-
1
-
-
21444448621
-
Strategies for compound selection
-
Olah, M.; Bologa, C.; Oprea, S.T. Strategies for compound selection. Curr. Drug Discov. Tech., 2004, 1, 211-220.
-
(2004)
Curr. Drug Discov. Tech.
, vol.1
, pp. 211-220
-
-
Olah, M.1
Bologa, C.2
Oprea, S.T.3
-
2
-
-
19644377421
-
Prediction methods and databases within chemoinformatics: Emphasis on drugs and drug candidates
-
Jónsdóttir, S.; Jørgensen, F.; Søren, B. Prediction methods and databases within chemoinformatics: emphasis on drugs and drug candidates. Bioinformatics, 2005, 21, 2145-2160.
-
(2005)
Bioinformatics
, vol.21
, pp. 2145-2160
-
-
Jónsdóttir, S.1
Jørgensen, F.2
Søren, B.3
-
3
-
-
0031152073
-
New technologies for high-throughput screening
-
Burbaum, J.; Sigal, N. New technologies for high throughput screening. Curr. Opin. Chem. Biol., 1997, 1, 72-78. (Pubitemid 127435148)
-
(1997)
Current Opinion in Chemical Biology
, vol.1
, Issue.1
, pp. 72-78
-
-
Burbaum, J.J.1
Sigal, N.H.2
-
4
-
-
33244478113
-
Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: An application of the Receptor-Dependent (RD) 4D-QSAR Formalism
-
DOI 10.1021/ci050326x
-
Santos-Filho, O.; Hopfinger, A. Structure-based QSAR analysis of a set of 4-hydroxy-5,6-dihydropyrones as inhibitors of HIV-1 protease: an application of the receptor dependent (RD) 4D-QSAR formalism. J. Chem. Inf. Model., 2006, 345-354. (Pubitemid 43282127)
-
(2006)
Journal of Chemical Information and Modeling
, vol.46
, Issue.1
, pp. 345-354
-
-
Santos-Filho, O.A.1
Hopfinger, A.J.2
-
5
-
-
0043235843
-
Self-organizing neural networks for pharmacophore mapping
-
DOI 10.1016/S0169-409X(03)00116-9
-
Polanski, J. Self-organizing neural networks for pharmacophore mapping, Adv. Drug. Deliver. Rev., 2003, 55, 1149-1162. (Pubitemid 37098281)
-
(2003)
Advanced Drug Delivery Reviews
, vol.55
, Issue.9
, pp. 1149-1162
-
-
Polanski, J.1
-
6
-
-
27744502081
-
A 4D-QSAR study on anti-HIV HEPT analogues
-
DOI 10.1016/j.bmc.2005.08.023, PII S0968089605007777
-
Bak, A.; Polanski, J. The 4D-QSAR study on anti-HIV HEPT analogues. Bioorg. Med. Chem., 2006, 14, 273-279. (Pubitemid 41635489)
-
(2006)
Bioorganic and Medicinal Chemistry
, vol.14
, Issue.1
, pp. 273-279
-
-
Bak, A.1
Polanski, J.2
-
7
-
-
34547657462
-
Modeling robust QSAR 3: SOM-4D-QSAR with iterative variable elimination IVE-PLS: Application to steroid, azo dye, and benzoic acid series
-
DOI 10.1021/ci700025m
-
Bak, A.; Polanski, J. Modeling robust QSAR 3: SOM-4D-QSAR with iterative variable elimination IVE-PLS: application to steroid, azo dye and benzoic acid series. J. Chem. Inf. Model., 2007, 47, 1469-1480. (Pubitemid 47210050)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.4
, pp. 1469-1480
-
-
Bak, A.1
Polanski, J.2
-
8
-
-
33845768010
-
Modeling robust QSAR J
-
Polanski, J.; Bak, A.; Gieleciak, R.; Magdziarz, T. Modeling robust QSAR J. Chem. Inf. Model., 2006, 46, 2310-2318.
-
(2006)
Chem. Inf. Model.
