-
1
-
-
10344230435
-
Molecular similarity: A key technique in molecular informatics
-
Bender A, Glen RC. Molecular similarity: a key technique in molecular informatics. Org Biomol Chem 2004;2:3204-18
-
(2004)
Org Biomol Chem
, vol.2
, pp. 3204-18
-
-
Bender, A.1
Glen, R.C.2
-
3
-
-
0036740917
-
Why do we need so many chemical similarity search methods?
-
Sheridan RP, Kearsley SK. Why do we need so many chemical similarity search methods? Drug Discov Today 2002;7:903-11
-
(2002)
Drug Discov Today
, vol.7
, pp. 903-11
-
-
Sheridan, R.P.1
Kearsley, S.K.2
-
4
-
-
48749127628
-
What has virtual screening ever done for drug discovery?
-
Clark DE. What has virtual screening ever done for drug discovery? Expert Opin Drug Discov 2008;3:841-51
-
(2008)
Expert Opin Drug Discov
, vol.3
, pp. 841-51
-
-
Clark, D.E.1
-
5
-
-
77749326688
-
Pharmacophore-based virtual screening: A review of recent applications
-
Kim KH, Kim KD, Seong BL. Pharmacophore-based virtual screening: a review of recent applications. Expert Opin Drug Discov 2010;5:205-22
-
(2010)
Expert Opin Drug Discov
, vol.5
, pp. 205-22
-
-
Kim, K.H.1
Kim, K.D.2
Seong, B.L.3
-
6
-
-
65549108234
-
Virtual screening-What does it give us?
-
Koeppen H. Virtual screening-What does it give us? Curr Opin Drug Discov Devel 2009;12:397-407
-
(2009)
Curr Opin Drug Discov Devel
, vol.12
, pp. 397-407
-
-
Koeppen, H.1
-
7
-
-
40049105721
-
Essential factors for successful virtual screening
-
Seifert MHJ, Lang M. Essential factors for successful virtual screening. Mini Rev Med Chem 2008;8:63-72
-
(2008)
Mini Rev Med Chem
, vol.8
, pp. 63-72
-
-
Mhj, S.1
Lang, M.2
-
8
-
-
77649220192
-
Current trends in ligand-based virtual screening: Molecular representations, data mining methods, new application areas, and performance evaluation
-
Geppert H, Vogt M, Bajorath J. Current trends in ligand-based virtual screening: molecular representations, data mining methods, new application areas, and performance evaluation. J Chem Inf Model 2010;50:205-16
-
(2010)
J Chem Inf Model
, vol.50
, pp. 205-16
-
-
Geppert, H.1
Vogt, M.2
Bajorath, J.3
-
10
-
-
84984766385
-
Databases: Compound bioactivities go public
-
Bender A. Databases: compound bioactivities go public. Nat Chem Biol 2010;6:309
-
(2010)
Nat Chem Biol
, vol.6
, pp. 309
-
-
Bender, A.1
-
11
-
-
0029744121
-
Molecular similarity based on DOCK-generated fingerprints
-
Briem H, Kuntz ID. Molecular similarity based on DOCK-generated fingerprints. J Med Chem 1996;39:3401-8
-
(1996)
J Med Chem
, vol.39
, pp. 3401-8
-
-
Briem, H.1
Kuntz, I.D.2
-
12
-
-
2942700377
-
Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures
-
Hert J, Willett P, Wilton DJ, et al. Comparison of fingerprint-based methods for virtual screening using multiple bioactive reference structures. J Chem Inf Comput Sci 2004;44:1177-85
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 1177-85
-
-
Hert, J.1
Willett, P.2
Wilton, D.J.3
-
14
-
-
65349136650
-
Maximum unbiased validation (MUV) data sets for virtual screening based on pubchem bioactivity data
-
Rohrer SG, Baumann K. Maximum unbiased validation (MUV) data sets for virtual screening based on pubchem bioactivity data. J Chem Inf Model 2009;49(2):169-84
-
(2009)
J Chem Inf Model
, vol.49
, Issue.2
, pp. 169-84
-
-
Rohrer, S.G.1
Baumann, K.2
-
15
-
-
77952780755
-
Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments
-
Sastry M, Lowrie JF, Dixon SL, et al. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J Chem Inf Model 2010;50:771-84
-
(2010)
J Chem Inf Model
, vol.50
, pp. 771-84
-
-
Sastry, M.1
Lowrie, J.F.2
Dixon, S.L.3
-
16
-
-
10244222365
-
Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
-
Hert J, Willett P, Wilton DJ, et al. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures. Org Biomol Chem 2004;2:3256-66
-
(2004)
Org Biomol Chem
, vol.2
, pp. 3256-66
-
-
Hert, J.1
Willett, P.2
Wilton, D.J.3
-
17
-
-
61949166066
-
How similar are similarity searching methods? A principal component analysis of molecular descriptor space
-
Bender A, Jenkins JL, Scheiber J, et al. How similar are similarity searching methods? A principal component analysis of molecular descriptor space. J Chem Inf Model 2009;49:108-19
-
(2009)
J Chem Inf Model
, vol.49
, pp. 108-19
-
-
Bender, A.1
Jenkins, J.L.2
Scheiber, J.3
-
18
-
-
0015655543
-
Analysis of structural characteristics of chemical compounds in a large computer-based file. Part II. Atom-centred fragments
-
Adamson GW, Lynch MF, Town WG. Analysis of structural characteristics of chemical compounds in a large computer-based file. Part II. Atom-centred fragments. J Chem Doc 1973;13(3):158-62
-
(1973)
J Chem Doc
, vol.13
, Issue.3
, pp. 158-62
-
-
Adamson, G.W.1
Lynch, M.F.2
Town, W.G.3
-
19
-
-
77952772341
-
Extended-connectivity fingerprints
-
Rogers D, Hahn M. Extended-connectivity fingerprints. J Chem Inf Model 2010;50:742-54
-
(2010)
J Chem Inf Model
, vol.50
, pp. 742-54
-
-
Rogers, D.1
Hahn, M.2
-
20
-
-
1842690601
-
Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier
-
Bender A, Mussa HY, Glen RC, et al. Molecular similarity searching using atom environments, information-based feature selection, and a naive bayesian classifier. J Chem Inf Comput Sci 2004;44:170-8
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 170-8
-
-
Bender, A.1
Mussa, H.Y.2
Glen, R.C.3
-
21
-
-
5544290537
-
Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
-
Bender A, Mussa HY, Glen RC, et al. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J Chem Inf Comput Sci 2004;44:1708-18
-
(2004)
J Chem Inf Comput Sci
, vol.44
, pp. 1708-18
-
-
Bender, A.1
Mussa, H.Y.2
Glen, R.C.3
-
22
-
-
26944445752
-
Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naive Bayesian classifier: Limitations of the descriptor and the importance of balanced chemistry in training and test sets
-
Bender A, Mussa HY, Glen RC. Screening for dihydrofolate reductase inhibitors using MOLPRINT 2D, a fast fragment-based method employing the naive Bayesian classifier: limitations of the descriptor and the importance of balanced chemistry in training and test sets. J Biomol Screen 2005;10:658-66
-
(2005)
J Biomol Screen
, vol.10
, pp. 658-66
-
-
Bender, A.1
Mussa, H.Y.2
Glen, R.C.3
-
23
-
-
77951675415
-
Prospective validation of a comprehensive in silico hERG model and its applications to commercial compound and drug databases
-
Doddareddy MR, Klaasse EC, Shagufta, et al. Prospective validation of a comprehensive in silico hERG model and its applications to commercial compound and drug databases. ChemMedChem 2010;5:716-29
-
(2010)
Chem Med Chem
, vol.5
, pp. 716-29
-
-
Doddareddy, M.R.1
Klaasse, E.C.2
Shagufta3
-
24
-
-
0029894013
-
The properties of known drugs. 1. Molecular frameworks
-
Bemis GW, Murcko MA. The properties of known drugs. 1. Molecular frameworks. J Med Chem 1996;39:2887-93
-
(1996)
J Med Chem
, vol.39
, pp. 2887-93
-
-
Bemis, G.W.1
Murcko, M.A.2
-
25
-
-
20444383539
-
Assessment of structural diversity in combinatorial synthesis
-
Fergus S, Bender A, Spring DR. Assessment of structural diversity in combinatorial synthesis. Curr Opin Chem Biol 2005;9:304-9
-
(2005)
Curr Opin Chem Biol
, vol.9
, pp. 304-9
-
-
Fergus, S.1
Bender, A.2
Spring, D.R.3
-
26
-
-
41149097628
-
