메뉴 건너뛰기




Volumn 14, Issue 10, 2011, Pages 840-860

Virtual high throughput screening in new lead identification

Author keywords

Kinase; Lead design; Molecular representations; Virtual screening

Indexed keywords

CILOMILAST; DORAMAPIMOD; G PROTEIN COUPLED RECEPTOR; IMATINIB; LAPATINIB; LIGAND; PHOSPHODIESTERASE V INHIBITOR; ROFLUMILAST; ROLIPRAM; SORAFENIB; THEOPHYLLINE;

EID: 80054930821     PISSN: 13862073     EISSN: 18755402     Source Type: Journal    
DOI: 10.2174/138620711797537102     Document Type: Article
Times cited : (78)

References (207)
  • 2
    • 67649225348 scopus 로고    scopus 로고
    • Efficient drug lead discovery and optimization
    • Jorgensen, W. L. Efficient drug lead discovery and optimization. Acc. Chem. Res., 2009, 42, 724-733.
    • (2009) Acc. Chem. Res. , vol.42 , pp. 724-733
    • Jorgensen, W.L.1
  • 3
    • 65549108234 scopus 로고    scopus 로고
    • Virtual screening: What does it give us?
    • Koppen, H. Virtual screening: what does it give us? Curr. Opin. Drug Discov. Devel., 2009, 12, 397-407.
    • (2009) Curr. Opin. Drug Discov. Devel. , vol.12 , pp. 397-407
    • Koppen, H.1
  • 4
    • 77950503976 scopus 로고    scopus 로고
    • Virtual screening: An endless staircase?
    • Schneider, G. Virtual screening: an endless staircase? Nat. Rev. Drug Discovery, 2010, 9, 273-276.
    • (2010) Nat. Rev. Drug Discovery , vol.9 , pp. 273-276
    • Schneider, G.1
  • 5
    • 0035292795 scopus 로고    scopus 로고
    • Selected concepts and investigations in compound classification, molecular descriptor analysis, and virtual screening
    • Bajorath, J. Selected concepts and investigations in compound classification, molecular descriptor analysis, and virtual screening. J. Chem. Inf. Comput. Sci., 2001, 41, 233-245. (Pubitemid 33717130)
    • (2001) Journal of Chemical Information and Computer Sciences , vol.41 , Issue.2 , pp. 233-245
    • Bajorath, J.1
  • 6
    • 61949166066 scopus 로고    scopus 로고
    • How Similar Are Similarity Searching Methods? A principal component analysis of molecular descriptor space
    • Bender, A.; Jenkins, J. L.; Scheiber, J.; Sukuru, S. C. K.; Glick, M.; Davies, J. W. How Similar Are Similarity Searching Methods? A principal component analysis of molecular descriptor space. J. Chem. Inf. Model., 2009, 49, 108-119.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 108-119
    • Bender, A.1    Jenkins, J.L.2    Scheiber, J.3    Sukuru, S.C.K.4    Glick, M.5    Davies, J.W.6
  • 7
    • 77952780755 scopus 로고    scopus 로고
    • Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments
    • Sastry, M.; Lowrie, J. F.; Dixon, S. L.; Sherman, W. Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. J. Chem. Inf. Model., 2010, 50, 771-784.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 771-784
    • Sastry, M.1    Lowrie, J.F.2    Dixon, S.L.3    Sherman, W.4
  • 8
    • 73449116746 scopus 로고    scopus 로고
    • Fingerprint recombination - Generating hybrid fingerprints for similarity searching from different fingerprint Types
    • Nisius, B.; Bajorath, J. Fingerprint recombination - generating hybrid fingerprints for similarity searching from different fingerprint Types. Chem. Med. Chem., 2009, 4, 1859-1863.
    • (2009) Chem. Med. Chem. , vol.4 , pp. 1859-1863
    • Nisius, B.1    Bajorath, J.2
  • 9
    • 49949100432 scopus 로고    scopus 로고
    • Protein ligand interaction database (PLID): Datamining analysis of structure-function relationships
    • Reddy, A. S.; Amarnath, H. S. D.; Bapi, R. S.; Sastry G. M.; Sastry, G. N. Protein ligand interaction database (PLID): Datamining analysis of structure-function relationships. Comp. Biol. Chem., 2008, 32, 387-390.
