-
1
-
-
0036603905
-
Chemical space navigation in lead discovery
-
DOI 10.1016/S1367-5931(02)00329-0
-
Oprea, T. I. Chemical space navigation in lead discovery. Curr. Ovin. Chem. Biol. 2002, 6, 384-389. (Pubitemid 34522066)
-
(2002)
Current Opinion in Chemical Biology
, vol.6
, Issue.3
, pp. 384-389
-
-
Oprea, T.I.1
-
2
-
-
11144320699
-
Navigating chemical space for biology and medicine
-
DOI 10.1038/nature03193
-
Lipinski, C.; Hopkins, A. Navigating chemical space for biology and medicine. Nature 2004, 432, 855-861. (Pubitemid 40037141)
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 855-861
-
-
Lipinski, C.1
Hopkins, A.2
-
4
-
-
0029783934
-
Neighborhood behavior: A useful concept for validation of 'molecular diversity' descriptors
-
DOI 10.1021/jm960290n
-
Patterson, D. E.; Cramer, R. D.; Ferguson, A. M.; Clark, R. D.; Weinberger, L. E. Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors. J. Med. Chem. 1996, 39, 3049-3059. (Pubitemid 26260310)
-
(1996)
Journal of Medicinal Chemistry
, vol.39
, Issue.16
, pp. 3049-3059
-
-
Patterson, D.E.1
Cramer, R.D.2
Ferguson, A.M.3
Clark, R.D.4
Weinberger, L.E.5
-
5
-
-
23844449940
-
Computer-based de novo design of drug-like molecules
-
DOI 10.1038/nrd1799
-
Schneider, G.; Fechner, U. Computer-based de novo design of druglike molecules. Nat. Rev. Drug Discovery 2005, 4, 649-663. (Pubitemid 41149759)
-
(2005)
Nature Reviews Drug Discovery
, vol.4
, Issue.8
, pp. 649-663
-
-
Schneider, G.1
Fechner, U.2
-
6
-
-
0033863669
-
High-throughput screening: New technology for the 21st century
-
DOI 10.1016/S1367-5931(00)00110-1
-
Hertzberg, R.; Pope, A. High-throughput screening: new technology for the 21st century. Curr. Opin. Chem. Biol. 2000, 4, 445-451. (Pubitemid 30621048)
-
(2000)
Current Opinion in Chemical Biology
, vol.4
, Issue.4
, pp. 445-451
-
-
Hertzberg, R.P.1
Pope, A.J.2
-
7
-
-
4344592378
-
Fragment-based lead discovery
-
Rees, D. C.; Congreve, M.; Murray, C. W.; Carr, R. Fragment-based lead discovery. Nat. Rev. Drug Discovery 2004, 3, 660-672. (Pubitemid 39173507)
-
(2004)
Nature Reviews Drug Discovery
, vol.3
, Issue.8
, pp. 660-672
-
-
Ress, D.C.1
Congreve, M.2
Murray, C.W.3
Carr, R.4
-
8
-
-
0036491696
-
Chemical database techniques in drug discovery
-
Miller, M. Chemical database techniques in drug discovery. Nat. Rev. Drug Discovery 2002, 1, 220-227. (Pubitemid 37361425)
-
(2002)
Nature Reviews Drug Discovery
, vol.1
, Issue.3
, pp. 220-227
-
-
Miller, M.A.1
-
9
-
-
0032572819
-
Can we learn to distinguish between 'drug-like' and 'nondrug-like' molecules?
-
DOI 10.1021/jm970666c
-
Ajay, A.; Walters, W. P.; Murcko, M. A. Can we learn to distinguish between "drug-like" and "nondrug-like" molecules. J. Med. Chem. 1998, 41, 3314-3324. (Pubitemid 28406538)
-
(1998)
Journal of Medicinal Chemistry
, vol.41
, Issue.18
, pp. 3314-3324
-
-
Ajay1
Walters, W.P.2
Murcko, M.A.3
-
12
-
-
0024010130
-
Structure generation by reduction: A new strategy for computer-assisted structure elucidation
-
Christie, B. D.; Munk, M. E. Structure generation by reduction: a new strategy for computer-assisted structure elucidation. J. Chem. Inf. omput. Sci. 1988, 28, 87-93.
