-
1
-
-
44649133861
-
A perspective of publicly accessible/open-access chemistry database
-
Williams, A. J. A perspective of publicly accessible/open-access chemistry database. Drug Discovery Today 13, 495-501 (2008).
-
(2008)
Drug Discovery Today
, vol.13
, pp. 495-501
-
-
Williams, A.J.1
-
2
-
-
84859201409
-
Chemistry's web of data expands
-
Noorden, R. V. Chemistry's web of data expands. Nature 483, 524 (2012).
-
(2012)
Nature
, vol.483
, pp. 524
-
-
Noorden, R.V.1
-
3
-
-
67849104638
-
PubChem: A public information system for analyzing bioac-tivities of small molecules
-
Wang, Y., Xiao, J., Suzek, T. O., Zhang, J. & Bryant, S. H. PubChem: A public information system for analyzing bioac-tivities of small molecules. Nucleic Acids Res. 37, W623-W633 (2009).
-
(2009)
Nucleic Acids Res
, vol.37
-
-
Wang, Y.1
Xiao, J.2
Suzek, T.O.3
Zhang, J.4
Bryant, S.H.5
-
4
-
-
84862192766
-
ChEMBL: A large-scale bio-activity database for drug discovery
-
Gaulton, A., Bellis, L. J., Bentro, A. P., Chambers, J., Davies, M., Hersey, A., Light, Y., McGlinchey, S., Michalovich, D., Al-Lazikani, B. & Overington, P. ChEMBL: A large-scale bio-activity database for drug discovery. Nucleic Acids Res. 40, D1100-D1107 (2011).
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Gaulton, A.1
Bellis, L.J.2
Bentro, A.P.3
Chambers, J.4
Davies, M.5
Hersey, A.6
Light, Y.7
McGlinchey, S.8
Michalovich, D.9
Al-Lazikani, B.10
Overington, P.11
-
5
-
-
11144323163
-
Virtual screening of chemical libraries
-
Shoichet, B.K. Virtual screening of chemical libraries. Nature 432, 862-865 (2004).
-
(2004)
Nature
, vol.432
, pp. 862-865
-
-
Shoichet, B.K.1
-
6
-
-
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. Cur. Opn. Biotech. 20, 429-436 (2009).
-
(2009)
Cur. Opn. Biotech
, vol.20
, pp. 429-436
-
-
Kolb, P.1
Ferreira, R.S.2
Irwin, J.J.3
Shoichet, B.K.4
-
7
-
-
77952809660
-
Virtual screening with AutoDock: Theory and practice
-
Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D.S. & Olson, A.J. Virtual screening with AutoDock: theory and practice. Expert. Opin. Drug Discov. 5, 597-607 (2010).
-
(2010)
Expert. Opin. Drug Discov
, vol.5
, pp. 597-607
-
-
Cosconati, S.1
Forli, S.2
Perryman, A.L.3
Harris, R.4
Goodsell, D.S.5
Olson, A.J.6
-
8
-
-
84856385436
-
B.O. Established and emerging trends in computational drug discovery in the structural genomics era
-
Taboureau, O., Baell, J. B., Fernandez-Recio, J. & Villoutreix, B.O. Established and emerging trends in computational drug discovery in the structural genomics era. Chem. Biol. 19, 29-41 (2012).
-
(2012)
Chem. Biol
, vol.19
-
-
Taboureau, O.1
Baell, J.B.2
Fernandez-Recio, J.3
Villoutreix4
-
9
-
-
77749298913
-
Advanced in-silico drug screening to achieve high hit ratio-Development of 3D-compound database-
-
Fukunishi, Y., Sugihara, Y., Mikami, Y., Sakai, K., Kusudo, H. & Nakamura, H. Advanced in-silico drug screening to achieve high hit ratio-Development of 3D-compound database-. Synthesiology 2, 64-72 (2009).
-
(2009)
Synthesiology
, vol.2
, pp. 64-72
-
-
Fukunishi, Y.1
Sugihara, Y.2
Mikami, Y.3
Sakai, K.4
Kusudo, H.5
Nakamura, H.6
-
10
-
-
66449110287
-
DOCK 6: Combining techniques to model RNA-small molecule complexes
-
Lang, P. T., Brozell, S. R., Mukherjee, S., Pettersen, E. F., Meng, E.C., Thomas, V., Rizzo, R. C., Case, D. A., James, T.L. & Kuntz, I. D. DOCK 6: Combining techniques to model RNA-small molecule complexes. RNA 15, 1219-1230 (2009).
-
(2009)
RNA
, vol.15
, pp. 1219-1230
-
-
Lang, P.T.1
Brozell, S.R.2
Mukherjee, S.3
Pettersen, E.F.4
Meng, E.C.5
Thomas, V.6
Rizzo, R.C.7
Case, D.A.8
James, T.L.9
Kuntz, I.D.10
-
11
-
-
70349932423
-
AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility
-
Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J. Comp. Chem. 30, 2785-2791 (2009).
