-
1
-
-
1042265247
-
Approaches to measure chemical similarity - A review
-
Nikolova, N.; Jaworska, J. Approaches to measure chemical similarity - A review. QSAR Comb. Sci. 2004, 22 (9-10), 1006-1026.
-
(2004)
QSAR Comb. Sci
, vol.22
, Issue.9-10
, pp. 1006-1026
-
-
Nikolova, N.1
Jaworska, J.2
-
3
-
-
10344230435
-
Molecular similarity: A key technique in molecular informatics
-
Bender, A.; Glen, R. C. Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2004, 2 (22), 3204-3218.
-
(2004)
Org. Biomol. Chem
, vol.2
, Issue.22
, pp. 3204-3218
-
-
Bender, A.1
Glen, R.C.2
-
4
-
-
0029783934
-
Neighborhood behavior: A useful concept for validation of "molecular diversity" descriptors
-
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 (16), 3049-3059.
-
(1996)
J. Med Chem
, 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
-
-
5344244908
-
Chemical similarity searching
-
Willett, P.; Barnard, J. M.; Downs, G. M. Chemical similarity searching. J. Chem. Inf. Comput. Sci. 1998, 38 (6), 983-996.
-
(1998)
J. Chem. Inf. Comput. Sci
, vol.38
, Issue.6
, pp. 983-996
-
-
Willett, P.1
Barnard, J.M.2
Downs, G.M.3
-
6
-
-
0037068532
-
Do structurally similar molecules have similar biological activity
-
Martin, Y. C.; Kofron, J. L.; Traphagen, L. M. Do structurally similar molecules have similar biological activity. J. Med. Chem. 2002, 45 (19), 4350-4358.
-
(2002)
J. Med. Chem
, vol.45
, Issue.19
, pp. 4350-4358
-
-
Martin, Y.C.1
Kofron, J.L.2
Traphagen, L.M.3
-
7
-
-
0038170311
-
Similarity metrics for ligands reflecting the similarity of the target proteins
-
Schuffenhauer, A.; Floersheim, P.; Acklin, P.; Jacoby, E. Similarity metrics for ligands reflecting the similarity of the target proteins. J. Chem. Inf. Comput. Sci. 2003, 43 (2), 391-405.
-
(2003)
J. Chem. Inf. Comput. Sci
, vol.43
, Issue.2
, pp. 391-405
-
-
Schuffenhauer, A.1
Floersheim, P.2
Acklin, P.3
Jacoby, E.4
-
8
-
-
33846876695
-
Relating protein pharmacology by ligand chemistry
-
Keiser, M. J.; Roth, B. L.; Armbruster, B. N.; Ernsberger, P.; Irwin, J. J.; Shoichet, B. K. Relating protein pharmacology by ligand chemistry. Nat. Biotechnol. 2007, 25 (2), 197-206.
-
(2007)
Nat. Biotechnol
, vol.25
, Issue.2
, pp. 197-206
-
-
Keiser, M.J.1
Roth, B.L.2
Armbruster, B.N.3
Ernsberger, P.4
Irwin, J.J.5
Shoichet, B.K.6
-
9
-
-
34547697192
-
Understanding False Positives in Reporter Gene Assays: In silico Chemogenomics Approaches to Prioritize Cell-based HTS Data
-
Crisman, T. J.; Parker, C. N.; Jenkins, J. L.; Scheiber, J.; Thoma, M.; Kang, Z. B.; Kim, R.; Bender, A.; Nettles, J. H.; Davies, J. W.; Glick, M. Understanding False Positives in Reporter Gene Assays: in silico Chemogenomics Approaches to Prioritize Cell-based HTS Data. J. Chem. Inf. Model. 2007, 47 (4), 1319-1327.
-
(2007)
J. Chem. Inf. Model
, vol.47
, Issue.4
, pp. 1319-1327
-
-
Crisman, T.J.1
Parker, C.N.2
Jenkins, J.L.3
Scheiber, J.4
Thoma, M.5
Kang, Z.B.6
Kim, R.7
Bender, A.8
Nettles, J.H.9
Davies, J.W.10
Glick, M.11
-
10
-
-
0034878886
-
A novel chemogenomics knowledge-based ligand design strategy - Application to G protein-coupled receptors
-
Jacoby, E. A novel chemogenomics knowledge-based ligand design strategy - Application to G protein-coupled receptors. Quant. Struct-Act. Relat. 2001, 20 (2), 115-123.