-
(1988)
J. Chem. Inf. Omput. Sci.
, vol.28
, pp. 87-93
-
-
Christie, B.D.1
Munk, M.E.2
-
14
-
-
0027193713
-
GroupBuild: A fragment-based method for de novo drug design
-
Rotstein, S.; Murcko, M. GroupBuild: a fragment-based method for de novo drug design. J. Med. Chem. 1993, 36, 1700-1710. (Pubitemid 23191297)
-
(1993)
Journal of Medicinal Chemistry
, vol.36
, Issue.12
, pp. 1700-1710
-
-
Rotstein, S.H.1
Murcko, M.A.2
-
15
-
-
0000217414
-
LigBuilder: A multi-purpose program for structure-based drug design
-
Wang, R.; Gao, Y.; Lai, L. LigBuilder: a multi-purpose program for structure-based drug design. J. Mol. Model. 2000, 6, 498-516.
-
(2000)
J. Mol. Model.
, vol.6
, pp. 498-516
-
-
Wang, R.1
Gao, Y.2
Lai, L.3
-
16
-
-
0026345685
-
Computer design of bioactive molecules: A method for receptor-based de novo ligand design
-
Moon, J.; Howe, W. Computer design of bioactive molecules: a method for receptor-based de novo ligand design. Proteins: Struct., Fun., Genet. 1991, 11, 314-328.
-
(1991)
Proteins: Struct., Fun., Genet.
, vol.11
, pp. 314-328
-
-
Moon, J.1
Howe, W.2
-
17
-
-
0029320812
-
BUILDER v. 2: Improving the chemistry of a de novo design strategy
-
Roe, D.; Kuntz, I. BUILDER v. 2: Improving the chemistry of a de novo design strategy. J. Comput.-Aided Mol. Des. 1995, 9, 269-282.
-
(1995)
J. Comput.-aided Mol. Des.
, vol.9
, pp. 269-282
-
-
Roe, D.1
Kuntz, I.2
-
18
-
-
0029242926
-
DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria
-
Ho, C.; Marshall, G. DBMAKER: A set of programs to generate three-dimensional databases based upon user-specified criteria. J. Comput.-Aided Mol. Des 1995, 9, 65-86.
-
(1995)
J. Comput.-aided Mol. des
, vol.9
, pp. 65-86
-
-
Ho, C.1
Marshall, G.2
-
19
-
-
0029988211
-
BOOMSLANG: A program for combinatorial structure generation
-
DOI 10.1016/0263-7855(95)00040-2
-
Cosgrove, D.; Kenny, P. BOOMSLANG: A program for combinatorial structure generation. J. Mol. Graphics 1996, 14, 1-5. (Pubitemid 26152969)
-
(1996)
Journal of Molecular Graphics
, vol.14
, Issue.1
, pp. 1-5
-
-
Cosgrove, D.A.1
Kenny, P.W.2
-
20
-
-
0029687909
-
MOLMAKER: De novo generation of 3D databases for use in drug design
-
Clark, D.; Firth, M.; Murray, C. MOLMAKER: de novo generation of 3D databases for use in drug design. J. Chem. Inf. Comput. Sci. 1996, 36, 137-145. (Pubitemid 126579145)
-
(1996)
Journal of Chemical Information and Computer Sciences
, vol.36
, Issue.1
, pp. 137-145
-
-
Clark, D.E.1
Firth, M.A.2
Murray, C.W.3
-
21
-
-
0032840569
-
DREAM++: Flexible docking program for virtual combinatorial libraries
-
DOI 10.1023/A:1008066310669
-
Makino, S.; Ewing, T.; Kuntz, I. DREAM++: flexible docking program for virtual combinatorial libraries. J. Comput.-Aided Mol. Des. 1999, 13, 513-532. (Pubitemid 29395565)
-
(1999)
Journal of Computer-Aided Molecular Design
, vol.13
, Issue.5
, pp. 513-532
-
-
Makino, S.1
Ewing, T.J.A.2
Kuntz, I.D.3
-
22
-
-
0034130399
-
De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
-
DOI 10.1023/A:1008184403558
-
Schneider, G.; Lee, M.; Stahl, M.; Schneider, P. De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks. J. Comput.-Aided Mol. Des. 2000, 14, 487-494. (Pubitemid 30386823)
-
(2000)
Journal of Computer-Aided Molecular Design
, vol.14
, Issue.5
, pp. 487-494
-
-
Schneider, G.1
Lee, M.-L.2
Stahl, M.3
Schneider, P.4
-
23
-
-
0037777697
-
SYNOPSIS: SYNthesize and OPti mize System in Silico
-
DOI 10.1021/jm030809x
-
Vinkers, H.; de Jonge, M.; Daeyaert, F.; Heeres, J.; Koymans, L.; van Lenthe, J.; Lewi, P.; Timmerman, H.; Van Aken, K.; Janssen, P. Synopsis: synthesize and optimize system in silico. J. Med. Chem. 2003, 46, 2765-2773. (Pubitemid 36702544)
