-
1
-
-
33646104414
-
The central role of chemoinformatics
-
Gasteiger, J. The central role of chemoinformatics. Chemom. Intell. Lab. Syst., 2006, 82(1-2), 200-209.
-
(2006)
Chemom. Intell. Lab. Syst.
, vol.82
, Issue.1-2
, pp. 200-209
-
-
Gasteiger, J.1
-
2
-
-
29144521676
-
Chemoinformatics: A new field with a long tradition
-
Gasteiger, J. Chemoinformatics: a new field with a long tradition. Anal. Bioanal. Chem., 2006, 384(1), 57-64.
-
(2006)
Anal. Bioanal. Chem.
, vol.384
, Issue.1
, pp. 57-64
-
-
Gasteiger, J.1
-
6
-
-
77950503976
-
Virtual screening: An endless staircase?
-
Schneider, G. Virtual screening: an endless staircase? Nat. Rev. Drug. Discov., 2010, 9(4), 273-276.
-
(2010)
Nat. Rev. Drug. Discov.
, vol.9
, Issue.4
, pp. 273-276
-
-
Schneider, G.1
-
7
-
-
77955767207
-
Virtual screening in drug design and development
-
Sousa, S.F.; Cerqueira, N.M.; Fernandes, P.A.; Ramos, M.J. Virtual screening in drug design and development. Comb. Chem. High Throughput Screen., 13(5), 442-453.
-
Comb. Chem. High Throughput Screen.
, vol.13
, Issue.5
, pp. 442-453
-
-
Sousa, S.F.1
Cerqueira, N.M.2
Fernandes, P.A.3
Ramos, M.J.4
-
8
-
-
33744539143
-
Chemical database preparation for compound acquisition or virtual screening
-
Bologa, C.G.; Olah, M.M.; Oprea, T.I. Chemical database preparation for compound acquisition or virtual screening. Methods Mol. Biol., 2006, 316(375-388).
-
(2006)
Methods Mol. Biol.
, vol.316
, pp. 375-388
-
-
Bologa, C.G.1
Olah, M.M.2
Oprea, T.I.3
-
9
-
-
79955024158
-
Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections
-
Del Rio, A.; Barbosa, A.; Caporuscio, F. Use of large multiconformational databases with structure-based pharmacophore models for fast screening of commercial compound collections. J. Cheminform., 2011, 3(Suppl 1), P27.
-
(2011)
J. Cheminform.
, vol.3
, Issue.SUPPL. 1
, pp. 27
-
-
Del Rio, A.1
Barbosa, A.2
Caporuscio, F.3
-
10
-
-
34548289911
-
Free resources to assist structure-based virtual ligand screening experiments
-
Villoutreix, B.O.; Renault, N.; Lagorce, D.; Sperandio, O.; Montes, M.; Miteva, M.A. Free resources to assist structure-based virtual ligand screening experiments. Curr. Protein Pept. Sci., 2007, 8(4), 381-411.
-
(2007)
Curr. Protein Pept. Sci.
, vol.8
, Issue.4
, pp. 381-411
-
-
Villoutreix, B.O.1
Renault, N.2
Lagorce, D.3
Sperandio, O.4
Montes, M.5
Miteva, M.A.6
-
11
-
-
72949101438
-
Structure and organization of drug-target networks: Insights from genomic approaches for drug discovery
-
Janga, S.C.; Tzakos, A. Structure and organization of drug-target networks: insights from genomic approaches for drug discovery. Mol. BioSyst., 2009, 5(12), 1536-1548.
-
(2009)
Mol. BioSyst.
, vol.5
, Issue.12
, pp. 1536-1548
-
-
Janga, S.C.1
Tzakos, A.2
-
12
-
-
34548189765
-
Large compound databases for structure-activity relationships studies in drug discovery
-
Scior, T.; Bernard, P.; Medina-Franco, J.L.; Maggiora, G.M. Large compound databases for structure-activity relationships studies in drug discovery. Mini Rev. Med. Chem., 2007, 7(8), 851-860.
-
(2007)
Mini Rev. Med. Chem.
, vol.7
, Issue.8
, pp. 851-860
-
-
Scior, T.1
Bernard, P.2
Medina-Franco, J.L.3
Maggiora, G.M.4
-
13
-
-
17844388776
-
-
Accessed on November
-
OpenEye Scientific Software. http://www.eyesopen.com [Accessed on November 2010]
-
(2010)
OpenEye Scientific Software
-
-
-
15
-
-
84860264514
-
-
Accessed on November
-
Xemistry Gmb H. http://xemistry.com/ [Accessed on November 2010]
-
(2010)
Xemistry GmbH
-
-
-
16
-
-
34249874435
-
The IUPAC International Chemical Identifier: InChl
-
McNaught, A. The IUPAC International Chemical Identifier: InChl. Chem. Int., 2006, 28(6), 12-15.
-
(2006)
Chem. Int.