, vol.46
, pp. 2310-2318
-
-
Polanski, J.1
Bak, A.2
Gieleciak, R.3
Magdziarz, T.4
-
9
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
Wishart, D.; Knox, C.; Guo, A.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Wollsey, J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 2006, 34, 668-672.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 668-672
-
-
Wishart, D.1
Knox, C.2
Guo, A.3
Shrivastava, S.4
Hassanali, M.5
Stothard, P.6
Chang, Z.7
Wollsey, J.8
-
10
-
-
27944507949
-
ChemDB: A public database of small molecules and related chemoinformatics resources
-
DOI 10.1093/bioinformatics/bti683
-
Chen, J.; Swamidass, S.; Dou, Y.; Bruand, J.; Baldi, P. ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinformatics. 2005, 21, 4133-4139. (Pubitemid 41672103)
-
(2005)
Bioinformatics
, vol.21
, Issue.22
, pp. 4133-4139
-
-
Chen, J.1
Swamidass, S.J.2
Dou, Y.3
Bruand, J.4
Baldi, P.5
-
11
-
-
77950817086
-
-
http://www.ebi.ac.uk/pdbe/docs/References.html
-
-
-
-
12
-
-
3042683783
-
-
Ed.; Swindon
-
Wu, B.; Tai, K.; Murdock, S.; Ng, M.; Johnston, S.; Fangohr, H.; Jeffreys, P.; Cox, S.; Essex, J.; Sansom, M. BioSimGrid: a distributed database for biomolecular simulations. In: Proceeings of the UK e-Science All Hands Meeting, Cox, J., Ed.; Swindon, 2003, 412-419.
-
(2003)
BioSimGrid: A Distributed Database for Biomolecular Simulations. In: Proceeings of the UK E-Science All Hands Meeting Cox J.
, pp. 412-419
-
-
Wu, B.1
Tai, K.2
Murdock, S.3
Ng, M.4
Johnston, S.5
Fangohr, H.6
Jeffreys, P.7
Cox, S.8
Essex, J.9
Sansom, M.10
-
13
-
-
33748182876
-
BioSimGrid: Grid-enabled biomolecular simulation data storage and analysis
-
DOI 10.1016/j.future.2005.10.005, PII S0167739X05001457
-
Ng, M.; Johnston, S.; Murdock, S.; Wu, B.; Tai, K.; Fangohr, H.; Cox, S.; Essex, J.; Sansom, M.; Jeffreys, P. Efficient data storage and analysis for generic biomolecular simulation data. In: Proceedings of UK e-Science All Hands Meeting. Cox, J., Ed.; Swindon, 2004, 443-450. (Pubitemid 44308062)
-
(2006)
Future Generation Computer Systems
, vol.22
, Issue.6
, pp. 657-664
-
-
Ng, M.H.1
Johnston, S.2
Wu, B.3
Murdock, S.E.4
Tai, K.5
Fangohr, H.6
Cox, S.J.7
Essex, J.W.8
Sansom, M.S.P.9
Jeffreys, P.10
-
14
-
-
34547668730
-
Web service infrastructure for chemoinformatics
-
DOI 10.1021/ci6004349
-
Dong, X.; Gilbert, E.; Guha, R.; Heiland, R.; Kim, J.; Pierce, E.; Fox, C.; Wild, J. Web service infrastructure for chemoinformatics. J. Chem. Inf. Model., 2007, 47, 1303-1307. (Pubitemid 47210034)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.4
, pp. 1303-1307
-
-
Xiao, D.1
Gilbert, K.E.2
Guha, R.3
Heiland, R.4
Jungkee, K.5
Pierce, M.E.6
Fox, G.C.7
Wild, D.J.8
-
15
-
-
77950821874
-
-
http://www.mysql.com/
-
-
-
-
16
-
-
77950844230
-
-
http://www.python.org
-
-
-
-
17
-
-
77950835977
-
-
http://dirac.cnrs-orleans.fr/MMTK/
-
-
-
-
18
-
-
77950800238
-
-
http://www.ks.uiuc.edu/Research/vmd/
-
-
-
-
19
-
-
77950848449
-
-
http://www.r-project.org/
-
-
-
-
20
-
-
26944486424
-
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity
-
DOI 10.1093/bioinformatics/bti1055
-
Swamidass, S.; Chen, J.; Bruand, J.; Phung, P.; Ralaivola, L.; Baldi, P. Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. Bioinformatics, 2005, 21, 359-368. (Pubitemid 41794509)
-
(2005)
Bioinformatics
, vol.21
, Issue.SUPPL. 1
-
-
Swamidass, S.J.1
Chen, J.2
Bruand, J.3
Phung, P.4
Ralaivola, L.5
Baldi, P.6
-
21
-
-
9344232230
-
Ligand Info small-molecule meta-database
-
von Grotthuss, M.; Koczyk, G.; Pas, J.; Wyrwicz, L.; Rychlewski, L. Ligand Info small-molecule meta-database. Comb. Chem. High Throughput Screen., 2004, 7, 757-761.