-
(2003)
Journal of Medicinal Chemistry
, vol.46
, Issue.13
, pp. 2765-2773
-
-
Vinkers, H.M.1
De Jonge, M.R.2
Daeyaert, F.F.D.3
Heeres, J.4
Koymans, L.M.H.5
Van Lenthe, J.H.6
Lewi, P.J.7
Timmerman, H.8
Van Aken, K.9
Janssen, P.A.J.10
-
24
-
-
33749250361
-
Molecular complexity analysis of de novo designed ligands
-
DOI 10.1021/jm050054p
-
Boda, K.; Johnson, A. P. Molecular complexity analysis of de novo designed ligands. J. Med. Chem. 2006, 49, 5869-5879. (Pubitemid 44484933)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5869-5879
-
-
Boda, K.1
Johnson, A.P.2
-
25
-
-
0031024171
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
DOI 10.1016/S0169-409X(96)00423-1, PII S0169409X96004231
-
Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25. (Pubitemid 27046991)
-
(1997)
Advanced Drug Delivery Reviews
, vol.23
, Issue.1-3
, pp. 3-25
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
26
-
-
68149124133
-
FOG fragment optimized growth algorithm for the de novo generation of molecules occupying druglike chemical space
-
Kutchukian, P.; Lou, D.; Shakhnovich, E. FOG Fragment Optimized Growth Algorithm for the de Novo Generation of Molecules Occupying Druglike Chemical Space. J. Chem. Inf. Model. 2009, 49, 1630-1642.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 1630-1642
-
-
Kutchukian, P.1
Lou, D.2
Shakhnovich, E.3
-
27
-
-
33845378719
-
Applications of graph theory in chemistry
-
Balaban, A. T. Applications of Graph Theory in Chemistry. J. Chem. Inf. Comput. Sci. 1985, 25, 334-343.
-
(1985)
J. Chem. Inf. Comput. Sci.
, vol.25
, pp. 334-343
-
-
Balaban, A.T.1
-
28
-
-
0035481807
-
On median graphs: Properties, algorithms, and applications
-
DOI 10.1109/34.954604
-
Jiang, X.; Munger, A.; Bunke, H. On Median Graphs: Properties, Algorithms and Applications. IEEE Trans. Pattern Anal. Mach. Intell. 2001, 23, 1144-1151. (Pubitemid 33047952)
-
(2001)
IEEE Transactions on Pattern Analysis and Machine Intelligence
, vol.23
, Issue.10
, pp. 1144-1151
-
-
Jiang, X.1
Munger, A.2
Bunke, H.3
-
29
-
-
67349093251
-
Median graphs: A genetic approach based on new theoretical properties
-
Ferrer, M.; Valveny, E.; Serratosa, F. Median graphs: A genetic approach based on new theoretical properties. Pattern Recoenit. 2009, 42, 2003-2012.
-
(2009)
Pattern Recoenit.
, vol.42
, pp. 2003-2012
-
-
Ferrer, M.1
Valveny, E.2
Serratosa, F.3
-
30
-
-
24644475842
-
A linear generative model for graph structure
-
Graph-Based Representations in Pattern Recognition - 5th IAPR International Workshop, GbRPR 2005, Proceedings
-
Luo, B.; Wilson, R. C.; Hancock, E. R. A Linear Generative Model for Graph Structure. Lect. Notes Comput. Sci. 2005, 3434, 54-62. (Pubitemid 41273831)
-
(2005)
Lecture Notes in Computer Science
, vol.3434
, pp. 54-62
-
-
Luo, B.1
Wilson, R.C.2
Hancock, E.R.3
-
31
-
-
33749635812
-
A spectral generative model for graph structure
-
Structural, Syntactic, and Statistical Pattern Recognition - Joint IAPR International Workshops, SSPR 2006 and SPR 2006, Proceedings
-
Xiao, B.; Hancock, E. R. A Spectral Generative Model for Graph Structure. Lect. Notes Comput. Sci. 2006, 4109, 173-181. (Pubitemid 44543104)
-
(2006)
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
, vol.4109
, pp. 173-181
-
-
Xiao, B.1
Hancock, E.R.2
-
32
-
-
48149091382
-
Spectral generative models for graphs
-
IEEE Computer Society: Washington, DC
-
White, D.; Wilson, R. C. Spectral Generative Models for Graphs. Proceedings of the 14th International Conference on Image Analysis and Processing (ICIAP), Modena, Italy, September 10-14, 2007; IEEE Computer Society: Washington, DC, 2007; pp 35-42.