Diversity-oriented synthesis; A spectrum of approaches and results
-
Spandl RJ, Bender A, Spring DR. Diversity-oriented synthesis; a spectrum of approaches and results. Org Biomol Chem 2008;6:1149-58
-
(2008)
Org Biomol Chem
, vol.6
, pp. 1149-58
-
-
Spandl, R.J.1
Bender, A.2
Spring, D.R.3
-
27
-
-
76049086854
-
Scaffold diversity analysis of compound data sets using an entropy-based measure
-
Medina-Franco JL, Martinez-Mayorga K, Bender A, et al. Scaffold diversity analysis of compound data sets using an entropy-based measure. QSAR Comb Sci 2009;28:1551-60
-
(2009)
QSAR Comb Sci
, vol.28
, pp. 1551-60
-
-
Medina-Franco, J.L.1
Martinez-Mayorga, K.2
Bender, A.3
-
28
-
-
26944443036
-
A discussion of measures of enrichment in virtual screening: Comparing the information content of descriptors with increasing levels of sophistication
-
Bender A, Glen RC. 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;45:1369-75
-
(2005)
J Chem Inf Model
, vol.45
, pp. 1369-75
-
-
Bender, A.1
Glen, R.C.2
-
29
-
-
1242274596
-
Noncovalent interactions: Defining cooperativity. Ligand binding aided by reduced dynamic behavior of receptors. Binding of bacterial cell wall analogues to ristocetin A
-
Williams DH, Davies NL, Zerella R, et al. Noncovalent interactions: defining cooperativity. Ligand binding aided by reduced dynamic behavior of receptors. Binding of bacterial cell wall analogues to ristocetin A. J Am Chem Soc 2004;126:2042-9
-
(2004)
J Am Chem Soc
, vol.126
, pp. 2042-9
-
-
Williams, D.H.1
Davies, N.L.2
Zerella, R.3
-
30
-
-
60849101543
-
Similarity-based virtual screening with a Bayesian inference network
-
Abdo A, Salim N. Similarity-based virtual screening with a Bayesian inference network. Chem Med Chem 2009;4:210-18
-
(2009)
Chem Med Chem
, vol.4
, pp. 210-18
-
-
Abdo, A.1
Salim, N.2
-
32
-
-
34547673017
-
Comparison of topological, shape, and docking methods in virtual screening
-
McGaughey GB, Sheridan RP, Bayly CI, et al. Comparison of topological, shape, and docking methods in virtual screening. J Chem Inf Model 2007;47:1504-19
-
(2007)
J Chem Inf Model
, vol.47
, pp. 1504-19
-
-
McGaughey, G.B.1
Sheridan, R.P.2
Bayly, C.I.3
-
33
-
-
65249142225
-
Comparison of ligand-and structure-based virtual screening on the DUD data set
-
Von Korff M, Freyss J, Sander T. Comparison of ligand-and structure-based virtual screening on the DUD data set. J Chem Inf Model 2009;49:209-31
-
(2009)
J Chem Inf Model
, vol.49
, pp. 209-31
-
-
Von Korff, M.1
Freyss, J.2
Sander, T.3
-
34
-
-
20844436604
-
Measuring CAMD technique performance: A virtual screening case study in the design of validation experiments
-
Good AC, Hermsmeier MA, Hindle SA. Measuring CAMD technique performance: a virtual screening case study in the design of validation experiments. J Comput Aided Mol Des 2004;18:529-36
-
(2004)
J Comput Aided Mol des
, vol.18
, pp. 529-36
-
-
Good, A.C.1
Hermsmeier, M.A.2
Hindle, S.A.3
-
35
-
-
70350501165
-
Critical comparison of virtual screening methods against the MUV data set
-
Tiikkainen P, Markt P, Wolber G, et al. Critical comparison of virtual screening methods against the MUV data set. J Chem Inf Model 2009;49:2168-78
-
(2009)
J Chem Inf Model
, vol.49
, pp. 2168-78
-
-
Tiikkainen, P.1
Markt, P.2
Wolber, G.3
-
36
-
-
70349601754
-
The effect of structural redundancy in validation sets on virtual screening performance
-
Clark RD, Shepphird JK, Holliday J. The effect of structural redundancy in validation sets on virtual screening performance. J Chemometrics 2009;9:471-8
-
(2009)
J Chemometrics
, vol.9
, pp. 471-8
-
-
Clark, R.D.1
Shepphird, J.K.2
Holliday, J.3
-
37
-
-
34250332663
-