    • (2008) Comp. Biol. Chem. , vol.32 , pp. 387-390
    • Reddy, A.S.1    Amarnath, H.S.D.2    Bapi, R.S.3    Sastry, G.M.4    Sastry, G.N.5
  • 10
    • 67849104638 scopus 로고    scopus 로고
    • PubChem: A public information system for analyzing bioactivities of small molecules
    • Wang, Y.; Xiao, J.; Suzek, T. O.; Zhang, J.; Wang, J.; Bryant, S. H. PubChem: A public information system for analyzing bioactivities of small molecules. Nucleic Acids Res., 2009, 37, W623-33.
    • (2009) Nucleic Acids Res. , vol.37
    • Wang, Y.1    Xiao, J.2    Suzek, T.O.3    Zhang, J.4    Wang, J.5    Bryant, S.H.6
  • 11
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto encyclopedia of genes and genomes
    • Kanehisa, M.; Goto, S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 2000, 28, 27-30. (Pubitemid 30047706)
    • (2000) Nucleic Acids Research , vol.28 , Issue.1 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 13
    • 13844312649 scopus 로고    scopus 로고
    • ZINC - A free database of commercially available compounds for virtual screening
    • DOI 10.1021/ci049714+
    • Irwin, J. J.; Shoichet, B. K. ZINC - A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model., 2005, 45, 177-182. (Pubitemid 40736970)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.1 , pp. 177-182
    • Irwin, J.J.1    Shoichet, B.K.2
  • 14
    • 67649619336 scopus 로고    scopus 로고
    • 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, 8732-8733.
    • (2009) J. Am. Chem. Soc. , vol.131 , pp. 8732-8733
    • Blum, L.C.1    Reymond, J.L.2
  • 15
    • 15744388954 scopus 로고    scopus 로고
    • Target identification and validation in drug discovery: The role of proteomics
    • DOI 10.1016/j.bcp.2005.01.004
    • Karla, K.; Donna, K.; Coyne, B.; Williams, M. Target identification and validation in drug discovery: The role of proteomics. Biochem. Pharmacol., 2005, 69, 1133-1139. (Pubitemid 40417484)
    • (2005) Biochemical Pharmacology , vol.69 , Issue.8 , pp. 1133-1139
    • Kopec, K.K.1    Bozyczko-Coyne, D.2    Williams, M.3
  • 16
    • 77955517509 scopus 로고    scopus 로고
    • Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery
    • Perot, S.; Sperandio, O.; Miteva, M. A.; Camproux, A. C.; Villoutreix, B. O. Druggable pockets and binding site centric chemical space: A paradigm shift in drug discovery. Drug Discov. Today, 2010, 15, 656-667.
    • (2010) Drug Discov. Today , vol.15 , pp. 656-667
    • Perot, S.1    Sperandio, O.2    Miteva, M.A.3    Camproux, A.C.4    Villoutreix, B.O.5
  • 17
    • 58849145512 scopus 로고    scopus 로고
    • Predicting druggable binding sites at the protein-protein interface
    • Fuller, J. C.; Burgoyne, N. J.; Jackson, R. M. Predicting druggable binding sites at the protein-protein interface. Drug Discov. Today, 2009, 14, 155-161.
    • (2009) Drug Discov. Today , vol.14 , pp. 155-161
    • Fuller, J.C.1    Burgoyne, N.J.2    Jackson, R.M.3
  • 18
    • 77955397914 scopus 로고    scopus 로고
    • Understanding and predicting druggability. A high throughput method for detection of drug binding sites
    • Schmidtke, P.; Barril, X. Understanding and predicting druggability. A high throughput method for detection of drug binding sites J. Med. Chem., 2010, 53, 5858-5867.
    • (2010) J. Med. Chem. , vol.53 , pp. 5858-5867
    • Schmidtke, P.1    Barril, X.2
  • 19
    • 60149096311 scopus 로고    scopus 로고
    • Properties and identification of human protein drug targets
    • Bakheet, T. M.; Doig, A. J. Properties and identification of human protein drug targets. Bioinformatics, 2009, 25, 451-457.