, vol.28
, Issue.6
, pp. 12-15
-
-
McNaught, A.1
-
17
-
-
84860267125
-
-
Accessed on November
-
Schrödinger, LLC. http://www.schrodinger.com/ [Accessed on November 2010]
-
(2010)
-
-
Schrödinger, L.L.C.1
-
18
-
-
84860296824
-
-
Chemical Computing Group, Accessed on November
-
Chemical Computing Group. http://www.chemcomp.com [Accessed on November 2010]
-
(2010)
-
-
-
19
-
-
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., 1988, 28(1), 31-36.
-
(1988)
J. Chem. Inf. Comput. Sci.
, vol.28
, Issue.1
, pp. 31-36
-
-
Weininger, D.1
-
20
-
-
0024664539
-
SMILES. 2. Algorithm for generation of unique SMILES notation
-
Weininger, D.; Weininger, A.; Weininger, J.L. SMILES. 2. Algorithm for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci., 1989, 29(2), 97-101.
-
(1989)
J. Chem. Inf. Comput. Sci.
, vol.29
, Issue.2
, pp. 97-101
-
-
Weininger, D.1
Weininger, A.2
Weininger, J.L.3
-
21
-
-
84986533812
-
Hash codes for the identification and classification of molecular structure elements
-
Ihlenfeldt, W.D.; Gasteiger, J. Hash codes for the identification and classification of molecular structure elements. J. Comput. Chem., 1994, 15(8), 793-813.
-
(1994)
J. Comput. Chem.
, vol.15
, Issue.8
, pp. 793-813
-
-
Ihlenfeldt, W.D.1
Gasteiger, J.2
-
22
-
-
84860267124
-
-
RDkit, Accessed on November
-
RDkit. http://rdkit.org [Accessed on November 2010]
-
(2010)
-
-
-
23
-
-
84860266745
-
-
Accelrys Inc., Accessed on November
-
Accelrys Inc. http://accelrys.com [Accessed on November 2010]
-
(2010)
-
-
-
24
-
-
37249065124
-
Generating conformer ensembles using a multiobjective genetic algorithm
-
Vainio, M.J.; Johnson, M.S. Generating conformer ensembles using a multiobjective genetic algorithm. J. Chem. Inf. Model., 2007, 47(6), 2462-2474.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.6
, pp. 2462-2474
-
-
Vainio, M.J.1
Johnson, M.S.2
-
25
-
-
84860296825
-
-
Tripos, Accessed on November
-
Tripos. http://www.tripos.com [Accessed on November 2010]
-
(2010)
-
-
-
26
-
-
78651287009
-
EDULISS: A small-molecule database with data-mining and pharmacophore searching capabilities
-
Database issue
-
Hsin, K.-Y.; Morgan, H.P.; Shave, S.R.; Hinton, A.C.; Taylor, P.; Walkinshaw, M.D. EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. Nucleic Acids Res., 2010, 39(Database issue):D1042-1048.
-
(2010)
Nucleic Acids Res
, vol.39
-
-
Hsin, K.-Y.1
Morgan, H.P.2
Shave, S.R.3
Hinton, A.C.4
Taylor, P.5
Walkinshaw, M.D.6
-
27
-
-
38549092091
-
Database resources of the National Center for Biotechnology Information
-
Database issue
-
Wheeler, D.L.; Barrett, T.; Benson, D.A.; Bryant, S.H.; Canese, K.; Chetvernin, V.; Church, D.M.; Dicuccio, M.; Edgar, R.; Federhen, S.; Feolo, M.; Geer, L.Y.; Helmberg, W.; Kapustin, Y.; Khovayko, O.; Landsman, D.; Lipman, D.J.; Madden, T.L.; Maglott, D.R.; Miller, V.; Ostell, J.; Pruitt, K.D.; Schuler, G.D.; Shumway, M.; Sequeira, E.; Sherry, S.T.; Sirotkin, K.; Souvorov, A.; Starchenko, G.; Tatusov, R.L.; Tatusova, T.A.; Wagner, L.; Yaschenko, E. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res., 2008, 36(Database issue): D13-21.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wheeler, D.L.1
Barrett, T.2
Benson, D.A.3
Bryant, S.H.4
Canese, K.5
Chetvernin, V.6
Church, D.M.7
Dicuccio, M.8
Edgar, R.9
Federhen, S.10
Feolo, M.11
Geer, L.Y.12
Helmberg, W.13
Kapustin, Y.14
Khovayko, O.15
Landsman, D.16
Lipman, D.J.17
Madden, T.L.18
Maglott, D.R.19
Miller, V.20
Ostell, J.21
Pruitt, K.D.22
Schuler, G.D.23
Shumway, M.24
Sequeira, E.25
Sherry, S.T.26
Sirotkin, K.27
Souvorov, A.28
Starchenko, G.29
Tatusov, R.L.30
Tatusova, T.A.31
Wagner, L.32
Yaschenko, E.33
more..
-
28
-
-
75149173490
-
The PubChem chemical structure sketcher
-
Ihlenfeldt, W.; Bolton, E.; Bryant, S. The PubChem chemical structure sketcher. J. Cheminform., 2009, 1(1), 20.
