-
1
-
-
84986522918
-
ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation
-
Abagyan R., Totrov M., Kuznetsov D. (1994) ICM - A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem. 15: 488-506.
-
(1994)
J. Comput. Chem
, vol.15
, pp. 488-506
-
-
Abagyan, R.1
Totrov, M.2
Kuznetsov, D.3
-
2
-
-
0001752768
-
The Cambridge Structural Database: A quarter of a million crystal structures and rising
-
Allen F.H. (2002) The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Crystallogr. B. 58: 380-388.
-
(2002)
Acta Crystallogr. B
, vol.58
, pp. 380-388
-
-
Allen, F.H.1
-
3
-
-
77955012685
-
Identification of new classes of ricin toxin inhibitors by virtual screening
-
Bai Y., Watt B., Wahome P.G., Mantis N.J., Robertus J.D. (2010) Identification of new classes of ricin toxin inhibitors by virtual screening. Toxicon. 56: 526-534.
-
(2010)
Toxicon
, vol.56
, pp. 526-534
-
-
Bai, Y.1
Watt, B.2
Wahome, P.G.3
Mantis, N.J.4
Robertus, J.D.5
-
5
-
-
37249079137
-
Search for nonnucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring
-
Barreiro G., Guimarães C.R.W., Tubert-Brohman I., Lyons T.M., Tirado-Rives J., Jorgensen W.L. (2007) Search for nonnucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring. J. Chem. Inf. Model. 47: 2416-2428.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 2416-2428
-
-
Barreiro, G.1
Guimarães, C.R.W.2
Tubert-Brohman, I.3
Lyons, T.M.4
Tirado-Rives, J.5
Jorgensen, W.L.6
-
6
-
-
38349030662
-
Multiple-step virtual screening using VSM-G: Overview and validation of fast geometrical matching enrichment
-
Beautrait A., Leroux V., Chavent M., Ghemtio L., Devignes L., Smaïl-Tabbone M., Cai W., Shao X., Moreau G., Bladon P. (2008) Multiple-step virtual screening using VSM-G: overview and validation of fast geometrical matching enrichment. J. Mol. Model. 14: 135-148.
-
(2008)
J. Mol. Model
, vol.14
, pp. 135-148
-
-
Beautrait, A.1
Leroux, V.2
Chavent, M.3
Ghemtio, L.4
Devignes, L.5
Smaïl-Tabbone, M.6
Cai, W.7
Shao, X.8
Moreau, G.9
Bladon, P.10
-
7
-
-
10344230435
-
Molecular similarity: A key technique in molecular informatics
-
Bender A., Glen R.C. (2004) Molecular similarity: a key technique in molecular informatics. Org. Biomol. Chem. 2: 3204-3218.
-
(2004)
Org. Biomol. Chem
, vol.2
, pp. 3204-3218
-
-
Bender, A.1
Glen, R.C.2
-
8
-
-
0033954256
-
The Protein Data Bank
-
Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E. (2000) The Protein Data Bank. Nucl. Acids Res. 28: 235-242.
-
(2000)
Nucl. Acids Res
, vol.28
, 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
-
9
-
-
0030039619
-
The art and practice of structure-based drug design: A molecular modeling perspective
-
Bohacek R.S., McMartin C., Guida W.C. (1996) The art and practice of structure-based drug design: a molecular modeling perspective. Med. Res. Rev. 16: 3-50.
-
(1996)
Med. Res. Rev
, vol.16
, pp. 3-50
-
-
Bohacek, R.S.1
McMartin, C.2
Guida, W.C.3
-
10
-
-
23844456151
-
Here be dragons: Docking and screening in an uncharted region of chemical space
-
Brenk R., Irwin J.J., Shoichet B.K. (2005) Here be dragons: docking and screening in an uncharted region of chemical space. J. Biomol. Screen. 10: 667-674.
-
(2005)
J. Biomol. Screen
, vol.10
, pp. 667-674
-
-
Brenk, R.1
Irwin, J.J.2
Shoichet, B.K.3
-
11
-
-
73349090936
-
Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization
-
Casey F.P., Pihan E., Shields D.C. (2009) Discovery of small molecule inhibitors of protein-protein interactions using combined ligand and target score normalization. J. Chem. Inf. Model. 49: 2708-2717.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 2708-2717
-
-
Casey, F.P.1
Pihan, E.2
Shields, D.C.3
-
12
-
-
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. (1999) Consensus scoring: A method for obtaining improved hit rates from docking databases of three-dimensional structures into proteins. J. Med. Chem. 42: 5100-5109.
-
(1999)
J. Med. Chem
, vol.42
, pp. 5100-5109
-
-
Charifson, P.S.1
Corkery, J.J.2
Murcko, M.A.3
Walters, W.P.4
-
13
-
-
0030954877
-
Structure-based discovery of ligands targeted to the RNA double helix
-
Chen Q., Shafer R.H., Kuntz I.D. (1997) Structure-based discovery of ligands targeted to the RNA double helix. Biochemistry 36: 11402-11407.
-
(1997)
Biochemistry
, vol.36
, pp. 11402-11407
-
-
Chen, Q.1
Shafer, R.H.2
Kuntz, I.D.3
-
14
-
-
84984532074
-
Structure-based discovery of triphenylmethane derivatives as inhibitors of hepatitis C virus helicase
-
Chen C.S., Chiou C.T., Chen G.S., Chen S.C., Hu C.Y., Chi W.K., Chu Y.D., Hwang L.H., Chen P.J., Chen D.S., Liaw S.H., Chern J.W. (2009a) Structure-based discovery of triphenylmethane derivatives as inhibitors of hepatitis C virus helicase. J. Med. Chem. 52: 2716-2723.
-
(2009)
J. Med. Chem
, vol.52
, pp. 2716-2723
-
-
Chen, C.S.1
Chiou, C.T.2
Chen, G.S.3
Chen, S.C.4
Hu, C.Y.5
Chi, W.K.6
Chu, Y.D.7
Hwang, L.H.8
Chen, P.J.9
Chen, D.S.10
Liaw, S.H.11
Chern, J.W.12
-
15
-
-
74949101324
-
Pharmacophore-based virtual screening versus docking-based virtual screening: A benchmark comparison against eight targets
-
Chen Z., Li H., Zhang Q., Bao X., Yu K., Luo X., Zhu W., Jiang H. (2009b) Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets. Acta Pharm. Sinic. 30: 1694-1708.
-
(2009)
Acta Pharm. Sinic
, vol.30
, pp. 1694-1708
-
-
Chen, Z.1
Li, H.2
Zhang, Q.3
Bao, X.4
Yu, K.5
Luo, X.6
Zhu, W.7
Jiang, H.8
-
16
-
-
41849121148
-
Combination of virtual screening and high throughput gene profiling for identification of novel liver X receptor modulators
-
Cheng J.F., Zapf J., Takedomi K., Fukushima C., Ogiku T., Zhang S.H., Yang G., Sakurai N., Barbosa M., Jack R., Xu K. (2008) Combination of virtual screening and high throughput gene profiling for identification of novel liver X receptor modulators. J. Med. Chem. 51: 2057-2061.