    • (2009) Bioinformatics , vol.25 , pp. 451-457
    • Bakheet, T.M.1    Doig, A.J.2
  • 20
    • 44049094415 scopus 로고    scopus 로고
    • Biocomputational strategies for microbial drug target identification
    • New Antibiotic Targets Edited by: W. Scott Champney, Humana Press Inc., Totowa, NJ
    • Sakharkar, K. R.; Sakharkar, M. K.; Vincent, Chow, T. K. Biocomputational strategies for microbial drug target identification. Methods in Molecular Medicine, 142, New Antibiotic Targets Edited by: W. Scott Champney, Humana Press Inc., Totowa, NJ. 1-9
    • Methods in Molecular Medicine , vol.142 , pp. 1-9
    • Sakharkar, K.R.1    Sakharkar, M.K.2    Vincent Chow, T.K.3
  • 22
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- and three-dimensional chemical structures
    • DOI 10.1021/jm0582165
    • Willett, P. Searching techniques for databases of two- and three dimensional chemical structures. J. Med. Chem., 2005, 48, 4183-4199. (Pubitemid 40884919)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.13 , pp. 4183-4199
    • Willett, P.1
  • 23
    • 33847207834 scopus 로고    scopus 로고
    • Molecular similarity analysis in virtual screening: Foundations, limitations and novel approaches
    • Eckert, H.; Bajorath J. Molecular similarity analysis in virtual screening: foundations, limitations and novel approaches. Drug Discov. Today, 2007, 12, 225-233.
    • (2007) Drug Discov. Today , vol.12 , pp. 225-233
    • Eckert, H.1    Bajorath, J.2
  • 24
    • 5244364312 scopus 로고    scopus 로고
    • The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding
    • Brown, R. D.; Martin, Y. C. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9. (Pubitemid 127601574)
    • (1997) Journal of Chemical Information and Computer Sciences , vol.37 , Issue.1 , pp. 1-9
    • Brown, R.D.1    Martin, Y.C.2
  • 25
  • 28
    • 5244364312 scopus 로고    scopus 로고
    • The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding
    • Brown, R. D.; Martin, Y. C. The information content of 2D and 3D structural descriptors relevant to ligand-receptor binding. J. Chem. Inf. Comput. Sci. 1997, 37, 1-9. (Pubitemid 127601574)
    • (1997) Journal of Chemical Information and Computer Sciences , vol.37 , Issue.1 , pp. 1-9
    • Brown, R.D.1    Martin, Y.C.2
  • 29
    • 0022620276 scopus 로고
    • A comparison of some measures for the determination of inter-molecular structural similarity measures of inter-molecular structural similarity
    • Willett, P.; Winterman, V. A comparison of some measures for the determination of intermolecular structural similarity measures of intermolecular structural similarity. Quan. Struct. Activ. Relat., 1986, 5, 18-25. (Pubitemid 16134330)
    • (1986) Quantitative Structure-Activity Relationships , vol.5 , Issue.1 , pp. 18-25
    • Willett, P.1    Winterman, V.2
  • 31
    • 67349104587 scopus 로고    scopus 로고
    • Targeted scoring functions for virtual screening
    • Seifert, M. H. Targeted scoring functions for virtual screening. Drug Discov. Today, 2009, 14, 562-569.
    • (2009) Drug Discov. Today , vol.14 , pp. 562-569
    • Seifert, M.H.1
  • 32
    • 0035971738 scopus 로고    scopus 로고
    • A smooth permittivity function for Poisson-Boltzmann solvation methods
    • DOI 10.1002/jcc.1032
    • Grant, J.A.; Pickup, B. T.; Nicholls, A. A smooth permitivity function for Poisson-Boltzman solvation methods. J. Comp. Chem., 2001, 22, 608-640. (Pubitemid 32382607)
    • (2001) Journal of Computational Chemistry , vol.22 , Issue.6 , pp. 608-640
    • Grant, J.A.1
  • 33
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based scoring function to predict protein-ligand interactions
    • DOI 10.1006/jmbi.1999.3371
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based scoring function to predict protein-ligand interactions. J. Mol. Biol., 2000, 295, 337-356. (Pubitemid 30045364)
    • (2000) Journal of Molecular Biology , vol.295 , Issue.2 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 34
    • 0033673508 scopus 로고    scopus 로고
    • A knowledge-based scoring function for protein-ligand interactions: Probing the reference state
    • Muegge, I. A knowledge-based scoring function for protein-ligand interactions: probing the reference state. Perspect. Drug Des. Discov., 2000, 20, 99-114.