-
(2009)
J. Cheminform.
, vol.1
, Issue.1
, pp. 20
-
-
Ihlenfeldt, W.1
Bolton, E.2
Bryant, S.3
-
29
-
-
84857192927
-
-
Accessed on November
-
Molinspiration cheminformatics. http://www.molinspiration.com [Accessed on November 2010]
-
(2010)
Molinspiration cheminformatics
-
-
-
30
-
-
84860266746
-
-
AMSOL, Accessed on November
-
AMSOL. http://comp.chem.umn.edu/amsol [Accessed on November 2010]
-
(2010)
-
-
-
31
-
-
13844312649
-
ZINC--a free database of commercially available compounds for virtual screening
-
Irwin, J.J.; Shoichet, B.K. ZINC--a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 2005, 45(1), 177-182.
-
(2005)
J. Chem. Inf. Model.
, vol.45
, Issue.1
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
32
-
-
58149203232
-
MMsINC: A large-scale chemoinformatics database
-
Database issue
-
Masciocchi, J.; Frau, G.; Fanton, M.; Sturlese, M.; Floris, M.; Pireddu, L.; Palla, P.; Cedrati, F.; Rodriguez-Tome, P.; Moro, S. MMsINC: a large-scale chemoinformatics database. Nucleic Acids Res., 2009, 37(Database issue), D284-290.
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Masciocchi, J.1
Frau, G.2
Fanton, M.3
Sturlese, M.4
Floris, M.5
Pireddu, L.6
Palla, P.7
Cedrati, F.8
Rodriguez-Tome, P.9
Moro, S.10
-
33
-
-
77951987154
-
ConfGen: A conformational search method for efficient generation of bioactive conformers
-
Watts, K.S.; Dalal, P.; Murphy, R.B.; Sherman, W.; Friesner, R.A.; Shelley, J.C. ConfGen: a conformational search method for efficient generation of bioactive conformers. J. Chem. Inf. Model., 2010, 50(4), 534-546.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.4
, pp. 534-546
-
-
Watts, K.S.1
Dalal, P.2
Murphy, R.B.3
Sherman, W.4
Friesner, R.A.5
Shelley, J.C.6
-
34
-
-
77957894400
-
CoCoCo: A free suite of multiconformational chemical databases for high-throughput virtual screening purposes
-
Del Rio, A.; Barbosa, A.J.; Caporuscio, F.; Mangiatordi, G.F. CoCoCo: a free suite of multiconformational chemical databases for high-throughput virtual screening purposes. Mol. BioSyst., 2010, 6(11), 2122-2128.
-
(2010)
Mol. BioSyst.
, vol.6
, Issue.11
, pp. 2122-2128
-
-
Del Rio, A.1
Barbosa, A.J.2
Caporuscio, F.3
Mangiatordi, G.F.4
-
35
-
-
33846108633
-
Binding DB: A web-accessible database of experimentally determined proteinligand binding affinities
-
Database issue
-
Liu, T.; Lin, Y.; Wen, X.; Jorissen, R.N.; Gilson, M.K. Binding DB: a web-accessible database of experimentally determined proteinligand binding affinities. Nucleic Acids Res., 2007, 35(Database issue): D198-201.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Liu, T.1
Lin, Y.2
Wen, X.3
Jorissen, R.N.4
Gilson, M.K.5
-
36
-
-
0037606114
-
Ligand-Info, searching for similar small compounds using index profiles
-
von Grotthuss, M.; Pas, J.; Rychlewski, L. Ligand-Info, searching for similar small compounds using index profiles. Bioinformatics, 2003, 19(8), 1041-1042.
-
(2003)
Bioinformatics
, vol.19
, Issue.8
, pp. 1041-1042
-
-
von Grotthuss, M.1
Pas, J.2
Rychlewski, L.3
-
37
-
-
38549151817
-
DrugBank: A knowledgebase for drugs, drug actions and drug targets
-
Database issue
-
Wishart, D.S.; Knox, C.; Guo, A.C.; Cheng, D.; Shrivastava, S.; Tzur, D.; Gautam, B.; Hassanali, M. DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res., 2008, 36(Database issue), D901-906.
-
(2008)
Nucleic Acids Res
, vol.36
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Cheng, D.4
Shrivastava, S.5
Tzur, D.6
Gautam, B.7
Hassanali, M.8
-
38
-
-
33644876210
-
DrugBank: A comprehensive resource for in silico drug discovery and exploration
-
Database issue
-
Wishart, D.S.; Knox, C.; Guo, A.C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J. DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic Acids Res., 2006, 34(Database issue), D668-672.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Wishart, D.S.1
Knox, C.2
Guo, A.C.3
Shrivastava, S.4
Hassanali, M.5
Stothard, P.6
Chang, Z.7
Woolsey, J.8
-
39
-
-
61749093196
-
ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBLEBI)
-
Warr, W. ChEMBL. An interview with John Overington, team leader, chemogenomics at the European Bioinformatics Institute Outstation of the European Molecular Biology Laboratory (EMBLEBI). J. Comput.-Aided Mol. Des., 2009, 23(4), 195-198.