-
(2008)
J. Med. Chem
, vol.51
, pp. 2057-2061
-
-
Cheng, J.F.1
Zapf, J.2
Takedomi, K.3
Fukushima, C.4
Ogiku, T.5
Zhang, S.H.6
Yang, G.7
Sakurai, N.8
Barbosa, M.9
Jack, R.10
Xu, K.11
-
17
-
-
66149103553
-
Comparative assessment of scoring functions on a diverse test set
-
Cheng T., Li X., Li Y., Liu Z., Wang R. (2009) Comparative assessment of scoring functions on a diverse test set. J. Chem. Inf. Model. 49: 1079-1093.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1079-1093
-
-
Cheng, T.1
Li, X.2
Li, Y.3
Liu, Z.4
Wang, R.5
-
18
-
-
53549091061
-
Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening
-
Cho Y., Ioerger T.R., Sacchettini J.C. (2008) Discovery of novel nitrobenzothiazole inhibitors for Mycobacterium tuberculosis ATP phosphoribosyl transferase (HisG) through virtual screening. J. Med. Chem. 51: 5984-5992.
-
(2008)
J. Med. Chem
, vol.51
, pp. 5984-5992
-
-
Cho, Y.1
Ioerger, T.R.2
Sacchettini, J.C.3
-
19
-
-
77954308481
-
Receptor-based virtual screening of EGFR kinase inhibitors from the NCI diversity database
-
Choowongkomon K., Sawatdichaikul O., Songtawee N., Limtrakul J. (2010) Receptor-based virtual screening of EGFR kinase inhibitors from the NCI diversity database. Molecules 15: 4041-4054.
-
(2010)
Molecules
, vol.15
, pp. 4041-4054
-
-
Choowongkomon, K.1
Sawatdichaikul, O.2
Songtawee, N.3
Limtrakul, J.4
-
20
-
-
67650097331
-
Comparison of several molecular docking programs: Pose prediction and virtual screening accuracy
-
Cross J.B., Thompson D.C., Rai B.K., Baber J.C., Fan K.Y., Hu Y., Humblet C. (2009) Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 49: 1455-1474.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1455-1474
-
-
Cross, J.B.1
Thompson, D.C.2
Rai, B.K.3
Baber, J.C.4
Fan, K.Y.5
Hu, Y.6
Humblet, C.7
-
21
-
-
67349140440
-
Structure-based drug design: From nucleic acid to membrane protein targets
-
Dailey M.M., Hait C., Holt P.A., Maguire J.M., Meier J.B., Miller M.C., Petraccone L., Trent J.O. (2009) Structure-based drug design: from nucleic acid to membrane protein targets. Exp. Mol. Pathol. 86: 141-150.
-
(2009)
Exp. Mol. Pathol
, vol.86
, pp. 141-150
-
-
Dailey, M.M.1
Hait, C.2
Holt, P.A.3
Maguire, J.M.4
Meier, J.B.5
Miller, M.C.6
Petraccone, L.7
Trent, J.O.8
-
22
-
-
58949095753
-
Structure-based virtual screening for novel inhibitors of the sarco/endoplasmic reticulum calcium ATPase and their experimental evaluation
-
Deye J., Elam C., Lape M., Ratliff R., Evans K., Paula S. (2009) Structure-based virtual screening for novel inhibitors of the sarco/endoplasmic reticulum calcium ATPase and their experimental evaluation. Bioorgan. Med. Chem. 17: 1353-1360.
-
(2009)
Bioorgan. Med. Chem
, vol.17
, pp. 1353-1360
-
-
Deye, J.1
Elam, C.2
Lape, M.3
Ratliff, R.4
Evans, K.5
Paula, S.6
-
23
-
-
0037161605
-
Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B
-
Doman T.N., McGovern S.L., Witherbee B.J., Kasten T.P., Kurumbail R., Stallings W.C., Connolly D.T., Shoichet B.K. (2002) Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. J. Med. Chem. 45: 2213-2221.
-
(2002)
J. Med. Chem
, vol.45
, pp. 2213-2221
-
-
Doman, T.N.1
McGovern, S.L.2
Witherbee, B.J.3
Kasten, T.P.4
Kurumbail, R.5
Stallings, W.C.6
Connolly, D.T.7
Shoichet, B.K.8
-
24
-
-
0037442962
-
HADDOCK: A protein-protein docking approach based on biochemical or biophysical information
-
Dominguez C., Boelens R., Bonvin A.M.J.J. (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J. Am. Chem. Soc. 125: 1731-1737.
-
(2003)
J. Am. Chem. Soc
, vol.125
, pp. 1731-1737
-
-
Dominguez, C.1
Boelens, R.2
Bonvin, A.M.J.J.3
-
25
-
-
77953092035
-
Fragment- based lead discovery: Screening and optimizing fragments for thermolysin inhibition
-
Englert L., Silber K., Steuber H., Brass S., Over B., Gerber H.D., Heine A., Diederich W.E., Klebe G. (2010) Fragment- based lead discovery: screening and optimizing fragments for thermolysin inhibition. ChemMedChem. 5: 930-940.
-
(2010)
ChemMedChem
, vol.5
, pp. 930-940
-
-
Englert, L.1
Silber, K.2
Steuber, H.3
Brass, S.4
Over, B.5
Gerber, H.D.6
Heine, A.7
Diederich, W.E.8
Klebe, G.9
-
26
-
-
33746740077
-
Quest for the rings. In silico exploration of ring universe to identify novel bioactive heteroaromatic scaffolds
-
Ertl P., Jelfs S., Muhlbacher J., Schuffenhauer A., Selzer P. (2006) Quest for the rings. In silico exploration of ring universe to identify novel bioactive heteroaromatic scaffolds. J. Med. Chem. 49: 4568-4573.
-
(2006)
J. Med. Chem
, vol.49
, pp. 4568-4573
-
-
Ertl, P.1
Jelfs, S.2
Muhlbacher, J.3
Schuffenhauer, A.4
Selzer, P.5
-
27
-
-
0024239320
-
Methods for drug discovery: Development of potent, selective, orally effective cholecystokinin antagonists
-
Evans B.E., Rittle K.E., Bock M.G., DiPardo R.M., Freidinger R.M., Whitter W.L., Lundell G.F., Veber D.F., Anderson P.S., Chang R.S., et al. (1988) Methods for drug discovery: development of potent, selective, orally effective cholecystokinin antagonists. J. Med. Chem. 31: 2235-2246.
-
(1988)
J. Med. Chem
, vol.31
, pp. 2235-2246
-
-
Evans, B.E.1
Rittle, K.E.2
Bock, M.G.3
Dipardo, R.M.4
Freidinger, R.M.5
Whitter, W.L.6
Lundell, G.F.7
Veber, D.F.8
Anderson, P.S.9
Chang, R.S.10
-
28
-
-
0242607645
-
Comparing performance of computational tools for combinatorial library design
-
Evensen E., Eksterowicz J.E., Stanton R.V., Oshiro C., Grootenhuis P.D., Bradley E.K. (2003) Comparing performance of computational tools for combinatorial library design. J. Med. Chem. 46: 5125-5128.