-
(2004)
Comb. Chem. High Throughput Screen.
, vol.7
, pp. 757-761
-
-
Von Grotthuss, M.1
Koczyk, G.2
Pas, J.3
Wyrwicz, L.4
Rychlewski, L.5
-
22
-
-
0001708959
-
Description of several chemical structure file formats used by computer programs developed at molecular design limited
-
Dalby, A.; Nourse, J.; Hounshell, W.; Gushurst, A.; Grier, D.; Leland, B.; Laufer, J. Description of several chemical structure file formats used by computer programs developed at molecular design limited. J. Chem. Inf. Comput. Sci., 1992, 32, 244-255.
-
(1992)
J. Chem. Inf. Comput. Sci.
, vol.32
, pp. 244-255
-
-
Dalby, A.1
Nourse, J.2
Hounshell, W.3
Gushurst, A.4
Grier, D.5
Leland, B.6
Laufer, J.7
-
23
-
-
0012034179
-
The substance module: The representation storage and searching of complex structures
-
Hushurst, A.; Nourse, J.; Hounshell, W.; Leland, B.; Raich, D. The substance module: the representation, storage and searching of complex structures. J. Chem. Inf. Comput. Sci., 1991, 31, 447-454.
-
(1991)
J. Chem. Inf. Comput. Sci.
, vol.31
, pp. 447-454
-
-
Hushurst, A.1
Nourse, J.2
Hounshell, W.3
Leland, B.4
Raich, D.5
-
24
-
-
13844312649
-
ZINC - A free database of commercially available compounds for virtual screening
-
DOI 10.1021/ci049714+
-
Irwin, J.; Shoichet, B. ZINC-A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 2005, 45, 177-182. (Pubitemid 40736970)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
25
-
-
34249040810
-
Physics-based methods for studying protein-ligand interactions
-
Huang, N.; Jacobson, M. Physics-based methods for studying protein-ligand interactions. Curr. Opin. Drug Discov. Devel., 2007, 10, 325-331. (Pubitemid 46800226)
-
(2007)
Current Opinion in Drug Discovery and Development
, vol.10
, Issue.3
, pp. 325-331
-
-
Huang, N.1
Jacobson, M.P.2
-
26
-
-
0034020917
-
STAR/mmCIF: An ontology for macromolecular structure
-
Westbrook, J.; Bourne, P. STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 2000, 16, 159-168. (Pubitemid 30248593)
-
(2000)
Bioinformatics
, vol.16
, Issue.2
, pp. 159-168
-
-
Westbrook, J.D.1
Bourne, P.E.2
-
27
-
-
0033954256
-
The protein data bank
-
Berman, H.; Westbrook, J.; Feng, Z.; Gilliand, G.; Bhat, T.; Wiessig, H.; Shindyalov, I.; Bourne, P. The Protein Data Bank. Nucleic Acids Res., 2000, 28, 235-243. (Pubitemid 30047768)
-
(2000)
Nucleic Acids Research
, vol.28
, Issue.1
, 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
-
28
-
-
0032214622
-
Protein Data Bank (PDB): Database of three-dimensional structural information of biological macromolecules
-
DOI 10.1107/S0907444998009378
-
Sussman, J.; Lin, D.; Jiang, J.; Manning, N.; Prilusky, J.; Ritter, O.; Abola, E. Protein Data Bank (PDB): database of three-dimensional structural information of biological macromolecules. Acta Crystallogr. D Biol. Crystallogr., 1998, 54, 1078-1084. (Pubitemid 29000162)
-
(1998)
Acta Crystallographica Section D: Biological Crystallography
, vol.54
, Issue.I6
, pp. 1078-1084
-
-
Sussman, J.L.1
Lin, D.2
Jiang, J.3
Manning, N.O.4
Prilusky, J.5
Ritter, O.6
Abola, E.E.7
-
29
-
-
33846036096
-
The worldwide Protein Data Bank (wwPDB): Ensuring a single, uniform archive of PDB data
-
DOI 10.1093/nar/gkl971
-
Berman, H.; Henrick, K.; Nakamura, H.; Markley, J. The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data. Nucleic Acids Res., 2007, 35, 301-303. (Pubitemid 46056219)
-
(2007)
Nucleic Acids Research
, vol.35
, Issue.SUPPL. 1
-
-
Berman, H.1
Henrick, K.2
Nakamura, H.3
Markley, J.L.4
-
30
-
-
16344364140
-
PDBML: The representation of archival macromolecular structure data in XML
-
DOI 10.1093/bioinformatics/bti082
-
Westbrook, J.; Ito, N.; Nakamura, H.; Henrick, K.; Berman, H. PDBML: the representation of archival macromolecular structure in XML. Bioinformatics, 2005, 21, 988-992. (Pubitemid 40467920)
-
(2005)
Bioinformatics
, vol.21
, Issue.7
, pp. 988-992
-
-
Westbrook, J.1
Ito, N.2
Nakamura, H.3
Henrick, K.4
Berman, H.M.5
-
31
-
-
13444270892
-
The RCSB Protein Databa Bank: A redesigned query system and relational database based on the mmCIF schema
-
DOI 10.1093/nar/gki057
-
Deshpande, N.; Addess, K.; Bluhm, W.; Merino-Ott, J.; Wownsend-Merino, W.; Qing, Z.; Knezevich, C.; Xie, L.; Chen, L.; Feng, Z.; Green, K.R.; Flippen-Anderson, J.; Westbrook, J.; Berman, H.; Bourne, P. The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res., 2005, 33, 223-237. (Pubitemid 40207868)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.DATABASE ISS.