-
(2001)
Quant. Struct-Act. Relat
, vol.20
, Issue.2
, pp. 115-123
-
-
Jacoby, E.1
-
11
-
-
36048992504
-
Chemogenomic data analysis: Prediction of small-molecule targets and the advent of biological fingerprint
-
Bender, A.; Young, D. W.; Jenkins, J. L.; Serrano, M.; Mikhailov, D.; Clemons, P. A.; Davies, J. W. Chemogenomic data analysis: prediction of small-molecule targets and the advent of biological fingerprint. Comb. Chem. High-Throughput Screening 2007, 10 (8), 719-731.
-
(2007)
Comb. Chem. High-Throughput Screening
, vol.10
, Issue.8
, pp. 719-731
-
-
Bender, A.1
Young, D.W.2
Jenkins, J.L.3
Serrano, M.4
Mikhailov, D.5
Clemons, P.A.6
Davies, J.W.7
-
12
-
-
1542358841
-
Kinomics-structural biology and chemogenomics of kinase inhibitors and targets
-
Vieth, M.; Higgs, R. E.; Robertson, D. H.; Shapiro, M.; Gragg, E. A.; Hemmerle, H. Kinomics-structural biology and chemogenomics of kinase inhibitors and targets. Biochim. Biophys. Acta 2004, 1697 (1-2), 243-257.
-
(2004)
Biochim. Biophys. Acta
, vol.1697
, Issue.1-2
, pp. 243-257
-
-
Vieth, M.1
Higgs, R.E.2
Robertson, D.H.3
Shapiro, M.4
Gragg, E.A.5
Hemmerle, H.6
-
13
-
-
21144440283
-
Chemical genetics to chemical genomics: Small molecules offer big insights
-
Spring, D. R. Chemical genetics to chemical genomics: small molecules offer big insights. Chem. Soc. Rev. 2005, 34 (6), 472-482.
-
(2005)
Chem. Soc. Rev
, vol.34
, Issue.6
, pp. 472-482
-
-
Spring, D.R.1
-
14
-
-
42449106583
-
Which aspects of HTS are empirically correlated with downstream success
-
Bender, A.; Bojanic, D.; Davies, J. W.; Crisman, T. J.; Mikhailov, D.; Scheiber, J.; Jenkins, J. L.; Deng, Z.; Hill, W. A.; Popov, M.; Jacoby, E.; Glick, M. Which aspects of HTS are empirically correlated with downstream success. Curr. Opin. Drug Discovery Dev. 2008, 11 (3), 327-337.
-
(2008)
Curr. Opin. Drug Discovery Dev
, vol.11
, Issue.3
, pp. 327-337
-
-
Bender, A.1
Bojanic, D.2
Davies, J.W.3
Crisman, T.J.4
Mikhailov, D.5
Scheiber, J.6
Jenkins, J.L.7
Deng, Z.8
Hill, W.A.9
Popov, M.10
Jacoby, E.11
Glick, M.12
-
16
-
-
33644963750
-
Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME
-
Glen, R. C.; Bender, A.; Arnby, C. H.; Carlsson, L.; Boyer, S.; Smith, J. Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs 2006, 9 (3), 199-204.
-
(2006)
IDrugs
, vol.9
, Issue.3
, pp. 199-204
-
-
Glen, R.C.1
Bender, A.2
Arnby, C.H.3
Carlsson, L.4
Boyer, S.5
Smith, J.6
-
18
-
-
26944443036
-
A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication
-
Bender, A.; Glen, R. C. A Discussion of Measures of Enrichment in Virtual Screening: Comparing the Information Content of Descriptors with Increasing Levels of Sophistication. J. Chem. Inf. Model. 2005, 45 (5), 1369-1375.
-
(2005)
J. Chem. Inf. Model
, vol.45
, Issue.5
, pp. 1369-1375
-
-
Bender, A.1
Glen, R.C.2
-
19
-
-
0035292795
-
Selected concepts and investigations in compound classification, molecular descriptor analysis, and virtual screening
-
Bajorath, J. Selected concepts and investigations in compound classification, molecular descriptor analysis, and virtual screening. J. Chem. Inf. Comput. Sci. 2001, 41 (2), 233-245.