-
(2003)
J. Med. Chem
, vol.46
, pp. 5125-5128
-
-
Evensen, E.1
Eksterowicz, J.E.2
Stanton, R.V.3
Oshiro, C.4
Grootenhuis, P.D.5
Bradley, E.K.6
-
29
-
-
0035025191
-
DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
-
Ewing T.J., Makino S., Skillman A.G., Kuntz I.D. (2001) DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases. J. Comput. Aid. Mol. Des. 15: 411-428.
-
(2001)
J. Comput. Aid. Mol. Des
, vol.15
, pp. 411-428
-
-
Ewing, T.J.1
Makino, S.2
Skillman, A.G.3
Kuntz, I.D.4
-
30
-
-
47649106947
-
Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics
-
Feder M., Purta E., Koscinski L., Cubrilo S., Maravic Vlahovicek G., Bujnicki J.M. (2008) Virtual screening and experimental verification to identify potential inhibitors of the ErmC methyltransferase responsible for bacterial resistance against macrolide antibiotics. ChemMedChem 3: 316-322.
-
(2008)
ChemMedChem
, vol.3
, pp. 316-322
-
-
Feder, M.1
Purta, E.2
Koscinski, L.3
Cubrilo, S.4
Maravic Vlahovicek, G.5
Bujnicki, J.M.6
-
31
-
-
33748667774
-
Consensus scoring for protein-ligand interactions
-
Feher M. (2006) Consensus scoring for protein-ligand interactions. Drug Discov. Today 11: 421-428.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 421-428
-
-
Feher, M.1
-
33
-
-
0033949057
-
Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR
-
Filikov A.V., Mohan V., Vickers T.A., Griffey R.H., Cook P.D., Abagyan R.A., James T.L. (2000) Identification of ligands for RNA targets via structure-based virtual screening: HIV-1 TAR. J. Comp. Aid. Mol. Des. 14: 593-610.
-
(2000)
J. Comp. Aid. Mol. Des
, vol.14
, pp. 593-610
-
-
Filikov, A.V.1
Mohan, V.2
Vickers, T.A.3
Griffey, R.H.4
Cook, P.D.5
Abagyan, R.A.6
James, T.L.7
-
34
-
-
12144289984
-
Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy
-
Friesner R.A., Banks J.L., Murphy R.B., Halgren T.A., Klicic J.J., Mainz D.T., Repasky M.P., Knoll E.H., Shelley M., Perry J.K., Shaw D.E., Francis P., Shenkin P.S. (2004) Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J. Med. Chem. 47: 1739-1749.
-
(2004)
J. Med. Chem
, vol.47
, pp. 1739-1749
-
-
Friesner, R.A.1
Banks, J.L.2
Murphy, R.B.3
Halgren, T.A.4
Klicic, J.J.5
Mainz, D.T.6
Repasky, M.P.7
Knoll, E.H.8
Shelley, M.9
Perry, J.K.10
Shaw, D.E.11
Francis, P.12
Shenkin, P.S.13
-
36
-
-
78651258569
-
Discovery of novel class 1 phosphatidylinositide 3-kinases (PI3K) fragment inhibitors through structure-based virtual screening
-
Giordanetto F., Kull B., Dellsén A. (2011) Discovery of novel class 1 phosphatidylinositide 3-kinases (PI3K) fragment inhibitors through structure-based virtual screening. Bioorg. Med. Chem. Lett. 21: 829-835.
-
(2011)
Bioorg. Med. Chem. Lett
, vol.21
, pp. 829-835
-
-
Giordanetto, F.1
Kull, B.2
Dellsén, A.3
-
37
-
-
39749181550
-
Generation of a set of simple, interpretable ADMET rules of thumb
-
Gleeson M.P. (2008) Generation of a set of simple, interpretable ADMET rules of thumb. J. Med. Chem. 51: 817-834.
-
(2008)
J. Med. Chem
, vol.51
, pp. 817-834
-
-
Gleeson, M.P.1
-
38
-
-
0037103119
-
Successful virtual screening for novel inhibitors of human carbonic anhydrase: Strategy and experimental confirmation
-
Gruneberg S., Stubbs M.T., Klebe G. (2002) Successful virtual screening for novel inhibitors of human carbonic anhydrase: strategy and experimental confirmation. J. Med. Chem. 45: 3588-3602.
-
(2002)
J. Med. Chem
, vol.45
, pp. 3588-3602
-
-
Gruneberg, S.1
Stubbs, M.T.2
Klebe, G.3
-
39
-
-
0031473847
-
SWISS-MODEL and the Swiss- PdbViewer: An environment for comparative protein modeling
-
Guex N., Peitsch M.C. (1997) SWISS-MODEL and the Swiss- PdbViewer: an environment for comparative protein modeling. Electrophoresis 18: 2714-2723.
-
(1997)
Electrophoresis
, vol.18
, pp. 2714-2723
-
-
Guex, N.1
Peitsch, M.C.2
-
40
-
-
33745359822
-
The Blue Obelisk - Interoperability in Chemical Informatics
-
Guha R., Howard M.T., Hutchison G.R., Murray-Rust P., Rzepa H., Steinbeck C., Wegner J.K., Willighagen E. (2006) The Blue Obelisk - Interoperability in Chemical Informatics. J. Chem. Inf. Model. 46(3): 991-998.
-
(2006)
J. Chem. Inf. Model
, vol.46
, Issue.3
, pp. 991-998
-
-
Guha, R.1
Howard, M.T.2
Hutchison, G.R.3
Murray-Rust, P.4
Rzepa, H.5
Steinbeck, C.6
Wegner, J.K.7
Willighagen, E.8
-
41
-
-
0024904643
-
Similarity measures in scientometric research: The Jaccard index versus Salton's cosine formula
-
Hamersa L., Hemerycka Y., Herweyersa G., Janssena M., Ketersa H., Rousseau R. (2002) Similarity measures in scientometric research: The Jaccard index versus Salton's cosine formula. Inform. Process Manag. 25: 315-318.
-
(2002)
Inform. Process Manag
, vol.25
, pp. 315-318
-
-
Hamersa, L.1
Hemerycka, Y.2
Herweyersa, G.3
Janssena, M.4
Ketersa, H.5
Rousseau, R.6
-
43
-
-
62549131251
-
Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform
-
Holt P.A., Ragazzon P., Strekowski L., Chaires J.B., Trent J.O. (2009) Discovery of novel triple helical DNA intercalators by an integrated virtual and actual screening platform. Nucl. Acids Res. 37: 1280-1287.
-
(2009)
Nucl. Acids Res
, vol.37
, pp. 1280-1287
-
-
Holt, P.A.1
Ragazzon, P.2
Strekowski, L.3
Chaires, J.B.4
Trent, J.O.5
-
44
-
-
77649221514
-
Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
-
Huang S.Y., Zou X. (2010) Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. J. Chem. Inf. Model. 50: 262-273.
-
(2010)
J. Chem. Inf. Model
, vol.50
, pp. 262-273
-
-
Huang, S.Y.1
Zou, X.2
-
45
-
-
77957898063
-
Scoring functions and their evaluation methods for protein-ligand docking: Recent advances and future directions
-
Huang S.Y., Grinter S.Z., Zou X. (2010) Scoring functions and their evaluation methods for protein-ligand docking: recent advances and future directions. Phys. Chem. Ch. Ph. 12: 12899-12908.