-
-
Deshpande, N.1
Addess, K.J.2
Bluhm, W.F.3
Merino-Ott, J.C.4
Townsend-Merino, W.5
Zhang, Q.6
Knezevich, C.7
Xie, L.8
Chen, L.9
Feng, Z.10
Green, R.K.11
Flippen-Anderson, J.L.12
Westbrook, J.13
Berman, H.M.14
Bourne, P.E.15
-
32
-
-
77950843111
-
-
http://mmcif.pdb.org/
-
-
-
-
33
-
-
0023965741
-
SMILES a chemical language and information system. 1. Introduction to methodology and encoding rules
-
Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. J. Chem. Inf. Comput. Sci., 1998, 28, 31-36.
-
(1998)
J. Chem. Inf. Comput. Sci.
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
34
-
-
0024664539
-
SMILES. 2. Algorithm for generation of unique SMILES notation
-
Weininger, D.; Weininger, A.; Weeininger, J. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci., 1989, 29, 97-101.
-
(1989)
J. Chem. Inf. Comput. Sci.
, Issue.29
, pp. 97-101
-
-
Weininger, D.1
Weininger, A.2
Weeininger, J.3
-
35
-
-
0000010226
-
Novel canonical coding method for representation of three-dimensional structures
-
Satoh, H.; Koshino, H.; Funatsu, K.; Nakata, T. Novel canonical coding method for representation of three-dimensional structures. J. Chem. Inf. Comput. Sci., 2000, 40, 622-630.
-
(2000)
J. Chem. Inf. Comput. Sci.
, vol.40
, pp. 622-630
-
-
Satoh, H.1
Koshino, H.2
Funatsu, K.3
Nakata, T.4
-
36
-
-
35248878598
-
Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmetric information
-
DOI 10.1021/ci600238j
-
Koichi, S.; Iwata, S.; Uno, T.; Koshino, H.; Satoh, H. Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmeteric information. J. Chem. Inf. Model., 2007, 45, 1734-1746. (Pubitemid 47561122)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.5
, pp. 1734-1746
-
-
Koichi, S.1
Iwata, S.2
Uno, T.3
Koshino, H.4
Satoh, H.5
-
38
-
-
77950793500
-
-
http://docs.python.org/tutorial/
-
-
-
-
39
-
-
77950852564
-
-
OEChem-Python Theory Manual, OpenEye Scientific Software Inc. 2008 Santa Fe, NM 87508
-
OEChem-Python Theory Manual, OpenEye Scientific Software Inc., 2008, Santa Fe, NM 87508.
-
-
-
-
40
-
-
41249091782
-
Pybel: A Python wrapper for the OpenBabel cheminformatics toolkit
-
O'Boyle, N.; Morley, C.; Hutchison, R. Pybel: a Python wrapper for the OpenBabel cheminformatics toolkit. Chem. Cent. J., 2008, 2, 1-7.
-
(2008)
Chem. Cent. J.