-
(2001)
J. Chem. Inf. Comput. Sci
, vol.41
, Issue.2
, pp. 233-245
-
-
Bajorath, J.1
-
20
-
-
0002480134
-
Characterization of Molecular Structures Using Topological Indices
-
Basak, S. C.; Gute, B. D. Characterization of Molecular Structures Using Topological Indices. SAR QSAR Environ. Res. 1997, 7, 1-21.
-
(1997)
SAR QSAR Environ. Res
, vol.7
, pp. 1-21
-
-
Basak, S.C.1
Gute, B.D.2
-
21
-
-
0001136343
-
Four associative constants for relating molecular similarity measures
-
Cheng, C.; Maggiora, G.; Lajiness, M.; Johnson, M. Four associative constants for relating molecular similarity measures. J. Chem. Inf. Comput. Sci. 1996, 36 (4), 909-915.
-
(1996)
J. Chem. Inf. Comput. Sci
, vol.36
, Issue.4
, pp. 909-915
-
-
Cheng, C.1
Maggiora, G.2
Lajiness, M.3
Johnson, M.4
-
22
-
-
33846013232
-
Scaffold-Hopping: How far can you jump
-
Schneider, G.; Schneider, P.; Renner, S. Scaffold-Hopping: How far can you jump. QSAR Comb. Sci. 2006, 25, 1162-1171.
-
(2006)
QSAR Comb. Sci
, vol.25
, pp. 1162-1171
-
-
Schneider, G.1
Schneider, P.2
Renner, S.3
-
23
-
-
33644862638
-
Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
-
Zhang, Q.; Muegge, I. Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring. J. Med. Chem. 2006, 49 (5), 1536-1548.
-
(2006)
J. Med. Chem
, vol.49
, Issue.5
, pp. 1536-1548
-
-
Zhang, Q.1
Muegge, I.2
-
25
-
-
61949426135
-
-
PipelinePilot, version 6.1, Accelrys: San Diego, 2007
-
PipelinePilot, version 6.1, Accelrys: San Diego, 2007.
-
-
-
-
26
-
-
2942700377
-
Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures
-
Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J. Chem. Inf. Comput. Sci. 2004, 44 (3), 1177-1185.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, Issue.3
, pp. 1177-1185
-
-
Hert, J.1
Willett, P.2
Wilton, D.J.3
Acklin, P.4
Azzaoui, K.5
Jacoby, E.6
Schuffenhauer, A.7
-
27
-
-
10244222365
-
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
-
Hert, J.; Willett, P.; Wilton, D. J.; Acklin, P.; Azzaoui, K.; Jacoby, E.; Schuffenhauer, A. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org. Biomol. Chem. 2004, 2 (22), 3256-3266.
-
(2004)
Org. Biomol. Chem
, vol.2
, Issue.22
, pp. 3256-3266
-
-
Hert, J.1
Willett, P.2
Wilton, D.J.3
Acklin, P.4
Azzaoui, K.5
Jacoby, E.6
Schuffenhauer, A.7
-
28
-
-
5544290537
-
Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
-
Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J. Chem. Inf. Comput. Sci. 2004, 44 (5), 1708-1718.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, Issue.5
, pp. 1708-1718
-
-
Bender, A.1
Mussa, H.Y.2
Glen, R.C.3
Reiling, S.4
-
29
-
-
61949276784
-
-
MDL Drug Data Report (MDDR) version 2005.3; MDL: San Ramon, CA, 2005
-
MDL Drug Data Report (MDDR) version 2005.3; MDL: San Ramon, CA, 2005.
-
-
-
-
30
-
-
44449122375
-
Impact of benchmark data set topology on the validation of virtual screening methods: Exploration and quantification by spatial statistics
-
Rohrer, S. G.; Baumann, K. Impact of benchmark data set topology on the validation of virtual screening methods: exploration and quantification by spatial statistics. J. Chem. Inf. Model. 2008, 48 (4), 704-718.