-
(2009)
J. Comput.-Aided Mol. Des.
, vol.23
, Issue.4
, pp. 195-198
-
-
Warr, W.1
-
40
-
-
84860313420
-
-
Accessed on November
-
NCI Open database. http://cactus.nci.nih.gov/download/nci [Accessed on November 2010]
-
(2010)
NCI Open database
-
-
-
42
-
-
78049349961
-
Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research
-
Fourches, D.; Muratov, E.; Tropsha, A. Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J. Chem. Inf. Model., 2010, 50(7), 1189-1204.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.7
, pp. 1189-1204
-
-
Fourches, D.1
Muratov, E.2
Tropsha, A.3
-
43
-
-
0035289779
-
Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
-
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., 2001, 46(1-3), 3-26.
-
(2001)
Adv. Drug Delivery Rev.
, vol.46
, Issue.1-3
, pp. 3-26
-
-
Lipinski, C.A.1
Lombardo, F.2
Dominy, B.W.3
Feeney, P.J.4
-
44
-
-
33751313329
-
Knowledge-based chemoinformatic approaches to drug discovery
-
Ghose, A.K.; Herbertz, T.; Salvino, J.M.; Mallamo, J.P. Knowledge-based chemoinformatic approaches to drug discovery. Drug Discov. Today, 2006, 11(23-24), 1107-1114.
-
(2006)
Drug Discov. Today
, vol.11
, Issue.23-24
, pp. 1107-1114
-
-
Ghose, A.K.1
Herbertz, T.2
Salvino, J.M.3
Mallamo, J.P.4
-
45
-
-
25844495011
-
Medicinal chemical properties of successful central nervous system drugs
-
Pajouhesh, H.; Lenz, G.R. Medicinal chemical properties of successful central nervous system drugs. Neurorx, 2005, 2(4), 541-553.
-
(2005)
Neurorx
, vol.2
, Issue.4
, pp. 541-553
-
-
Pajouhesh, H.1
Lenz, G.R.2
-
46
-
-
0343869724
-
SYBYL line notation (SLN): A versatile language for chemical structure representation
-
Ash, S.; Cline, M.A.; Homer, R.W.; Hurst, T.; Smith, G.B. SYBYL line notation (SLN): A versatile language for chemical structure representation. J. Chem. Inf. Comput. Sci., 1997, 37(1), 71-79.
-
(1997)
J. Chem. Inf. Comput. Sci.
, vol.37
, Issue.1
, pp. 71-79
-
-
Ash, S.1
Cline, M.A.2
Homer, R.W.3
Hurst, T.4
Smith, G.B.5
-
47
-
-
0028336046
-
Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility
-
Ihlenfeldt, W.D.; Takahashi, Y.; Abe, H.; Sasaki, S. Computation and management of chemical properties in CACTVS: An extensible networked approach toward modularity and compatibility. J. Chem. Inf. Comput. Sci., 1994, 34(1), 109-116.
-
(1994)
J. Chem. Inf. Comput. Sci.
, vol.34
, Issue.1
, pp. 109-116
-
-
Ihlenfeldt, W.D.1
Takahashi, Y.2
Abe, H.3
Sasaki, S.4
-
48
-
-
19644392743
-
Application of InChI to curate, index, and query 3-D structures
-
Prasanna, M.; Vondrasek, J.; Wlodawer, A.; Bhat, T. Application of InChI to curate, index, and query 3-D structures. Proteins Struct. Funct. Bioinformat., 2005, 60(1), 1-4.
-
(2005)
Proteins Struct. Funct. Bioinformat.
, vol.60
, Issue.1
, pp. 1-4
-
-
Prasanna, M.1
Vondrasek, J.2
Wlodawer, A.3
Bhat, T.4
-
49
-
-
0036025426
-
Enhanced CACTVS Browser of the Open NCI Database
-
Ihlenfeldt, W.-D.; Voigt, J.H.; Bienfait, B.; Oellien, F.; Nicklaus, M.C. Enhanced CACTVS Browser of the Open NCI Database. J. Chem. Inf. Comput. Sci., 2002, 42(1), 46-57.
-
(2002)
J. Chem. Inf. Comput. Sci.
, vol.42
, Issue.1
, pp. 46-57
-
-
Ihlenfeldt, W.-D.1
Voigt, J.H.2
Bienfait, B.3
Oellien, F.4
Nicklaus, M.C.5
-
50
-
-
19944419184
-
Enhancement of the chemical semantic web through the use of InChI identifiers
-
Coles, S.J.; Day, N.E.; Murray-Rust, P.; Rzepa, H.S.; Zhang, Y. Enhancement of the chemical semantic web through the use of InChI identifiers. Org. Biomol. Chem., 2005, 3(10), 1832-1834.
-
(2005)
Org. Biomol. Chem.
, vol.3
, Issue.10
, pp. 1832-1834
-
-
Coles, S.J.1
Day, N.E.2
Murray-Rust, P.3
Rzepa, H.S.4
Zhang, Y.5
-
51
-
-
78049428484
-
Tautomer identification and tautomer structure generation based on the InChI Code
-
Thalheim, T.; Vollmer, A.; Ebert, R.-U.; Kuhne, R.; Schuurmann, G. Tautomer identification and tautomer structure generation based on the InChI Code. J. Chem. Inf. Model., 2010, 50(7), 1223-1232.