-
(2010)
Phys. Chem. Ch. Ph
, vol.12
, pp. 12899-12908
-
-
Huang, S.Y.1
Grinter, S.Z.2
Zou, X.3
-
47
-
-
13844312649
-
ZINC - a free database of commercially available compounds for virtual screening
-
Irwin J.J., Shoichet B.K. (2005) ZINC - a free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 45: 177-182.
-
(2005)
J. Chem. Inf. Model
, vol.45
, pp. 177-182
-
-
Irwin, J.J.1
Shoichet, B.K.2
-
48
-
-
0037434582
-
Surflex: Fully automatic flexible molecular docking using a molecular similarity-based search engine
-
Jain A.N. (2003) Surflex: fully automatic flexible molecular docking using a molecular similarity-based search engine. J. Med. Chem. 46: 499-511.
-
(2003)
J. Med. Chem
, vol.46
, pp. 499-511
-
-
Jain, A.N.1
-
49
-
-
34247343346
-
Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledgebased search
-
Jain A.N. (2007) Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledgebased search. J. Comp. Aid. Mol. Des. 21: 281-306.
-
(2007)
J. Comp. Aid. Mol. Des
, vol.21
, pp. 281-306
-
-
Jain, A.N.1
-
50
-
-
67349261359
-
Effects of protein conformation in docking: Improved pose prediction through protein pocket adaptation
-
Jain A.N. (2009) Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation. J. Comp. Aid. Mol. Des. 23: 355-374.
-
(2009)
J. Comp. Aid. Mol. Des
, vol.23
, pp. 355-374
-
-
Jain, A.N.1
-
51
-
-
0037235881
-
Virtual screening to enrich hit lists from high-throughput screening: A case study on small-molecule inhibitors of angiogenin
-
Jenkins J.L., Kao R.Y., Shapiro R. (2003) Virtual screening to enrich hit lists from high-throughput screening: a case study on small-molecule inhibitors of angiogenin. Proteins 50: 81-93.
-
(2003)
Proteins
, vol.50
, pp. 81-93
-
-
Jenkins, J.L.1
Kao, R.Y.2
Shapiro, R.3
-
52
-
-
4544367743
-
Comparative evaluation of eight docking tools for docking and virtual screening accuracy
-
Kellenberger E., Rodrigo J., Muller P., Rognan D. (2004) Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins 57: 225-242.
-
(2004)
Proteins
, vol.57
, pp. 225-242
-
-
Kellenberger, E.1
Rodrigo, J.2
Muller, P.3
Rognan, D.4
-
53
-
-
56649086404
-
Identification of novel HCV RNA-dependent RNA polymerase inhibitors using pharmacophore-guided virtual screening
-
Kim J., Kim K., Kim D.E., Chong Y. (2008) Identification of novel HCV RNA-dependent RNA polymerase inhibitors using pharmacophore-guided virtual screening. Chem. Biol. Drug. Des. 72: 585-591.
-
(2008)
Chem. Biol. Drug. Des
, vol.72
, pp. 585-591
-
-
Kim, J.1
Kim, K.2
Kim, D.E.3
Chong, Y.4
-
54
-
-
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. (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection--what can we learn from earlier mistakes? J. Comp. Aid. Mol. Des. 22: 213-228.
-
(2008)
J. Comp. Aid. Mol. Des
, vol.22
, pp. 213-228
-
-
Kirchmair, J.1
Markt, P.2
Distinto, S.3
Wolber, G.4
Langer, T.5
-
55
-
-
44949168495
-
Discovery of novel human histamine H4 receptor ligands by large-scale structure- based virtual screening
-
Kiss R., Kiss B., Könczöl A., Szalai F., Jelinek I., László V., Noszál B., Falus A., Keseru G.M. (2008) Discovery of novel human histamine H4 receptor ligands by large-scale structure- based virtual screening. J. Med. Chem. 51: 3145-3153.
-
(2008)
J. Med. Chem
, vol.51
, pp. 3145-3153
-
-
Kiss, R.1
Kiss, B.2
Könczöl, A.3
Szalai, F.4
Jelinek, I.5
László, V.6
Noszál, B.7
Falus, A.8
Keseru, G.M.9
-
56
-
-
33745199815
-
Virtual ligand screening: Strategies, perspectives and limitations
-
Klebe G. (2006) Virtual ligand screening: strategies, perspectives and limitations. Drug Discov. Today 11: 580-594.
-
(2006)
Drug Discov. Today
, vol.11
, pp. 580-594
-
-
Klebe, G.1
-
57
-
-
57349130997
-
Discovery of new inhibitors of Dalanine: D-alanine ligase by structure-based virtual screening
-
Kovac A., Konc J., Vehar B., Bostock J.M., Chopra I., Janezic D., Gobec S. (2008) Discovery of new inhibitors of Dalanine: D-alanine ligase by structure-based virtual screening. J. Med. Chem. 51: 7442-7448.
-
(2008)
J. Med. Chem
, vol.51
, pp. 7442-7448
-
-
Kovac, A.1
Konc, J.2
Vehar, B.3
Bostock, J.M.4
Chopra, I.5
Janezic, D.6
Gobec, S.7
-
59
-
-
0020491251
-
A geometric approach to macromolecule-ligand interactions
-
Kuntz I.D., Blaney J.M., Oatley S.J., Langridge R., Ferrin T.E. (1982) A geometric approach to macromolecule-ligand interactions. J. Mol. Biol. 161: 269-288.
-
(1982)
J. Mol. Biol
, vol.161
, pp. 269-288
-
-
Kuntz, I.D.1
Blaney, J.M.2
Oatley, S.J.3
Langridge, R.4
Ferrin, T.E.5
-
60
-
-
77950058867
-
The development and validation of a novel virtual screening cascade protocol to identify potential serotonin 5-HT(7)R antagonists
-
Kurczab R., Nowak M., Chilmonczyk Z., Sylte I., Bojarski A.J. (2010) The development and validation of a novel virtual screening cascade protocol to identify potential serotonin 5-HT(7)R antagonists. Bioorg. Med. Chem. Lett. 20: 2465-2468.
-
(2010)
Bioorg. Med. Chem. Lett
, vol.20
, pp. 2465-2468
-
-
Kurczab, R.1
Nowak, M.2
Chilmonczyk, Z.3
Sylte, I.4
Bojarski, A.J.5
-
61
-
-
78650721466
-
Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening
-
Lalonde J.M., Elban M.A., Courter J.R., Sugawara A., Soeta T., Madani N., Princiotto A.M., Kwon Y.D., Kwong P.D., Schön A., Freire E., Sodroski J., Smith A.B., 3rd (2011) Design, synthesis and biological evaluation of small molecule inhibitors of CD4-gp120 binding based on virtual screening. Bioorg. Med. Chem. 19: 91-101.
-
(2011)
Bioorg. Med. Chem
, vol.19
, pp. 91-101
-
-
Lalonde, J.M.1
Elban, M.A.2
Courter, J.R.3
Sugawara, A.4
Soeta, T.5
Madani, N.6
Princiotto, A.M.7
Kwon, Y.D.8
Kwong, P.D.9
Schön, A.10
Freire, E.11
Sodroski, J.12
Smith III, A.B.13
-
62
-
-
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. (2009) DOCK 6: combining techniques to model RNA-small molecule complexes. RNA. 15: 1219-1230.