-
(2009)
J. Comp. Chem
, vol.30
, pp. 2785-2791
-
-
Morris, G.M.1
Huey, R.2
Lindstrom, W.3
Sanner, M.F.4
Belew, R.K.5
Goodsell, D.S.6
Olson, A.7
-
12
-
-
24944576105
-
Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening
-
Fukunishi, Y., Mikami, Y. & Nakamura, H. Similarities among receptor pockets and among compounds: Analysis and application to in silico ligand screening. J. Mol. Graph. Model. 24, 34-35 (2005).
-
(2005)
J. Mol. Graph. Model
, vol.24
, pp. 34-35
-
-
Fukunishi, Y.1
Mikami, Y.2
Nakamura, H.3
-
13
-
-
13844312649
-
ZINC-a free database of commercially available compounds for virtual screening
-
Irwin, J. I. & Shoichet, B. K. ZINC-a free database of commercially available compounds for virtual screening. J. Chem. Info. Model. 45, 177-182 (2005).
-
(2005)
J. Chem. Info. Model
, vol.45
, pp. 177-182
-
-
Irwin, J.I.1
Shoichet, B.K.2
-
14
-
-
84864199587
-
ZINC: A free tool to discover chemistry for biology
-
Irwin, J. I., Sterling, T., Mysinger, M.M., Bolstad, E. S. & Coleman, R.G. ZINC: A free tool to discover chemistry for biology. J. Chem. Info. Model. 52, 1757-1768 (2012).
-
(2012)
J. Chem. Info. Model
, vol.52
, pp. 1757-1768
-
-
Irwin, J.I.1
Sterling, T.2
Mysinger, M.M.3
Bolstad, E.S.4
Coleman, R.G.5
-
15
-
-
58149203232
-
MMsINC: A large-scale chemoinformatics database
-
Masciocchi, J., Frau, G., Fanton, M., Sturlese, M., Floris, M., Pireddu, L., Palla, P., Cedrati, F., Rodriguez-Tomé, P. & Moro, S. MMsINC: A large-scale chemoinformatics database. Nucleic Acids Res. 37, D284-D290 (2009).
-
(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-Tomé, P.9
Moro, S.10
-
16
-
-
77957894400
-
CoCoCo: A free suite of multiconformational chemical databases for high-throughput virtual screening purposes
-
Del Rio, A., Barbosa, A.J. M., Caporuscio, F. & Mangiatordi, G. F. CoCoCo: A free suite of multiconformational chemical databases for high-throughput virtual screening purposes. Mol. BioSyst. 6, 2122-2128 (2010).
-
(2010)
Mol. BioSyst
, vol.6
, pp. 2122-2128
-
-
Del Rio, A.1
Barbosa, A.J.M.2
Caporuscio, F.3
Mangiatordi, G.F.4
-
17
-
-
80053175990
-
PubChem3D: A new resource for scientists
-
Bolton, E. E., Chen, J., Kim, S., Han, L., He, S., Shi, W., Simonyan, V., Sun, Y., Thiessen, P. A., Wang, J., Yu, B., Zhang, J. & Bryant, S.H. PubChem3D: A new resource for scientists. J. Cheminform. 3, 32 (2011).
-
(2011)
J. Cheminform
, vol.3
, pp. 32
-
-
Bolton, E.E.1
Chen, J.2
Kim, S.3
Han, L.4
He, S.5
Shi, W.6
Simonyan, V.7
Sun, Y.8
Thiessen, P.A.9
Wang, J.10
Yu, B.11
Zhang, J.12
Bryant, S.H.13
-
18
-
-
0000490166
-
From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders
-
Sadowski, J. & Gasteiger, J. From atoms and bonds to three-dimensional atomic coordinates: Automatic model builders. Chem. Rev. 93, 2567-2581 (1993).
-
(1993)
Chem. Rev
, vol.93
, pp. 2567-2581
-
-
Sadowski, J.1
Gasteiger, J.2
-
19
-
-
77951986384
-
Conformer generation with OMEGA: Algorithm and validation using high quality structures from the protein databank and Cambridge structure database
-
Hawkins, P. C. D., Skillman, G., Warren, G. L., Ellingson, B.A. & Stahl, M. T. Conformer generation with OMEGA: Algorithm and validation using high quality structures from the protein databank and Cambridge structure database. J. Chem. Info. Model. 50, 572-584 (2010).
-
(2010)
J. Chem. Info. Model
, vol.50
, pp. 572-584
-
-
Hawkins, P.C.D.1
Skillman, G.2
Warren, G.L.3
Ellingson, B.A.4
Stahl, M.T.5
-
20
-
-
80051966794
-
Build-up algorithm for atomic correspondence between chemical structures
-
Kawabata, T. Build-up algorithm for atomic correspondence between chemical structures. J. Chem. Info. Model. 51, 1775-1787 (2011).