-
(2010)
J. Chem. Inf. Model.
, vol.50
, Issue.7
, pp. 1223-1232
-
-
Thalheim, T.1
Vollmer, A.2
Ebert, R.-U.3
Kuhne, R.4
Schuurmann, G.5
-
52
-
-
33845723240
-
SemanticEye: A semantic web application to rationalize and enhance chemical electronic publishing
-
Casher, O.; Rzepa, H.S. SemanticEye: A semantic web application to rationalize and enhance chemical electronic publishing. J. Chem. Inf. Model., 2006, 46(6), 2396-2411.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, Issue.6
, pp. 2396-2411
-
-
Casher, O.1
Rzepa, H.S.2
-
53
-
-
67649970229
-
Exploring enantioselective molecular recognition mechanisms with chemoinformatic techniques
-
Del Rio, A. Exploring enantioselective molecular recognition mechanisms with chemoinformatic techniques. J. Sep. Sci., 2009, 32(10), 1566-1584.
-
(2009)
J. Sep. Sci.
, vol.32
, Issue.10
, pp. 1566-1584
-
-
Del Rio, A.1
-
54
-
-
58149131487
-
Encoding absolute configurations with chiral enantiophore descriptors. application to the order of elution of enantiomers in liquid chromatography
-
Del Rio, A.; Gasteiger, J. Encoding absolute configurations with chiral enantiophore descriptors. application to the order of elution of enantiomers in liquid chromatography. QSAR Comb. Sci., 2008, 27(11-12), 1326-1336.
-
(2008)
QSAR Comb. Sci.
, vol.27
, Issue.11-12
, pp. 1326-1336
-
-
Del Rio, A.1
Gasteiger, J.2
-
55
-
-
70350560811
-
Activity prediction and structural insights of extracellular signal-regulated kinase 2 inhibitors with molecular dynamics simulations
-
Del Rio, A.; Baldi, B.F.; Rastelli, G. Activity prediction and structural insights of extracellular signal-regulated kinase 2 inhibitors with molecular dynamics simulations. Chem. Biol. Drug Des., 2009, 74(6), 630-635.
-
(2009)
Chem. Biol. Drug Des.
, vol.74
, Issue.6
, pp. 630-635
-
-
Del Rio, A.1
Baldi, B.F.2
Rastelli, G.3
-
56
-
-
3242733866
-
Theoretical reassessment of Whelk-O1 as an enantioselective receptor for 1-(4-halogeno-phenyl)-1-ethylamine derivatives
-
Del Rio, A.; Hayes, J.M.; Stein, M.; Piras, P.; Roussel, C. Theoretical reassessment of Whelk-O1 as an enantioselective receptor for 1-(4-halogeno-phenyl)-1-ethylamine derivatives. Chirality, 2004, 16 (Suppl)S1-11.
-
(2004)
Chirality
, vol.16
, Issue.SUPPL.
-
-
Del Rio, A.1
Hayes, J.M.2
Stein, M.3
Piras, P.4
Roussel, C.5
-
58
-
-
84860300724
-
-
Accessed on November
-
Molecular Networks GmbH. http://www.molecular-networks.com [Accessed on November 2010]
-
(2010)
Molecular Networks GmbH
-
-
-
59
-
-
37249043664
-
Impact of ligand protonation on virtual screening against beta-secretase (BACE1)
-
Polgar, T.; Magyar, C.; Simon, I.; Keseru, G.M. Impact of ligand protonation on virtual screening against beta-secretase (BACE1). J. Chem. Inf. Model., 2007, 47(6), 2366-2373.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.6
, pp. 2366-2373
-
-
Polgar, T.1
Magyar, C.2
Simon, I.3
Keseru, G.M.4
-
60
-
-
67650077383
-
Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results
-
ten Brink, T.; Exner, T.E. Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J. Chem. Inf. Model., 2009, 49(6), 1535-1546.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.6
, pp. 1535-1546
-
-
ten Brink, T.1
Exner, T.E.2
-
61
-
-
33845779764
-
The impact of tautomer forms on pharmacophore-based virtual screening
-
Oellien, F.; Cramer, J.; Beyer, C.; Ihlenfeldt, W.D.; Selzer, P.M. The impact of tautomer forms on pharmacophore-based virtual screening. J. Chem. Inf. Model., 2006, 46(6), 2342-2354.
-
(2006)
J. Chem. Inf. Model.
, vol.46
, Issue.6
, pp. 2342-2354
-
-
Oellien, F.1
Cramer, J.2
Beyer, C.3
Ihlenfeldt, W.D.4
Selzer, P.M.5
-
62
-
-
61949390938
-
Tautomer enumeration and stability prediction for virtual screening on large chemical databases
-
Milletti, F.; Storchi, L.; Sforna, G.; Cross, S.; Cruciani, G. Tautomer enumeration and stability prediction for virtual screening on large chemical databases. J. Chem. Inf. Model., 2009, 49(1), 68-75.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.1
, pp. 68-75
-
-
Milletti, F.1
Storchi, L.2
Sforna, G.3
Cross, S.4
Cruciani, G.5
-
63
-
-
76249106208
-
Let's not forget tautomers
-
Martin, Y.C. Let's not forget tautomers. J. Comput.-Aided Mol. Des., 2009, 23(10), 693-704.