, vol.2
, pp. 1-7
-
-
O'Boyle, N.1
Morley, C.2
Hutchison, R.3
-
41
-
-
77950824496
-
-
http://soiland.no/i/src/forgetsql2/
-
-
-
-
42
-
-
77950832059
-
-
http://www.eyesopen.com/docs/html/api/
-
-
-
-
43
-
-
77950811575
-
-
http://www.sqlobject.org/SQLBuilder.html
-
-
-
-
44
-
-
34247228558
-
Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time
-
DOI 10.1021/ci600358f
-
Swamidass, S.; Baldi, P. Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sub-linear time. J. Chem. Inf. Model., 2007, 47, 302-317. (Pubitemid 46615935)
-
(2007)
Journal of Chemical Information and Modeling
, vol.47
, Issue.2
, pp. 302-317
-
-
Swamidass, S.J.1
Baldi, P.2
-
45
-
-
20444410051
-
Database clustering with a combination of fingerprint and maximum common substructure methods
-
DOI 10.1021/ci050011h
-
Stahl, M.; Mauser, H. Database clustering with a combination of fingerprint and maximum common substructure methods. J. Chem. Inf. Model., 2005, 45, 542-548. (Pubitemid 40795160)
-
(2005)
Journal of Chemical Information and Modeling
, vol.45
, Issue.3
, pp. 542-548
-
-
Stahl, M.1
Mauser, H.2
-
46
-
-
77950802067
-
-
Daylight Theory Manual, http://www.daylight.com/dayhtml/doc/theory/ theory.toc.html
-
-
-
Theory Manual, D.1
-
47
-
-
0001232509
-
On the properties of bit string-based measures of chemical similarity
-
Flower, D. On the properties of bit-string based measures of chemical similarity. J. Chem. Inf. Comput. Sci., 1998, 38, 379-386. (Pubitemid 128594448)
-
(1998)
Journal of Chemical Information and Computer Sciences
, vol.38
, Issue.3
, pp. 379-386
-
-
Flower, D.R.1
-
48
-
-
61949359014
-
Common pharmacophore identification using Frequent Clique detection algorithm
-
Podolyan, Y.; Karypis, G. Common pharmacophore identification using Frequent Clique detection algorithm. J. Chem. Inf. Model., 2009, 49, 13-21.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, pp. 13-21
-
-
Podolyan, Y.1
Karypis, G.2
-
49
-
-
46249123633
-
A maximum common substructure-based algorithm for searching and predicting drug-like compounds
-
DOI 10.1093/bioinformatics/btn186
-
Cao, Y.; Jiang, T.; Girke, T. A maximum common substructure-based algorithm for searching and predicting drug-like compounds, Bioinformatics, 2008, 24, 366-374. (Pubitemid 351911692)
-
(2008)
Bioinformatics
, vol.24
, Issue.13
-
-
Cao, Y.1
Jiang, T.2
Girke, T.3
-
50
-
-
0035289779
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
DOI 10.1016/S0169-409X(00)00129-0, PII S0169409X00001290
-
Lipinski, C.; Lombardo, F.; Dominy, B.; Feeney, P. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Del. Res., 2001, 46, 3-26. (Pubitemid 33653411)
-
(2000)
Advanced Drug Delivery Reviews
, vol.46
, Issue.1-3
, pp. 3-26
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
51
-
-
0035438391
-
Is There a Difference between Leads and Drugs? A Historical Perspective
-
Oprea, T.; Davis, A.; Teague, S.; Leeson, P. Is there a difference between leads and drugs? A historical perspective. J. Chem. Inf. Comput., 2001, s1, 1308-1315. (Pubitemid 33663896)
-
(2001)
Journal of Chemical Information and Computer Sciences
, vol.41
, Issue.3-6
, pp. 1308-1315
-
-
Oprea, T.I.1
Davis, A.M.2
Teague, S.J.3
Leeson, P.D.4
-
52
-
-
2942564021
-
Pursuing the leadlikeness concept in pharmaceutical research
-
DOI 10.1016/j.cbpa.2004.04.003, PII S1367593104000493
-
Hann, M.; Oprea, T. Pursuing the leadlikeness concept in pharmaceutical research. Curr. Opin. Chem. Biol., 2004, 8, 255-263. (Pubitemid 38759400)
-
(2004)
Current Opinion in Chemical Biology
, vol.8
, Issue.3
, pp. 255-263
-
-
Hann, M.M.1
Oprea, T.I.2
-
53
-
-
77950789490
-
-
http://openbabel.org/wiki/Main-Page
-
-
-
-
54
-
-
77950843838
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http://www.eyesopen.com/
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-
55
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70349554501
-
The use of MoStBioDat for rapid screening of molecular diversity
-
Bak, A.; Polanski, J.; Kurczyk, A. The use of MoStBioDat for rapid screening of molecular diversity. Molecules, 2009, 14, 3436-3445.
-
(2009)
Molecules
, vol.14
, pp. 3436-3445
-
-
Bak, A.1
Polanski, J.2
Kurczyk, A.3
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