-
(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
-
64
-
-
33749245117
-
Prediction of protein-ligand interactions. Docking and scoring: Successes and gaps
-
Leach A.R., Shoichet B.K., Peishoff C.E. (2006) Prediction of protein-ligand interactions. Docking and scoring: successes and gaps. J. Med. Chem. 49: 5851-5855.
-
(2006)
J. Med. Chem
, vol.49
, pp. 5851-5855
-
-
Leach, A.R.1
Shoichet, B.K.2
Peishoff, C.E.3
-
65
-
-
0031894779
-
Modeling RNA-ligand interactions: The Rev-binding element RNA-aminoglycoside complex
-
Leclerc F., Cedergren R. (1998) Modeling RNA-ligand interactions: the Rev-binding element RNA-aminoglycoside complex. J. Med. Chem. 41: 175-182.
-
(1998)
J. Med. Chem
, vol.41
, pp. 175-182
-
-
Leclerc, F.1
Cedergren, R.2
-
66
-
-
78649893079
-
Accommodating protein flexibility for structurebased drug design
-
Lin J.H. (2011) Accommodating protein flexibility for structurebased drug design. Curr. Top Med. Chem. 11: 171-178.
-
(2011)
Curr. Top Med. Chem
, vol.11
, pp. 171-178
-
-
Lin, J.H.1
-
67
-
-
79957642077
-
Efficient In Silico Assay of Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase by Structure-Based Virtual Screening and In Vitro Evaluation
-
Lin Y.T., Huang K.J., Tseng C.K., Chen K.J., Wang H.M., Lee J.C. (2011) Efficient In Silico Assay of Inhibitors of Hepatitis C Virus RNA-Dependent RNA Polymerase by Structure-Based Virtual Screening and In Vitro Evaluation. Assay Drug Dev. Tech. 3: 290-298.
-
(2011)
Assay Drug Dev. Tech
, vol.3
, pp. 290-298
-
-
Lin, Y.T.1
Huang, K.J.2
Tseng, C.K.3
Chen, K.J.4
Wang, H.M.5
Lee, J.C.6
-
68
-
-
13844316622
-
Virtual screening of novel noncovalent inhibitors for SARS-CoV 3Clike proteinase
-
Liu Z., Huang C., Fan K., Wei P., Chen H., Liu S., Pei J., Shi L., Li B., Yang K., Liu Y., Lai L. (2005) Virtual screening of novel noncovalent inhibitors for SARS-CoV 3Clike proteinase. J. Chem. Inf. Model. 45: 10-17.
-
(2005)
J. Chem. Inf. Model
, vol.45
, pp. 10-17
-
-
Liu, Z.1
Huang, C.2
Fan, K.3
Wei, P.4
Chen, H.5
Liu, S.6
Pei, J.7
Shi, L.8
Li, B.9
Yang, K.10
Liu, Y.11
Lai, L.12
-
69
-
-
77957956614
-
Identification of Selective Norbornane-Type Aspartate Analogue Inhibitors of the Glutamate Transporter 1 (GLT-1) from the Chemical Universe Generated Database (GDB)
-
Luethi E., Nguyen K.T., Bürzle M., Blum L.C., Suzuki Y., Hediger M., Reymond J.L. (2010) Identification of Selective Norbornane-Type Aspartate Analogue Inhibitors of the Glutamate Transporter 1 (GLT-1) from the Chemical Universe Generated Database (GDB). J. Med. Chem. 53: 7236-7250.
-
(2010)
J. Med. Chem
, vol.53
, pp. 7236-7250
-
-
Luethi, E.1
Nguyen, K.T.2
Bürzle, M.3
Blum, L.C.4
Suzuki, Y.5
Hediger, M.6
Reymond, J.L.7
-
70
-
-
33846933784
-
Optimizing fragment and scaffold docking by use of molecular interaction fingerprints
-
Marcou G., Rognan D. (2007) Optimizing fragment and scaffold docking by use of molecular interaction fingerprints. J. Chem. Inf. Model. 47: 195-207.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 195-207
-
-
Marcou, G.1
Rognan, D.2
-
71
-
-
34447617713
-
The AnnoLite and Anno- Lyze programs for comparative annotation of protein structures
-
Marti-Renom M.A., Rossi A., Al-Shahrour F., Davis F.P., Pieper U., Dopazo J., Sali A. (2007) The AnnoLite and Anno- Lyze programs for comparative annotation of protein structures. BMC Bioinformatics 8(Suppl 4): S4.
-
(2007)
BMC Bioinformatics
, vol.8
, Issue.SUPPL. 4
-
-
Marti-Renom, M.A.1
Rossi, A.2
Al-Shahrour, F.3
Davis, F.P.4
Pieper, U.5
Dopazo, J.6
Sali, A.7
-
72
-
-
0031181346
-
QXP: Powerful, rapid computer algorithms for structure-based drug design
-
McMartin C., Bohacek R.S. (1997) QXP: powerful, rapid computer algorithms for structure-based drug design. J. Comp. Aid. Mol. Des. 11: 333-344.
-
(1997)
J. Comp. Aid. Mol. Des
, vol.11
, pp. 333-344
-
-
McMartin, C.1
Bohacek, R.S.2
-
73
-
-
78650947751
-
Discovery of modulators of protein-protein interactions: Current approaches and limitations
-
Meireles L.M.C., Mustata G. (2011) Discovery of modulators of protein-protein interactions: current approaches and limitations. Curr. Top Med. Chem. 11: 248-257.
-
(2011)
Curr. Top Med. Chem
, vol.11
, pp. 248-257
-
-
Meireles, L.M.C.1
Mustata, G.2
-
74
-
-
0033662998
-
Similarity versus docking in 3D virtual screening
-
Mestres J., Knegtel R. (2000) Similarity versus docking in 3D virtual screening. Persp. Drug Disc. Des. 20: 191-207.
-
(2000)
Persp. Drug Disc. Des
, vol.20
, pp. 191-207
-
-
Mestres, J.1
Knegtel, R.2
-
75
-
-
14044262243
-
Docking: Successes and challenges
-
Mohan V., Gibbs A.C., Cummings M.D., Jaeger E.P., DesJarlais R.L. (2005) Docking: successes and challenges. Curr. Pharm. Des. 11: 323-333.
-
(2005)
Curr. Pharm. Des
, vol.11
, pp. 323-333
-
-
Mohan, V.1
Gibbs, A.C.2
Cummings, M.D.3
Jaeger, E.P.4
Desjarlais, R.L.5
-
76
-
-
40349087133
-
Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
-
Moitessier N., Englebienne P., Lee D., Lawandi J., Corbeil C.R. (2009) Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Pharmacol. 153: S7-S26.
-
(2009)
Br. J. Pharmacol
, vol.153
-
-
Moitessier, N.1
Englebienne, P.2
Lee, D.3
Lawandi, J.4
Corbeil, C.R.5
-
77
-
-
61849150037
-
Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs)
-
Moro W.B., Yang Z., Kane T.A., Brouillette C.G., Brouillette W.J. (2009) Virtual screening to identify lead inhibitors for bacterial NAD synthetase (NADs). Bioorg. Med. Chem. Lett. 19: 2001-2005.
