273-276.
-
(2010)
Nat. Rev. Drug Discov.
, vol.9
, pp. 273-276
-
-
Schneider, G.1
-
244
-
-
66249097778
-
Scaffold-hopping potential of fragmentbased de novo design: the chances and limits of variation
-
Krüger, B.A., Dietrich, A., Baringhaus, K.H., and Schneider, G. (2009) Scaffold-hopping potential of fragmentbased de novo design: the chances and limits of variation. Comb. Chem. High Throughput Screening, 12, 383-396.
-
(2009)
Comb. Chem. High Throughput Screening
, vol.12
, pp. 383-396
-
-
Krüger, B.A.1
Dietrich, A.2
Baringhaus, K.H.3
Schneider, G.4
-
245
-
-
0004976810
-
Searching for pharmacophores in large coordinate data bases and its use in drug design
-
Sheridan, R.P., Rusinko, A. III, Nilakantan, R., and Venkataraghavan, R. (1989) Searching for pharmacophores in large coordinate data bases and its use in drug design. Proc. Natl. Acad. Sci. U.S.A., 86, 8165-8169.
-
(1989)
Proc. Natl. Acad. Sci. U.S.A.
, vol.86
, pp. 8165-8169
-
-
Sheridan, R.P.1
Rusinko, A.2
Nilakantan, R.3
Venkataraghavan, R.4
|