Computer-aided drug design: Integration of structure-based and ligand-based approaches in drug design
-
Prathipati P, Dixit A, Saxena AK. Computer-aided drug design: integration of structure-based and ligand-based approaches in drug design. Curr Comp Aided Drug Des 2007;3:133-48
-
(2007)
Curr Comp Aided Drug des
, vol.3
, pp. 133-48
-
-
Prathipati, P.1
Dixit, A.2
Saxena, A.K.3
-
38
-
-
74849085203
-
Comparison of structure-and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors
-
Kruger DM, Evers A. Comparison of structure-and ligand-based virtual screening protocols considering hit list complementarity and enrichment factors. Chem Med Chem 2010;5:148-58
-
(2010)
Chem Med Chem
, vol.5
, pp. 148-58
-
-
Kruger, D.M.1
Evers, A.2
-
39
-
-
0037361941
-
Combination of fingerprint-based similarity coefficients using data fusion
-
Salim N, Holliday J, Willett P. Combination of fingerprint-based similarity coefficients using data fusion. J Chem Inf Comput Sci 2003;43:435-42
-
(2003)
J Chem Inf Comput Sci
, vol.43
, pp. 435-42
-
-
Salim, N.1
Holliday, J.2
Willett, P.3
-
40
-
-
66849121861
-
Bayesian modeling in virtual high throughput screening
-
Klon AE. Bayesian modeling in virtual high throughput screening. Comb Chem High Throughput Screen 2009;12:469-83
-
(2009)
Comb Chem High Throughput Screen
, vol.12
, pp. 469-83
-
-
Klon, A.E.1
-
41
-
-
65549112317
-
Improving the search performance of extended connectivity fingerprints through activity-oriented feature filtering and application of a bit-density-dependent similarity function
-
Hu Y, Lounkine E, Bajorath J. Improving the search performance of extended connectivity fingerprints through activity-oriented feature filtering and application of a bit-density-dependent similarity function. Chem Med Chem 2009;4:540-8
-
(2009)
Chem Med Chem
, vol.4
, pp. 540-8
-
-
Hu, Y.1
Lounkine, E.2
Bajorath, J.3
-
42
-
-
73449116746
-
Molecular fingerprint recombination: Generating hybrid fingerprints for similarity searching from different fingerprint types
-
Nisius B, Bajorath J. Molecular fingerprint recombination: generating hybrid fingerprints for similarity searching from different fingerprint types. Chem Med Chem 2009;4:1859-63
-
(2009)
Chem Med Chem
, vol.4
, pp. 1859-63
-
-
Nisius, B.1
Bajorath, J.2
-
43
-
-
34547260921
-
Ultrafast shape recognition to search compound databases for similar molecular shapes
-
Ballester PJ, Richards WG. Ultrafast shape recognition to search compound databases for similar molecular shapes. J Comput Chem 2007;28:1711-23
-
(2007)
J Comput Chem
, vol.28
, pp. 1711-23
-
-
Ballester, P.J.1
Richards, W.G.2
-
44
-
-
70449120267
-
Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors
-
Wilson JA, Bender A, Kaya T, et al. Alpha shapes applied to molecular shape characterization exhibit novel properties compared to established shape descriptors. J Chem Inf Model 2009;49:2231-41
-
(2009)
J Chem Inf Model
, vol.49
, pp. 2231-41
-
-
Wilson, J.A.1
Bender, A.2
Kaya, T.3
-
45
-
-
26944489929
-
McMaster university data-mining and docking competition-Computational models on the catwalk
-
Parker CN. McMaster university data-mining and docking competition-Computational models on the catwalk. J Biomol Screen 2005;10:647-8
-
(2005)
J Biomol Screen
, vol.10
, pp. 647-8
-
-
Parker, C.N.1
-
46
-
-
68149101393
-
Comparison data sets for benchmarking QSAR methodologies in lead optimization
-
Mittal RR, McKinnon RA, Sorich MJ. Comparison data sets for benchmarking QSAR methodologies in lead optimization. J Chem Inf Model 2009;49:1810-20
-
(2009)
J Chem Inf Model
, vol.49
, pp. 1810-20
-
-
Mittal, R.R.1
McKinnon, R.A.2
Sorich, M.J.3
|