-
(2009)
Bioorg. Med. Chem. Lett
, vol.19
, pp. 2001-2005
-
-
Moro, W.B.1
Yang, Z.2
Kane, T.A.3
Brouillette, C.G.4
Brouillette, W.J.5
-
78
-
-
11644261806
-
Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
-
Morris G.M., Goodsell D.S., Halliday R.S., Huey R., Hart W.E., Belew R.K., Olson A.J. (1998) Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19: 1639-1662.
-
(1998)
J. Comput. Chem
, vol.19
, pp. 1639-1662
-
-
Morris, G.M.1
Goodsell, D.S.2
Halliday, R.S.3
Huey, R.4
Hart, W.E.5
Belew, R.K.6
Olson, A.J.7
-
79
-
-
33845873363
-
Development and validation of a modular, extensible docking program: DOCK 5
-
Moustakas D.T., Lang P.T., Pegg S., Pettersen E., Kuntz I.D., Brooijmans N., Rizzo R.C. (2006) Development and validation of a modular, extensible docking program: DOCK 5. J. Comp. Aid. Mol. Des. 20: 601-619.
-
(2006)
J. Comp. Aid. Mol. Des
, vol.20
, pp. 601-619
-
-
Moustakas, D.T.1
Lang, P.T.2
Pegg, S.3
Pettersen, E.4
Kuntz, I.D.5
Brooijmans, N.6
Rizzo, R.C.7
-
80
-
-
13944253576
-
Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors
-
Mozziconacci J.C., Arnoult E., Bernard P., Do Q.T., Marot C., Morin-Allory L. (2005) Optimization and validation of a docking-scoring protocol; application to virtual screening for COX-2 inhibitors. J. Med. Chem. 48: 1055-1068.
-
(2005)
J. Med. Chem
, vol.48
, pp. 1055-1068
-
-
Mozziconacci, J.C.1
Arnoult, E.2
Bernard, P.3
Do, Q.T.4
Marot, C.5
Morin-Allory, L.6
-
81
-
-
77951993951
-
Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors
-
Musmuca I., Caroli A., Mai A., Kaushik-Basu N., Arora P., Ragno R. (2010) Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors. J. Chem. Inf. Model. 50: 662-676.
-
(2010)
J. Chem. Inf. Model
, vol.50
, pp. 662-676
-
-
Musmuca, I.1
Caroli, A.2
Mai, A.3
Kaushik-Basu, N.4
Arora, P.5
Ragno, R.6
-
82
-
-
0037499658
-
A structure-based design approach for the identification of novel inhibitors: Application to an alanine racemase
-
Mustata G.I., Briggs J.M. (2002) A structure-based design approach for the identification of novel inhibitors: application to an alanine racemase. J. Comp. Aid. Mol. Des. 16: 935-953.
-
(2002)
J. Comp. Aid. Mol. Des
, vol.16
, pp. 935-953
-
-
Mustata, G.I.1
Briggs, J.M.2
-
83
-
-
79952200622
-
Design of screening collections for successful fragment-based lead discovery
-
Na J., Hu Q. (2011) Design of screening collections for successful fragment-based lead discovery. Meth. Mol. Biol. 685: 219-240.
-
(2011)
Meth. Mol. Biol
, vol.685
, pp. 219-240
-
-
Na, J.1
Hu, Q.2
-
84
-
-
58549110871
-
Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening
-
Neres J., Brewer M.L., Ratier L., Botti H., Buschiazzo A., Edwards P.N., Mortenson P.N., Charlton M.H., Alzari P.M., Frasch A.C., Bryce R.A., Douglas K.T. (2009) Discovery of novel inhibitors of Trypanosoma cruzi trans-sialidase from in silico screening. Bioorg. Med. Chem. Lett. 19: 589-596.
-
(2009)
Bioorg. Med. Chem. Lett
, vol.19
, pp. 589-596
-
-
Neres, J.1
Brewer, M.L.2
Ratier, L.3
Botti, H.4
Buschiazzo, A.5
Edwards, P.N.6
Mortenson, P.N.7
Charlton, M.H.8
Alzari, P.M.9
Frasch, A.C.10
Bryce, R.A.11
Douglas, K.T.12
-
85
-
-
78649843968
-
Evaluation of docking calculations on Xray structures using CONSENSUS-DOCK
-
Okamoto M., Masuda Y., Muroya A., Yasuno K., Takahashi O., Furuya T. (2010) Evaluation of docking calculations on Xray structures using CONSENSUS-DOCK. Chem. Pharm. Bull. 58: 1655-1657.
-
(2010)
Chem. Pharm. Bull
, vol.58
, pp. 1655-1657
-
-
Okamoto, M.1
Masuda, Y.2
Muroya, A.3
Yasuno, K.4
Takahashi, O.5
Furuya, T.6
-
87
-
-
0036137713
-
Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in AutoDock
-
Osterberg F., Morris G.M., Sanner M.F., Olson A.J., Goodsell D.S. (2002) Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins 46: 34-40.
-
(2002)
Proteins
, vol.46
, pp. 34-40
-
-
Osterberg, F.1
Morris, G.M.2
Sanner, M.F.3
Olson, A.J.4
Goodsell, D.S.5
-
88
-
-
0035830767
-
Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis
-
Paiva A.M., Vanderwall D.E., Blanchard J.S., Kozarich J.W., Williamson J.M., Kelly T.M. (2001) Inhibitors of dihydrodipicolinate reductase, a key enzyme of the diaminopimelate pathway of Mycobacterium tuberculosis. Biochim. Biophys. Acta 1545: 67-77.
-
(2001)
Biochim. Biophys. Acta
, vol.1545
, pp. 67-77
-
-
Paiva, A.M.1
Vanderwall, D.E.2
Blanchard, J.S.3
Kozarich, J.W.4
Williamson, J.M.5
Kelly, T.M.6
-
89
-
-
52449110024
-
Discovery of novel Cdc25 phosphatase inhibitors with micromolar activity based on the structure-based virtual screening
-
Park H., Bahn Y.J., Jung S.K., Jeong D.G., Lee S.H., Seo I., Yoon T.S., Kim S.J., Ryu S.E. (2008) Discovery of novel Cdc25 phosphatase inhibitors with micromolar activity based on the structure-based virtual screening. J. Med. Chem. 51: 5533-5541.
-
(2008)
J. Med. Chem
, vol.51
, pp. 5533-5541
-
-
Park, H.1
Bahn, Y.J.2
Jung, S.K.3
Jeong, D.G.4
Lee, S.H.5
Seo, I.6
Yoon, T.S.7
Kim, S.J.8
Ryu, S.E.9
-
90
-
-
0036606204
-
ConsDock: A new program for the consensus analysis of protein-ligand interactions
-
Paul N., Rognan D. (2002) ConsDock: A new program for the consensus analysis of protein-ligand interactions. Proteins 47: 521-533.
-
(2002)
Proteins
, vol.47
, pp. 521-533
-
-
Paul, N.1
Rognan, D.2
-
91
-
-
77955517509
-
Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
-
Pérot S., Sperandio O., Miteva M.A., Camproux A.C., Villoutreix B.O. (2010) Druggable pockets and binding site centric chemical space: a paradigm shift in drug discovery. Drug Discov. Today 15: 656-667.