-
Proceedings of the 14th International Conference on Image Analysis and Processing (ICIAP), Modena, Italy, September 10-14, 2007
, vol.2007
, pp. 35-42
-
-
White, D.1
Wilson, R.C.2
-
33
-
-
77957937638
-
Parts based generative models for graphs
-
IEEE Computer Society: Washington, DC
-
White, D.; Wilson, R. C. Parts Based Generative Models for Graphs. In Proceedings of the 19th International Conference on Pattern Recognition(ICPR), Tampa, FL, June 5-7, 2008; IEEE Computer Society: Washington, DC, 2008; pp 1-4.
-
(2008)
Proceedings of the 19th International Conference on Pattern Recognition(ICPR), Tampa, FL, June 5-7, 2008
, pp. 1-4
-
-
White, D.1
Wilson, R.C.2
-
36
-
-
1842426385
-
An eigenspace projection clustering method for inexact graph matching
-
Caelli, T.; Kosinov, S. An Eigenspace Projection Clustering Method for Inexact Graph Matching. IEEE Trans. Pattern Anal. Mach. Intell. 2004, 26, 515-519.
-
(2004)
IEEE Trans. Pattern Anal. Mach. Intell.
, vol.26
, pp. 515-519
-
-
Caelli, T.1
Kosinov, S.2
-
37
-
-
0002601045
-
Indexing usine a spectral codine of topoloeical structure
-
IEEE Computer Society: Washington, DC
-
Shokoufandeh, A.; Dickinson, S. J.; Siddiqi, K.; Zucker, S. W. Indexing usine a Spectral Codine of Topoloeical Structure. In 1999 Conference on Computer Vision and Pattern Recognition (CVPR), Ft. Collins, CO, June 23-25, 1999; IEEE Computer Society: Washington, DC, 1999; pp 2491-2497.
-
1999 Conference on Computer Vision and Pattern Recognition (CVPR), Ft. Collins, CO, June 23-25, 1999
, vol.1999
, pp. 2491-2497
-
-
Shokoufandeh, A.1
Dickinson, S.J.2
Siddiqi, K.3
Zucker, S.W.4
-
38
-
-
22944487937
-
Pattern vectors from algebraic graph theory
-
DOI 10.1109/TPAMI.2005.145
-
Wilson, R. C.; Hancock, E. R.; Luo, B. Pattern Vectors from Algebraic Graph Theory. IEEE Trans. Pattern Anal. Mach. Intell. 2005, 27, 1112-1124. (Pubitemid 41046906)
-
(2005)
IEEE Transactions on Pattern Analysis and Machine Intelligence
, vol.27
, Issue.7
, pp. 1112-1124
-
-
Wilson, R.C.1
Hancock, E.R.2
Luo, B.3
-
39
-
-
38149011441
-
Graph embedding in vector spaces by means of prototype selection
-
Riesen, K.; Neuhaus, M.; Bunke, H. Graph Embedding in Vector Spaces by Means Of Prototype Selection. Lect. Notes Comput. Sci. 2007, 4538, 383-393.
-
(2007)
Lect. Notes Comput. Sci.
, vol.4538
, pp. 383-393
-
-
Riesen, K.1
Neuhaus, M.2
Bunke, H.3
-
40
-
-
34147166028
-
Mixing spectral representations of graphs
-
IEEE Computer Society: Washington, DC
-
White, D.; Wilson, R. C. Mixing Spectral Representations of Graphs. In Proceedings of the 18th International Conference on Pattern Recognition(ICPR), Hong Kong, China, August 20-24, 2006; IEEE Computer Society: Washington, DC, 2006; pp 140-144.
-
Proceedings of the 18th International Conference on Pattern Recognition(ICPR), Hong Kong, China, August 20-24, 2006
, vol.2006
, pp. 140-144
-
-
White, D.1
Wilson, R.C.2
-
41
-
-
33644590420
-
Random computer generation of 3D molecular structures: Theoretical and statistical analysis
-
Porquet, A.; Duval, J. F. L.; Buffle, J. Random Computer Generation of 3D Molecular Structures: Theoretical and Statistical Analysis. Macromol. Theoey Simul. 2006, 15, 147-162.