-
(2009)
J. Comput.-Aided Mol. Des.
, vol.23
, Issue.10
, pp. 693-704
-
-
Martin, Y.C.1
-
64
-
-
70349768241
-
Docking and chemoinformatic screens for new ligands and targets
-
Kolb, P.; Ferreira, R.S.; Irwin, J.J.; Shoichet, B.K. Docking and chemoinformatic screens for new ligands and targets. Curr. Opin. Biotechnol., 2009, 20(4), 429-436.
-
(2009)
Curr. Opin. Biotechnol.
, vol.20
, Issue.4
, pp. 429-436
-
-
Kolb, P.1
Ferreira, R.S.2
Irwin, J.J.3
Shoichet, B.K.4
-
65
-
-
73449145345
-
Docking screens: Right for the right reasons?
-
Kolb, P.; Irwin, J.J. Docking screens: right for the right reasons? Curr. Top. Med. Chem., 2009, 9(9), 755-770.
-
(2009)
Curr. Top. Med. Chem.
, vol.9
, Issue.9
, pp. 755-770
-
-
Kolb, P.1
Irwin, J.J.2
-
66
-
-
34250839505
-
Conformational sampling of bioactive molecules: A comparative study
-
Agrafiotis, D.K.; Gibbs, A.C.; Zhu, F.; Izrailev, S.; Martin, E. Conformational sampling of bioactive molecules: a comparative study. J. Chem. Inf. Model., 2007, 47(3), 1067-1086.
-
(2007)
J. Chem. Inf. Model.
, vol.47
, Issue.3
, pp. 1067-1086
-
-
Agrafiotis, D.K.1
Gibbs, A.C.2
Zhu, F.3
Izrailev, S.4
Martin, E.5
-
67
-
-
70350501158
-
Conformational sampling for large-scale virtual screening: Accuracy versus ensemble size
-
Griewel, A.; Kayser, O.; Schlosser, J.; Rarey, M. Conformational sampling for large-scale virtual screening: accuracy versus ensemble size. J. Chem. Inf. Model., 2009, 49(10), 2303-2311.
-
(2009)
J. Chem. Inf. Model.
, vol.49
, Issue.10
, pp. 2303-2311
-
-
Griewel, A.1
Kayser, O.2
Schlosser, J.3
Rarey, M.4
-
68
-
-
58149186582
-
Do molecularly targeted agents in oncology have reduced attrition rates?
-
Walker, I.; Newell, H. Do molecularly targeted agents in oncology have reduced attrition rates? Nat. Rev. Drug Discov., 2009, 8(1), 15-16.
-
(2009)
Nat. Rev. Drug Discov.
, vol.8
, Issue.1
, pp. 15-16
-
-
Walker, I.1
Newell, H.2
-
69
-
-
84860276760
-
EDULISS: A small-molecule database with data-mining and pharmacophore searching capabilities
-
Hsin, K.Y.; Morgan, H.P.; Shave, S.R.; Hinton, A.C.; Taylor, P.; Walkinshaw, M.D. EDULISS: a small-molecule database with data-mining and pharmacophore searching capabilities. Nucleic Acids Res., 2010.
-
(2010)
Nucleic Acids Res
-
-
Hsin, K.Y.1
Morgan, H.P.2
Shave, S.R.3
Hinton, A.C.4
Taylor, P.5
Walkinshaw, M.D.6
-
70
-
-
84860285246
-
-
Accessed on November
-
The Chemistry Development Kit. http://sourceforge. net/projects/cdk [Accessed on November 2010]
-
(2010)
The Chemistry Development Kit
-
-
-
71
-
-
33748807805
-
-
Accessed on November
-
The PubChem Project. http://pubchem.ncbi.nlm.nih.gov [Accessed on November 2010]
-
(2010)
The PubChem Project
-
-
-
72
-
-
84860266748
-
-
Accessed on November
-
ZINC database. http://zinc.docking.org [Accessed on November 2010]
-
(2010)
ZINC database
-
-
-
73
-
-
84860283389
-
-
Accessed on November
-
ChemAxon Kft. http://www.chemaxon.com [Accessed on November 2010]
-
(2010)
ChemAxon Kft
-
-
-
74
-
-
33749628876
-
Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers
-
Monge, A.; Arrault, A.; Marot, C.; Morin-Allory, L. Managing, profiling and analyzing a library of 2.6 million compounds gathered from 32 chemical providers. Mol. Divers., 2006, 10(3), 389-403.
-
(2006)
Mol. Divers.