-
(2010)
Drug Discov. Today
, vol.15
, pp. 656-667
-
-
Pérot, S.1
Sperandio, O.2
Miteva, M.A.3
Camproux, A.C.4
Villoutreix, B.O.5
-
92
-
-
4444221565
-
UCSF Chimera-a visualization system for exploratory research and analysis
-
Pettersen E.F., Goddard T.D., Huang C.C., Couch G.S., Greenblatt D.M., Meng E.C., Ferrin T.E. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J. Comput. Chem. 25: 1605-1612.
-
(2004)
J. Comput. Chem
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
93
-
-
82155191018
-
HarmonyDOCK: The structural analysis of poses in protein-ligand docking
-
Plewczynski D., Philips A., von Grotthuss M., Rychlewski L., Ginalski K. (2010) HarmonyDOCK: the structural analysis of poses in protein-ligand docking. J. Comp. Biol. 18: 1-10.
-
(2010)
J. Comp. Biol
, vol.18
, pp. 1-10
-
-
Plewczynski, D.1
Philips, A.2
von Grotthuss, M.3
Rychlewski, L.4
Ginalski, K.5
-
94
-
-
79251524915
-
Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database
-
Plewczynski D., Łaźniewski M., Augustyniak R., Ginalski K. (2011a) Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database. J. Comput. Chem. 32: 742-755.
-
(2011)
J. Comput. Chem
, vol.32
, pp. 742-755
-
-
Plewczynski, D.1
łaźniewski, M.2
Augustyniak, R.3
Ginalski, K.4
-
95
-
-
79251524201
-
VoteDock: Consensus docking method for prediction of protein-ligand interactions
-
Plewczynski D., Łaźniewski M., von Grotthuss M., Rychlewski L., Ginalski K. (2011b) VoteDock: consensus docking method for prediction of protein-ligand interactions. J. Comput. Chem. 32: 568-581.
-
(2011)
J. Comput. Chem
, vol.32
, pp. 568-581
-
-
Plewczynski, D.1
łaźniewski, M.2
von Grotthuss, M.3
Rychlewski, L.4
Ginalski, K.5
-
96
-
-
33845965722
-
Towards in silico lead optimization: Scores from ensembles of protein/ ligand conformations reliably correlate with biological activity
-
Popov V.M., Yee W.A., Anderson A.C. (2007) Towards in silico lead optimization: scores from ensembles of protein/ ligand conformations reliably correlate with biological activity. Proteins 66: 375-387.
-
(2007)
Proteins
, vol.66
, pp. 375-387
-
-
Popov, V.M.1
Yee, W.A.2
Anderson, A.C.3
-
97
-
-
0030599010
-
A fast flexible docking method using an incremental construction algorithm
-
Rarey M., Kramer B., Lengauer T., Klebe G. (1996) A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 261: 470-489.
-
(1996)
J. Mol. Biol
, vol.261
, pp. 470-489
-
-
Rarey, M.1
Kramer, B.2
Lengauer, T.3
Klebe, G.4
-
98
-
-
0037784010
-
Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors
-
Rastelli G., Pacchioni S., Sirawaraporn W., Sirawaraporn R., Parenti M.D., Ferrari A.M. (2003) Docking and database screening reveal new classes of Plasmodium falciparum dihydrofolate reductase inhibitors. J. Med. Chem. 46: 2834-2845.
-
(2003)
J. Med. Chem
, vol.46
, pp. 2834-2845
-
-
Rastelli, G.1
Pacchioni, S.2
Sirawaraporn, W.3
Sirawaraporn, R.4
Parenti, M.D.5
Ferrari, A.M.6
-
99
-
-
69549090094
-
Docking studies on DNA-ligand interactions: Building and application of a protocol to identify the binding mode
-
Ricci C.G., Netz P.A. (2009) Docking studies on DNA-ligand interactions: building and application of a protocol to identify the binding mode. J. Chem. Inf. Model. 49: 1925-1935.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1925-1935
-
-
Ricci, C.G.1
Netz, P.A.2
-
100
-
-
34548317031
-
Chemogenomic approaches to rational drug design
-
Rognan D. (2007) Chemogenomic approaches to rational drug design. Br. J. Pharmacol. 152: 38-52.
-
(2007)
Br. J. Pharmacol
, vol.152
, pp. 38-52
-
-
Rognan, D.1
-
101
-
-
0028466540
-
Comparison of automatic three-dimensional model builders using 639 X-ray structures
-
Sadowski J., Gasteiger J., Klebe G. (1994) Comparison of automatic three-dimensional model builders using 639 X-ray structures. J. Chem. Inf. Comp. Sci. 34: 1000-1008.
-
(1994)
J. Chem. Inf. Comp. Sci
, vol.34
, pp. 1000-1008
-
-
Sadowski, J.1
Gasteiger, J.2
Klebe, G.3
-
102
-
-
0033522646
-
The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: Implications for the reaction mechanism
-
Schluckebier G., Zhong P., Stewart K.D., Kavanaugh T.J., Abad-Zapatero C. (1999) The 2.2 A structure of the rRNA methyltransferase ErmC' and its complexes with cofactor and cofactor analogs: implications for the reaction mechanism. J. Mol. Biol. 289: 277-291.
-
(1999)
J. Mol. Biol
, vol.289
, pp. 277-291
-
-
Schluckebier, G.1
Zhong, P.2
Stewart, K.D.3
Kavanaugh, T.J.4
Abad-Zapatero, C.5
-
103
-
-
33645422011
-
Are target-family-privileged substructures truly privileged
-
Schnur D.M., Hermsmeier M.A., Tebben A.J. (2006) Are target-family-privileged substructures truly privileged? J. Med. Chem. 49: 2000-2009.
-
(2006)
J. Med. Chem
, vol.49
, pp. 2000-2009
-
-
Schnur, D.M.1
Hermsmeier, M.A.2
Tebben, A.J.3
-
104
-
-
31544450787
-
Novel procedure for modeling ligand/receptor induced fit effects
-
Sherman W., Day T., Jacobson M.P., Friesner R.A., Farid R. (2006) Novel procedure for modeling ligand/receptor induced fit effects. J. Med. Chem. 49: 534-553.
-
(2006)
J. Med. Chem
, vol.49
, pp. 534-553
-
-
Sherman, W.1
Day, T.2
Jacobson, M.P.3
Friesner, R.A.4
Farid, R.5
-
105
-
-
11144323163
-
Virtual screening of chemical libraries
-
Shoichet B.K. (2004) Virtual screening of chemical libraries. Nature 432: 862-865.
-
(2004)
Nature
, vol.432
, pp. 862-865
-
-
Shoichet, B.K.1
-
106
-
-
33748276474
-
Protein-ligand docking: Current status and future challenges
-
Sousa S.F., Fernandes P.A., Ramos M.J. (2006) Protein-ligand docking: current status and future challenges. Proteins 65: 15-26.
-
(2006)
Proteins
, vol.65
, pp. 15-26
-
-
Sousa, S.F.1
Fernandes, P.A.2
Ramos, M.J.3
-
107
-
-
77955627131
-
How to choose relevant multiple receptor conformations for virtual screening: A test case of Cdk2 and normal mode analysis
-
Sperandio O., Mouawad L., Pinto E., Villoutreix B.O., Perahia D., Miteva M.A. (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur. Biophys. J. 39: 1365-1372.