    • (2000) Perspect. Drug Des. Discov. , vol.20 , pp. 99-114
    • Muegge, I.1
  • 36
    • 34548009855 scopus 로고    scopus 로고
    • CH/π interactions in DNA and proteins. A theoretical study
    • DOI 10.1021/jp0717847
    • Gil, A.; Branchadell, V.; Bertran, J.; Oliva, A. CH-π interactions in DNA and proteins. A theoretical study. J. Phys. Chem. B., 2007, 111, 9372-9379. (Pubitemid 47280538)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.31 , pp. 9372-9379
    • Gil, A.1    Branchadell, V.2    Bertran, J.3    Oliva, A.4
  • 37
    • 0242417008 scopus 로고    scopus 로고
    • Interactions with aromatic rings in chemical and biological recognition
    • DOI 10.1002/anie.200390319
    • Meyar, E. A.; Castellano, R. K.; Diederich, F. Interactions with aromatic rings in chemical and biological recognition. Angew. Chem. Int. Ed. Engl., 2003, 42, 1210-1250. (Pubitemid 36410287)
    • (2003) Angewandte Chemie - International Edition , vol.42 , Issue.11 , pp. 1210-1250
    • Meyer, E.A.1    Castellano, R.K.2    Diederich, F.3
  • 38
    • 4243468938 scopus 로고    scopus 로고
    • The Cation-π interactions
    • Ma, J. C.; Dougherty, D. A. The Cation-π interactions. Chem. Rev., 1997, 97, 1303-1324.
    • (1997) Chem. Rev. , vol.97 , pp. 1303-1324
    • Ma, J.C.1    Dougherty, D.A.2
  • 39
    • 26844482366 scopus 로고    scopus 로고
    • Cation [M=H+, Li+, Na+, K+, Ca+, Mg2+, NH4 +, and NMe4 +] interactions with the aromatic motifs of naturally occurring amino acids: A theoretical study
    • Reddy, A. S.; Sastry, G. N. Cation [M=H+, Li+, Na+, K+, Ca+, Mg2+, NH4 +, and NMe4 +] interactions with the aromatic motifs of naturally occurring amino acids: A theoretical study. J. Phys. Chem. A, 2005, 109, 8893-8903.
    • (2005) J. Phys. Chem. A , vol.109 , pp. 8893-8903
    • Reddy, A.S.1    Sastry, G.N.2
  • 41
    • 15944379585 scopus 로고    scopus 로고
    • Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases
    • DOI 10.1093/nar/gki317
    • Mignon, P.; Loverix, S.; Steyaert, J.; Geerlings, P. Influence of the π-π interaction on the hydrogen bonding capacity of stacked DNA/RNA bases. Nucleic Acids Res., 2005, 33, 1779-1789. (Pubitemid 41754207)
    • (2005) Nucleic Acids Research , vol.33 , Issue.6 , pp. 1779-1789
    • Mignon, P.1    Loverix, S.2    Steyaert, J.3    Geerlings, P.4
  • 42
    • 49349111901 scopus 로고    scopus 로고
    • On the cooperativity of cation-π and hydrogen bonding interactions
    • Vijay, D.; Zipse, H.; Sastry, G. N. On the cooperativity of cation-?c and hydrogen bonding interactions. J. Phys. Chem. B, 2008, 112, 8863-8867.
    • (2008) J. Phys. Chem. B , vol.112 , pp. 8863-8867
    • Vijay, D.1    Zipse, H.2    Sastry, G.N.3
  • 43
    • 73149108003 scopus 로고    scopus 로고
    • The cooperativity of cation-π and π-π Interactions
    • Vijay, D.; Sastry, G. N. The cooperativity of cation-π and π-π interactions. Chem. Phys. Lett., 2010, 485, 235-242.
    • (2010) Chem. Phys. Lett. , vol.485 , pp. 235-242
    • Vijay, D.1    Sastry, G.N.2
  • 44
    • 79953286743 scopus 로고    scopus 로고
    • Aromatic-aromatic database A2ID: An analysis of aromatic π-networks in proteins
    • Chourasia, M.; Sastry, G. M.; Sastry, G. N. Aromatic-Aromatic Database, A2ID: An analysis of aromatic π-networks in proteins. Int. J. Biol. Macromol., 2011, 48, 540-552.
    • (2011) Int. J. Biol. Macromol. , vol.48 , pp. 540-552
    • Chourasia, M.1    Sastry, G.M.2    Sastry, G.N.3
  • 46
    • 33748627714 scopus 로고    scopus 로고
    • m (X = N and P): Contrasting preferences between nitrogen and phosphorous-substituted rings
    • DOI 10.1021/jp062448d
    • Vijay, D.; Sastry, G. N. A computational study on π and π modes of metal ion binding to heteroaromatics (CH)5-mXm and (CH)6-mXm (X = N and P): Contrasting preferences between nitrogen and phosphorous substituted rings. J. Phys. Chem. A, 2006, 110, 10148-10154. (Pubitemid 44376322)
    • (2006) Journal of Physical Chemistry A , vol.110 , Issue.33 , pp. 10148-10154
    • Vijay, D.1    Sastry, G.N.2
  • 47
    • 77956339455 scopus 로고    scopus 로고
    • Insights into MAPK p38a DFG flip mechanism by accelerated molecular dynamics
    • Filomia, F.; Rienzo, F. D.; Menziani, M. C. Insights into MAPK p38a DFG flip mechanism by accelerated molecular dynamics. Bioorg. Med. Chem., 2010, 18, 6805-6812.