-
(2011)
J. Chem. Info. Model
, vol.51
, pp. 1775-1787
-
-
Kawabata, T.1
-
21
-
-
84858983547
-
KEGG for integration and interpretation of large-scale molecular data sets
-
Kanehisa, M., Goto, S., Sato, Y., Furumichi, M. & Tanabe, M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 34, D109-D114 (2012).
-
(2012)
Nucleic Acids Res
, vol.34
-
-
Kanehisa, M.1
Goto, S.2
Sato, Y.3
Furumichi, M.4
Tanabe, M.5
-
22
-
-
2942532422
-
Developing and testing of a general amber force field
-
Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P.A. & Case, D. A. Developing and testing of a general amber force field. J. Comp. Chem. 25, 1157-1174 (2004).
-
(2004)
J. Comp. Chem
, vol.25
, pp. 1157-1174
-
-
Wang, J.1
Wolf, R.M.2
Caldwell, J.W.3
Kollman, P.A.4
Case, D.A.5
-
23
-
-
79960239942
-
Definition of drug-likeness for compound affinity
-
Fukunishi, Y. & Nakamura, H. Definition of drug-likeness for compound affinity. J. Chem. Info. Model. 51, 1012-1016 (2011).
-
(2011)
J. Chem. Info. Model
, vol.51
, pp. 1012-1016
-
-
Fukunishi, Y.1
Nakamura, H.2
-
24
-
-
84881285631
-
Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction
-
Mashimo, T., Fukunishi, Y., Orita, M., Katayama, N., Fujita, S. & Nakamura, H. Quantitative analysis of aggregation-solubility relationship by in-silico solubility prediction. International J. High Throughput Screening 1, 99-107 (2010).
-
(2010)
International J. High Throughput Screening
, vol.1
, pp. 99-107
-
-
Mashimo, T.1
Fukunishi, Y.2
Orita, M.3
Katayama, N.4
Fujita, S.5
Nakamura, H.6
-
25
-
-
84862238809
-
Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format
-
Kinjo, A. R., Suzuki, H., Yamashita, R., Ikegawa, Y., Kudou, T., Igarashi, R., Kengaku, Y., Cho, H., Standley, D. M., Nakagawa, A. & Nakamura, H. Protein Data Bank Japan (PDBj): Maintaining a structural data archive and resource description framework format. Nucleic Acids Res. 40, D453-D460 (2011).
-
(2011)
Nucleic Acids Res
, vol.40
-
-
Kinjo, A.R.1
Suzuki, H.2
Yamashita, R.3
Ikegawa, Y.4
Kudou, T.5
Igarashi, R.6
Kengaku, Y.7
Cho, H.8
Standley, D.M.9
Nakagawa, A.10
Nakamura, H.11
-
26
-
-
0023965741
-
SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. 2
-
Weininger, D. SMILES, a chemical language and information system. 1. Introduction to methodology and encoding rules. 2. J. Chem. Inf.Comput. Sci. 28, 31-36 (1988).
-
(1988)
J. Chem. Inf.Comput. Sci
, vol.28
, pp. 31-36
-
-
Weininger, D.1
-
27
-
-
0024664539
-
SMILES. 2. A lgorithms for generation of unique SMILES notation
-
Weininger, D., Weininger, A. & Weininger, J.L. SMILES. 2. a lgorithms for generation of unique SMILES notation. J. Chem. Inf. Comput. Sci. 29, 97-101 (1989).
-
(1989)
J. Chem. Inf. Comput. Sci
, vol.29
, pp. 97-101
-
-
Weininger, D.1
Weininger, A.2
Weininger, J.L.3
-
28
-
-
33845379303
-
Atom pairs as molecular features in structure-activity studies: Definition and applications
-
Carhart, R. E., Smith, H. S. & Venkataraghavan, R. Atom pairs as molecular features in structure-activity studies: Definition and applications. J. Chem. Inf. Comput. Sci. 25, 64-73 (1985).
-
(1985)
J. Chem. Inf. Comput. Sci
, vol.25
, pp. 64-73
-
-
Carhart, R.E.1
Smith, H.S.2
Venkataraghavan, R.3
-
29
-
-
78149241414
-
Molecular structure input on the web
-
Ertl, P. Molecular structure input on the web. J. Cheminfo. 2, 1 (2010).
-
(2010)
J. Cheminfo
, vol.2
, pp. 1
-
-
Ertl, P.1
-
30
-
-
76249106208
-
Let's not forget tautomers
-
Martin, Y. C. Let's not forget tautomers. J. Comput. Aided. Mol. Des. 23, 693-704 (2009).
-
(2009)
J. Comput. Aided. Mol. Des
, vol.23
, pp. 693-704
-
-
Martin, Y.C.1
|