-
(2010)
Eur. Biophys. J
, vol.39
, pp. 1365-1372
-
-
Sperandio, O.1
Mouawad, L.2
Pinto, E.3
Villoutreix, B.O.4
Perahia, D.5
Miteva, M.A.6
-
108
-
-
34548276887
-
Improved cyclodextrin- based receptors for camptothecin by inverse virtual screening
-
Steffen A., Thiele C., Tietze S., Strassnig C., Kämper A., Lengauer T., Wenz G., Apostolakis J. (2007) Improved cyclodextrin- based receptors for camptothecin by inverse virtual screening. Chemistry 13: 6801-6809.
-
(2007)
Chemistry
, vol.13
, pp. 6801-6809
-
-
Steffen, A.1
Thiele, C.2
Tietze, S.3
Strassnig, C.4
Kämper, A.5
Lengauer, T.6
Wenz, G.7
Apostolakis, J.8
-
109
-
-
67650077383
-
Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results
-
Ten Brink T., Exner T.E. (2009) Influence of protonation, tautomeric, and stereoisomeric states on protein-ligand docking results. J. Chem. Inf. Model. 49: 1535-1546.
-
(2009)
J. Chem. Inf. Model
, vol.49
, pp. 1535-1546
-
-
Ten Brink, T.1
Exner, T.E.2
-
110
-
-
41949132916
-
Flexible ligand docking to multiple receptor conformations: A practical alternative
-
Totrov M., Abagyan R. (2008) Flexible ligand docking to multiple receptor conformations: a practical alternative. Curr. Opin. Struct. Biol. 18: 178-184.
-
(2008)
Curr. Opin. Struct. Biol
, vol.18
, pp. 178-184
-
-
Totrov, M.1
Abagyan, R.2
-
111
-
-
76149120388
-
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring func-tion, efficient optimization, and multithreading
-
Trott O., Olson A.J. (2010) AutoDock Vina: improving the speed and accuracy of docking with a new scoring func-tion, efficient optimization, and multithreading. J. Comput. Chem. 31: 455-461.
-
(2010)
J. Comput. Chem
, vol.31
, pp. 455-461
-
-
Trott, O.1
Olson, A.J.2
-
113
-
-
0041919542
-
Improved protein-ligand docking using GOLD
-
Verdonk M.L., Cole J.C., Hartshorn M.J., Murray C.W., Taylor R.D. (2003) Improved protein-ligand docking using GOLD. Proteins 52: 609-623.
-
(2003)
Proteins
, vol.52
, pp. 609-623
-
-
Verdonk, M.L.1
Cole, J.C.2
Hartshorn, M.J.3
Murray, C.W.4
Taylor, R.D.5
-
114
-
-
26444586139
-
Modeling water molecules in protein-ligand docking using GOLD
-
Verdonk M.L., Chessari G., Cole J.C., Hartshorn M.J., Murray C.W., Nissink J.W.M., Taylor R.D., Taylor R. (2005) Modeling water molecules in protein-ligand docking using GOLD. J. Med. Chem. 48: 6504-6515.
-
(2005)
J. Med. Chem
, vol.48
, pp. 6504-6515
-
-
Verdonk, M.L.1
Chessari, G.2
Cole, J.C.3
Hartshorn, M.J.4
Murray, C.W.5
Nissink, J.W.M.6
Taylor, R.D.7
Taylor, R.8
-
116
-
-
5344244908
-
Chemical Similarity Searching
-
Willet P. (1998) Chemical Similarity Searching. J. Chem. Inf. Comp. Sci. 38: 983-996.
-
(1998)
J. Chem. Inf. Comp. Sci
, vol.38
, pp. 983-996
-
-
Willet, P.1
-
117
-
-
34250829729
-
Alternative to consensus scoring - a new approach toward the qualitative combination of docking algorithms
-
Wolf A., Zimmermann M., Hofmann-Apitius M. (2007) Alternative to consensus scoring - a new approach toward the qualitative combination of docking algorithms. J. Chem. Inf. Model. 47: 1036-1044.
-
(2007)
J. Chem. Inf. Model
, vol.47
, pp. 1036-1044
-
-
Wolf, A.1
Zimmermann, M.2
Hofmann-Apitius, M.3
-
118
-
-
62749083700
-
In silico screening for PTPN22 inhibitors: Active hits from an inactive phosphatase conformation
-
Wu S., Bottini M., Rickert R.C., Mustelin T., Tautz L. (2009) In silico screening for PTPN22 inhibitors: active hits from an inactive phosphatase conformation. ChemMedChem 4: 440-444.
-
(2009)
ChemMedChem
, vol.4
, pp. 440-444
-
-
Wu, S.1
Bottini, M.2
Rickert, R.C.3
Mustelin, T.4
Tautz, L.5
-
119
-
-
77957591555
-
Identification of a submicromolar, non-peptide inhibitor of $-secretase with low neural cytotoxicity through in silico screening
-
Xu W., Chen G., Zhu W., Zuo Z. (2010) Identification of a submicromolar, non-peptide inhibitor of $-secretase with low neural cytotoxicity through in silico screening. Bioorg. Med. Chem. Lett. 20: 5763-5766.
-
(2010)
Bioorg. Med. Chem. Lett
, vol.20
, pp. 5763-5766
-
-
Xu, W.1
Chen, G.2
Zhu, W.3
Zuo, Z.4
-
120
-
-
0345735309
-
Shape signatures: A new approach to computer-aided ligand- and receptor-based drug design
-
Zauhar R.J., Moyna G., Tian L., Li Z., Welsh W.J. (2003) Shape signatures: a new approach to computer-aided ligand- and receptor-based drug design. J. Med. Chem. 46: 5674-5690.
-
(2003)
J. Med. Chem
, vol.46
, pp. 5674-5690
-
-
Zauhar, R.J.1
Moyna, G.2
Tian, L.3
Li, Z.4
Welsh, W.J.5
-
122
-
-
33644862638
-
Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: Ranking, voting, and consensus scoring
-
Zhang Q., Muegge I. (2006) Scaffold hopping through virtual screening using 2D and 3D similarity descriptors: ranking, voting, and consensus scoring. J. Med. Chem. 49: 1536-1548.
-
(2006)
J. Med. Chem
, vol.49
, pp. 1536-1548
-
-
Zhang, Q.1
Muegge, I.2
-
123
-
-
77649218736
-
Structure-based rational screening of novel hit compounds with structural diversity for cytochrome P450 sterol 14alpha-demethylase from Penicillium digitatum
-
Zhang Q., Li D., Wei P., Zhang J., Wan J., Ren Y., Chen Z., Liu D., Yu Z., Feng L. (2010) Structure-based rational screening of novel hit compounds with structural diversity for cytochrome P450 sterol 14alpha-demethylase from Penicillium digitatum. J. Chem. Inf. Model. 50: 317-325.
-
(2010)
J. Chem. Inf. Model
, vol.50
, pp. 317-325
-
-
Zhang, Q.1
Li, D.2
Wei, P.3
Zhang, J.4
Wan, J.5
Ren, Y.6
Chen, Z.7
Liu, D.8
Yu, Z.9
Feng, L.10
|