-
(2008)
J. Chem. Inf. Model
, vol.48
, Issue.4
, pp. 704-718
-
-
Rohrer, S.G.1
Baumann, K.2
-
31
-
-
0036827075
-
Reoptimization of MDL keys for use in drug discovery
-
Durant, J. L.; Leland, B. A.; Henry, D. R.; Nourse, J. G. Reoptimization of MDL keys for use in drug discovery. J. Chem. Inf. Comput. Sci. 2002, 42 (6), 1273-1280.
-
(2002)
J. Chem. Inf. Comput. Sci
, vol.42
, Issue.6
, pp. 1273-1280
-
-
Durant, J.L.1
Leland, B.A.2
Henry, D.R.3
Nourse, J.G.4
-
32
-
-
34247198331
-
Clustering and rule-based classifications of chemical structures evaluated in the biological activity space
-
Schuffenhauer, A.; Brown, N.; Ertl, P.; Jenkins, J. L.; Selzer, P.; Hamon, J. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space. J. Chem. Inf. Model. 2007, 47 (2), 325-336.
-
(2007)
J. Chem. Inf. Model
, vol.47
, Issue.2
, pp. 325-336
-
-
Schuffenhauer, A.1
Brown, N.2
Ertl, P.3
Jenkins, J.L.4
Selzer, P.5
Hamon, J.6
-
33
-
-
9744222830
-
A 3D similarity method for scaffold hopping from the known drugs or natural ligands to new chemotypes
-
Jenkins, J. L.; Glick, M.; Davies, J. W. A 3D similarity method for scaffold hopping from the known drugs or natural ligands to new chemotypes. J. Med. Chem. 2004, 47 (25), 6144-6159.
-
(2004)
J. Med. Chem
, vol.47
, Issue.25
, pp. 6144-6159
-
-
Jenkins, J.L.1
Glick, M.2
Davies, J.W.3
-
34
-
-
61949442060
-
-
Spotfire, version 8.0; TIBCO: Palo Alto, CA, 2007
-
Spotfire, version 8.0; TIBCO: Palo Alto, CA, 2007.
-
-
-
-
35
-
-
27644440282
-
Comparison of Three Holographic Fingerprint Descriptors and their Binary Counterparts
-
Fechner, U.; Paetz, J.; Schneider, G. Comparison of Three Holographic Fingerprint Descriptors and their Binary Counterparts. QSAR Comb. Sci. 2005, 24 (8), 961-967.
-
(2005)
QSAR Comb. Sci
, vol.24
, Issue.8
, pp. 961-967
-
-
Fechner, U.1
Paetz, J.2
Schneider, G.3
-
36
-
-
85135599249
-
-
Purvis, G. D. 3rd Size-intensive descriptors. J. Comput.-Aided Mol. Des. 2008, 22 (6-7), 461-468.
-
Purvis, G. D. 3rd Size-intensive descriptors. J. Comput.-Aided Mol. Des. 2008, 22 (6-7), 461-468.
-
-
-
-
37
-
-
33845800485
-
Novel 2D fingerprints for ligand-based virtual screening
-
Ewing, T.; Baber, J. C.; Feher, M. Novel 2D fingerprints for ligand-based virtual screening. J. Chem. Inf. Model. 2006, 46 (6), 2423-2431.
-
(2006)
J. Chem. Inf. Model
, vol.46
, Issue.6
, pp. 2423-2431
-
-
Ewing, T.1
Baber, J.C.2
Feher, M.3
-
38
-
-
1542712834
-
Comparison of correlation vector methods for ligand-based similarity searching
-
Fechner, U.; Franke, L.; Renner, S.; Schneider, P.; Schneider, G. Comparison of correlation vector methods for ligand-based similarity searching. J. Comput.-Aided Mol. Des. 2003, 17 (10), 687-698.
-
(2003)
J. Comput.-Aided Mol. Des
, vol.17
, Issue.10
, pp. 687-698
-
-
Fechner, U.1
Franke, L.2
Renner, S.3
Schneider, P.4
Schneider, G.5
-
39
-
-
0033606988
-
New 4-point pharmacophore method for molecular similarity and diversity applications: Overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures
-
Mason, J. S.; Morize, I.; Menard, P. R.; Cheney, D. L.; Hulme, C.; Labaudiniere, R. F. New 4-point pharmacophore method for molecular similarity and diversity applications: overview of the method and applications, including a novel approach to the design of combinatorial libraries containing privileged substructures. J. Med. Chem. 1999, 42 (17), 3251-3264.