-
(2006)
Macromol. Theoey Simul.
, vol.15
, pp. 147-162
-
-
Porquet, A.1
Duval, J.F.L.2
Buffle, J.3
-
44
-
-
33750991346
-
Benchmarking sets for molecular docking
-
DOI 10.1021/jm0608356
-
Huang, N.; Shoichet, B. K.; Irwin, J. J. Benchmarking sets for molecular docking. J. Med. Chem. 2006, 49, 6789-6801. (Pubitemid 44749746)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.23
, pp. 6789-6801
-
-
Huang, N.1
Shoichet, B.K.2
Irwin, J.J.3
-
45
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
DOI 10.1006/jmbi.1996.0477
-
Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489. (Pubitemid 26335901)
-
(1996)
Journal of Molecular Biology
, vol.261
, Issue.3
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
46
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz, I. D.; Blaney, J. M.; Oatley, S. J.; Langridge, R.; Ferrin, T. E. A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 1982, 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
-
47
-
-
0037212102
-
LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
-
DOI 10.1016/S1093-3263(02)00164-X, PII S109332630200164X
-
Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graphics Modell. 2003, 21, 289-307. (Pubitemid 35441326)
-
(2003)
Journal of Molecular Graphics and Modelling
, vol.21
, Issue.4
, pp. 289-307
-
-
Venkatachalam, C.M.1
Jiang, X.2
Oldfield, T.3
Waldman, M.4
-
48
-
-
0031552362
-
Development and validation of a genetic algorithm for flexible docking
-
DOI 10.1006/jmbi.1996.0897
-
Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol. 1997, 267, 727-748. (Pubitemid 27170693)
-
(1997)
Journal of Molecular Biology
, vol.267
, Issue.3
, pp. 727-748
-
-
Jones, G.1
Willett, P.2
Glen, R.C.3
Leach, A.R.4
Taylor, R.5
-
49
-
-
79951548600
-
-
version 2.2.3; OpenEye Scientific Software: Santa Fe, NM. Accessed May 27, 2010
-
FRED (Fast Rigid Exhaustive Docking), version 2.2.3; OpenEye Scientific Software: Santa Fe, NM, 2009; http://www.eyesopen.com/products/applications/ fred.html. Accessed May 27, 2010.
-
(2009)
FRED (Fast Rigid Exhaustive Docking)
-
-
-
51
-
-
79951546680
-
-
version 1.1.1; OpenEye Scientific Software: Santa Fe, NM. Accessed May 27, 2010
-
Chomp, version 1.1.1; OpenEye Scientific Software: Santa Fe, NM, 2009; http://www.eyesopen.com/docs/brood/LL2/html/manual/node30.html. Accessed May 27, 2010.
-
(2009)
Chomp
-
-
-
52
-
-
79951538789
-
-
version 2.3.0; OpenEye Scientific Software: Santa Fe, NM. Accessed May 27, 2010
-
Omega, version 2.3.0; OpenEye Scientific Software: Santa Fe, NM, 2009; http://www.eyesopen.com/products/applications/omega.html. Accessed May 27, 2010.
-
(2009)
Omega
-
-
-
53
-
-
33749260698
-
A critical assessment of docking programs and scoring functions
-
DOI 10.1021/jm050362n
-
Warren, G. L.; Andrews, C. W.; Capelli, A. M.; Clarke, B.; LaLonde, J.; Lambert, M. H.; Lindvall, M.; Nevins, N.; Semus, S. F.; Senger, S.; Tedesco, G.; Wall, I. D.; Woolven, J. M.; Peishoff, C. E.; Head, M. S. A critical assessment of docking programs and scoring functions. J. Med. Chem. 2006, 49, 5912-5931. (Pubitemid 44484938)
-
(2006)
Journal of Medicinal Chemistry
, vol.49
, Issue.20
, pp. 5912-5931
-
-
Warren, G.L.1
Andrews, C.W.2
Capelli, A.-M.3
Clarke, B.4
LaLonde, J.5
Lambert, M.H.6
Lindvall, M.7
Nevins, N.8
Semus, S.F.9
Senger, S.10
Tedesco, G.11
Wall, I.D.12
Woolven, J.M.13
Peishoff, C.E.14
Head, M.S.15
-
54
-
-
84871976073
-
-
version 2.2.3. Accessed May 27, 2010
-
The Open Babel Package, version 2.2.3; http://openbabel.sourceforge.net. Accessed May 27, 2010.
-
The Open Babel Package
-
-
|