, vol.10
, Issue.3
, pp. 389-403
-
-
Monge, A.1
Arrault, A.2
Marot, C.3
Morin-Allory, L.4
-
75
-
-
84860296828
-
-
Accessed on November
-
KNIME.com GmbH http://www.knime.org [Accessed on November 2010]
-
(2010)
KNIME.com GmbH
-
-
-
76
-
-
70349211752
-
Automated docking screens: A feasibility study
-
Irwin, J.J.; Shoichet, B.K.; Mysinger, M.M.; Huang, N.; Colizzi, F.; Wassam, P.; Cao, Y. Automated docking screens: a feasibility study. J. Med. Chem., 2009, 52(18), 5712-5720.
-
(2009)
J. Med. Chem.
, vol.52
, Issue.18
, pp. 5712-5720
-
-
Irwin, J.J.1
Shoichet, B.K.2
Mysinger, M.M.3
Huang, N.4
Colizzi, F.5
Wassam, P.6
Cao, Y.7
-
77
-
-
3242884966
-
High-throughput docking as a source of novel drug leads
-
Alvarez, J.C. High-throughput docking as a source of novel drug leads. Curr. Opin. Chem. Biol., 2004, 8(4), 365-370.
-
(2004)
Curr. Opin. Chem. Biol.
, vol.8
, Issue.4
, pp. 365-370
-
-
Alvarez, J.C.1
-
78
-
-
77954945271
-
A computational workflow for the design of irreversible inhibitors of protein kinases
-
Del Rio, A.; Sgobba, M.; Parenti, M.D.; Degliesposti, G.; Forestiero, R.; Percivalle, C.; Conte, P.F.; Freccero, M.; Rastelli, G. A computational workflow for the design of irreversible inhibitors of protein kinases. J. Comput.-Aided Mol. Des., 2010, 24(3), 183-194.
-
(2010)
J. Comput.-Aided Mol. Des.
, vol.24
, Issue.3
, pp. 183-194
-
-
Del Rio, A.1
Sgobba, M.2
Parenti, M.D.3
Degliesposti, G.4
Forestiero, R.5
Percivalle, C.6
Conte, P.F.7
Freccero, M.8
Rastelli, G.9
-
79
-
-
41349106585
-
Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection- -what can we learn from earlier mistakes?
-
Kirchmair, J.; Markt, P.; Distinto, S.; Wolber, G.; Langer, T. Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection- -what can we learn from earlier mistakes? J. Comput. Aided Mol. Des., 2008, 22(3-4), 213-228.
-
(2008)
J. Comput. Aided Mol. Des.
, vol.22
, Issue.3-4
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
80
-
-
60349105674
-
Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening
-
Rastelli, G.; Degliesposti, G.; Del Rio, A.; Sgobba, M. Binding estimation after refinement, a new automated procedure for the refinement and rescoring of docked ligands in virtual screening. Chem. Biol. Drug Des., 2009, 73(3), 283-286.
-
(2009)
Chem. Biol. Drug Des.
, vol.73
, Issue.3
, pp. 283-286
-
-
Rastelli, G.1
Degliesposti, G.2
Del Rio, A.3
Sgobba, M.4
-
81
-
-
76249112547
-
Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA
-
Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA. J. Comput. Chem., 2010, 31(4), 797-810.
-
(2010)
J. Comput. Chem.
, vol.31
, Issue.4
, pp. 797-810
-
-
Rastelli, G.1
Del Rio, A.2
Degliesposti, G.3
Sgobba, M.4
-
82
-
-
79959410458
-
Structure- Based design of potent aromatase inhibitors by high-throughput docking
-
Caporuscio, F.; Rastelli, G.; Imbriano, C.; Del Rio, A. Structure- Based Design of Potent Aromatase Inhibitors by High-Throughput Docking. J. Med. Chem., 2011, 54(12), 4006-4017.
-
(2011)
J. Med. Chem.
, vol.54
, Issue.12
, pp. 4006-4017
-
-
Caporuscio, F.1
Rastelli, G.2
Imbriano, C.3
Del Rio, A.4
-
83
-
-
85026053788
-
Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998)
-
Wermuth, C.G.; Ganellin, C.R.; P., L.; A., M.L. Glossary of terms used in medicinal chemistry (IUPAC Recommendations 1998). Pure Appl. Chem., 1998, 70(5), 1129-1143.
-
(1998)
Pure Appl. Chem.
, vol.70
, Issue.5
, pp. 1129-1143
-
-
Wermuth, C.G.1
Ganellin, C.R.2
-
84
-
-
77956951744
-
Pharmacophores in Drug Research
-
Langer, T. Pharmacophores in Drug Research. Mol. Inf., 2010, 29(6-7), 470-475.
-
(2010)
Mol. Inf.
, vol.29
, Issue.6-7
, pp. 470-475
-
-
Langer, T.1
-
86
-
-
77249106566
-
Threedimensional pharmacophore methods in drug discovery
-
Leach, A.R.; Gillet, V.J.; Lewis, R.A.; Taylor, R. Threedimensional pharmacophore methods in drug discovery. J. Med. Chem., 2010, 53(2), 539-558.