-
(1999)
J. Med. Chem
, vol.42
, Issue.17
, pp. 3251-3264
-
-
Mason, J.S.1
Morize, I.2
Menard, P.R.3
Cheney, D.L.4
Hulme, C.5
Labaudiniere, R.F.6
-
40
-
-
20844436604
-
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
-
Good, A. C.; Hermsmeier, M. A.; Hindle, S. A. Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments. J. Comput.-Aided Mol. Des. 2004, 18 (7), 529-536.
-
(2004)
J. Comput.-Aided Mol. Des
, vol.18
, Issue.7
, pp. 529-536
-
-
Good, A.C.1
Hermsmeier, M.A.2
Hindle, S.A.3
-
41
-
-
0033576680
-
Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins
-
Charifson, P. S.; Corkery, J. J.; Murcko, M. A.; Walters, W. P. Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 1999, 42 (25), 5100-5109.
-
(1999)
J. Med. Chem
, vol.42
, Issue.25
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
42
-
-
33344465112
-
The Use of Consensus Scoring in Ligand-Based Virtual Screening
-
Baber, J. C.; Shirley, W. A.; Gao, Y.; Feher, M. The Use of Consensus Scoring in Ligand-Based Virtual Screening. J. Chem. Inf. Model. 2005, 46 (1), 277-288.
-
(2005)
J. Chem. Inf. Model
, vol.46
, Issue.1
, pp. 277-288
-
-
Baber, J.C.1
Shirley, W.A.2
Gao, Y.3
Feher, M.4
-
43
-
-
33845787616
-
Analysis of data fusion methods in virtual screening: Theoretical model
-
Whittle, M.; Gillet, V. J.; Willett, P.; Loesel, J. Analysis of data fusion methods in virtual screening: theoretical model. J. Chem. Inf. Model. 2006, 46 (6), 2193-2205.
-
(2006)
J. Chem. Inf. Model
, vol.46
, Issue.6
, pp. 2193-2205
-
-
Whittle, M.1
Gillet, V.J.2
Willett, P.3
Loesel, J.4
-
44
-
-
33845782959
-
Analysis of data fusion methods in virtual screening: Similarity and group fusion
-
Whittle, M.; Gillet, V. J.; Willett, P.; Loesel, J. Analysis of data fusion methods in virtual screening: similarity and group fusion. J. Chem. Inf. Model. 2006, 46 (6), 2206-2219.
-
(2006)
J. Chem. Inf. Model
, vol.46
, Issue.6
, pp. 2206-2219
-
-
Whittle, M.1
Gillet, V.J.2
Willett, P.3
Loesel, J.4
-
45
-
-
0035438402
-
How does consensus scoring work for virtual library screening? An idealized computer experiment
-
Wang, R.; Wang, S. How does consensus scoring work for virtual library screening? An idealized computer experiment. J. Chem. Inf. Comput. Sci. 2001, 41 (5), 1422-6.
-
(2001)
J. Chem. Inf. Comput. Sci
, vol.41
, Issue.5
, pp. 1422-1426
-
-
Wang, R.1
Wang, S.2
-
46
-
-
0033669056
-
Combination of molecular similarity measures using data fusion
-
Ginn, C. M. R.; Willett, P.; Bradshaw, J. Combination of molecular similarity measures using data fusion. Perspect. Drug Discovery Des. 2000, 20 (1), 1-16.
-
(2000)
Perspect. Drug Discovery Des
, vol.20
, Issue.1
, pp. 1-16
-
-
Ginn, C.M.R.1
Willett, P.2
Bradshaw, J.3
-
47
-
-
1842690601
-
Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier
-
Bender, A.; Mussa, H. Y.; Glen, R. C.; Reiling, S. Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J. Chem. Inf. Comput. Sci. 2004, 44 (1), 170-178.
-
(2004)
J. Chem. Inf. Comput. Sci
, vol.44
, Issue.1
, pp. 170-178
-
-
Bender, A.1
Mussa, H.Y.2
Glen, R.C.3
Reiling, S.4
|