-
(2010)
J. Med. Chem.
, vol.53
, Issue.2
, pp. 539-558
-
-
Leach, A.R.1
Gillet, V.J.2
Lewis, R.A.3
Taylor, R.4
-
87
-
-
84860266749
-
-
eMolecules Inc, Accessed on November
-
eMolecules Inc. http://www.emolecules.com [Accessed on November 2010]
-
(2010)
-
-
-
88
-
-
11144341956
-
Chemical space and biology
-
Dobson, C.M. Chemical space and biology. Nature, 2004, 432(7019), 824-828.
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 824-828
-
-
Dobson, C.M.1
-
89
-
-
74049098222
-
Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds
-
Southan, C.; Varkonyi, P.; Muresan, S. Quantitative assessment of the expanding complementarity between public and commercial databases of bioactive compounds. J. Cheminform., 2009, 1(1), 10.
-
(2009)
J. Cheminform.
, vol.1
, Issue.1
, pp. 10
-
-
Southan, C.1
Varkonyi, P.2
Muresan, S.3
-
90
-
-
11144320699
-
Navigating chemical space for biology and medicine
-
Lipinski, C.; Hopkins, A. Navigating chemical space for biology and medicine. Nature, 2004, 432(7019), 855-861.
-
(2004)
Nature
, vol.432
, Issue.7019
, pp. 855-861
-
-
Lipinski, C.1
Hopkins, A.2
-
91
-
-
0035324932
-
Comparison of the NCI open database with seven large chemical structural databases
-
Voigt, J.H.; Bienfait, B.; Wang, S.; Nicklaus, M.C. Comparison of the NCI open database with seven large chemical structural databases. J. Chem. Inf. Comput. Sci., 2001, 41(3), 702-712.
-
(2001)
J. Chem. Inf. Comput. Sci.
, vol.41
, Issue.3
, pp. 702-712
-
-
Voigt, J.H.1
Bienfait, B.2
Wang, S.3
Nicklaus, M.C.4
-
92
-
-
77952552641
-
Cheminformatics approaches to analyze diversity in compound screening libraries
-
Akella, L.B.; DeCaprio, D. Cheminformatics approaches to analyze diversity in compound screening libraries. Curr. Opin. Chem. Biol., 14(3), 325-330.
-
Curr. Opin. Chem. Biol.
, vol.14
, Issue.3
, pp. 325-330
-
-
Akella, L.B.1
Decaprio, D.2
-
93
-
-
74049126603
-
Prospective virtual screening with Ultrafast Shape Recognition: The identification of novel inhibitors of arylamine N-acetyltransferases
-
Ballester, P.J.; Westwood, I.; Laurieri, N.; Sim, E.; Richards, W.G. Prospective virtual screening with Ultrafast Shape Recognition: the identification of novel inhibitors of arylamine N-acetyltransferases. J. Royal Soc. Interface, 2010, 7(43), 335-342.
-
(2010)
J. Royal Soc. Interface
, vol.7
, Issue.43
, pp. 335-342
-
-
Ballester, P.J.1
Westwood, I.2
Laurieri, N.3
Sim, E.4
Richards, W.G.5
-
94
-
-
84860276765
-
-
Blaster v1.0.2., Accessed on November
-
Blaster v1.0.2. http://blaster.docking.org [Accessed on November 2010]
-
(2010)
-
-
-
95
-
-
36949019801
-
Computer-aided drug design: The next 20 years
-
Van Drie, J. Computer-aided drug design: the next 20 years. J. Comput.-Aided Mol. Des., 2007, 21(10), 591-601.
-
(2007)
J. Comput.-Aided Mol. Des.
, vol.21
, Issue.10
, pp. 591-601
-
-
van Drie, J.1
-
96
-
-
67649619336
-
970 million druglike small molecules for virtual screening in the chemical universe database GDB-13
-
Blum, L.C.; Reymond, J.L. 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13. J. Am. Chem. Soc., 2009, 131(25), 8732-8733.
-
(2009)
J. Am. Chem. Soc.
, vol.131
, Issue.25
, pp. 8732-8733
-
-
Blum, L.C.1
Reymond, J.L.2
-
97
-
-
77957920721
-
Chemical space as a source for new drugs
-
Reymond, J.-L.; van Deursen, R.; Blum, L.C.; Ruddigkeit, L. Chemical space as a source for new drugs. Med. Chem. Commun., 2010, 1(1), 30-38.
-
(2010)
Med. Chem. Commun.
, vol.1
, Issue.1
, pp. 30-38
-
-
Reymond, J.-L.1
van Deursen, R.2
Blum, L.C.3
Ruddigkeit, L.4
-
98
-
-
0027136267
-
The NEWLEAD program: A new method for the design of candidate structures from pharmacophoric hypotheses
-
Tschinke, V.; Cohen, N.C. The NEWLEAD program: a new method for the design of candidate structures from pharmacophoric hypotheses. J. Med. Chem., 1993, 36(24), 3863-3870.
-
(1993)
J. Med. Chem.
, vol.36
, Issue.24
, pp. 3863-3870
-
-
Tschinke, V.1
Cohen, N.C.2
-
99
-
-
84860296829
-
-
Newlead, Accessed on November
-
Newlead. http://web.me.com/baobao/newlead/Software.html [Accessed on November 2010].
-
(2010)
-
-
|