    • (2010) Bioorg. Med. Chem. , vol.18 , pp. 6805-6812
    • Filomia, F.1    Rienzo, F.D.2    Menziani, M.C.3
  • 48
    • 2442687873 scopus 로고    scopus 로고
    • Stair motifs at protein-DNA interfaces: Nonadditivity of H-bond, stacking, and cation-π interactions
    • DOI 10.1021/ja049620g
    • Biot, C.; Wintjens, R.; Rooman, M. Stair motifs at protein-DNA interfaces: nonadditivity of H-bond, stacking, and cation-π interactions. J. Am. Chem. Soc., 2004, 126, 6220-6221. (Pubitemid 38657035)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.20 , pp. 6220-6221
    • Biot, C.1    Wintjens, R.2    Rooman, M.3
  • 49
    • 0842332235 scopus 로고    scopus 로고
    • A practical approach to docking of zinc metalloproteinase inhibitors
    • DOI 10.1016/j.jmgm.2003.11.002
    • Hu, X.; Balaz, S.; Shelver, W. H. A practical approach to docking of zinc metalloproteinase inhibitors. J. Mol. Graph. Model., 2004, 22, 293-307. (Pubitemid 38183099)
    • (2004) Journal of Molecular Graphics and Modelling , vol.22 , Issue.4 , pp. 293-307
    • Hu, X.1    Balaz, S.2    Shelver, W.H.3
  • 50
    • 24944529911 scopus 로고    scopus 로고
    • Virtual screening against metalloenzymes for inhibitors and substrates
    • DOI 10.1021/bi050801k
    • Irwin, J. J.; Raushel, F. M.; Shoichet, B. K. Virtual screening against metalloenzymes for inhibitors and substrates. Biochemistry, 2005, 44, 12316-12328. (Pubitemid 41324325)
    • (2005) Biochemistry , vol.44 , Issue.37 , pp. 12316-12328
    • Irwin, J.J.1    Raushel, F.M.2    Shoichet, B.K.3
  • 51
    • 23944459025 scopus 로고    scopus 로고
    • A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands
    • DOI 10.1021/jm049050v
    • Khandelwal, A.; Lukacova, V.; Comez, D.; Kroll, D. M.; Raha, S.; Balaz, S. A combination of docking, QM/MM methods, and MD simulation for binding affinity estimation of metalloprotein ligands. J. Med. Chem., 2005, 48, 5437-5447. (Pubitemid 41209242)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.17 , pp. 5437-5447
    • Khandelwal, A.1    Lukacova, V.2    Comez, D.3    Kroll, D.M.4    Raha, S.5    Balaz, S.6
  • 52
    • 34248596450 scopus 로고    scopus 로고
    • Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes
    • DOI 10.1002/prot.21332
    • Jain, T.; Jayaram, B. Computational protocol for predicting the binding affinities of zinc containing metalloprotein-ligand complexes. Proteins: Struct Funct Genet, 2007, 67, 1167-1178. (Pubitemid 46753961)
    • (2007) Proteins: Structure, Function and Genetics , vol.67 , Issue.4 , pp. 1167-1178
    • Jain, T.1    Jayaram, B.2
  • 53
    • 79952594739 scopus 로고    scopus 로고
    • Effect of solvation on ion binding to imidazole and methylimidazole
    • Sharma, B.; Rao, J. S.; Sastry, G. N. Effect of Solvation on Ion Binding to Imidazole and Methylimidazole. J. Phys. Chem. A, 2011, 115, 1971-1984.
    • (2011) J. Phys. Chem. A , vol.115 , pp. 1971-1984
    • Sharma, B.1    Rao, J.S.2    Sastry, G.N.3
  • 54
    • 84962448918 scopus 로고    scopus 로고
    • A theoretical study on interaction of cyclopentadienyl ligand with akali and alkaline earth metals
    • Mahadevi, A. S.; Sastry, G. N. A theoretical study on interaction of cyclopentadienyl ligand with akali and alkaline earth metals. J. Phys. Chem. B, 2011, 115, 703-710.
    • (2011) J. Phys. Chem. B , vol.115 , pp. 703-710
    • Mahadevi, A.S.1    Sastry, G.N.2
  • 55
    • 58149145441 scopus 로고    scopus 로고
    • A comprehensive study on the solvation of mono and di valent metal ions: Li+ Na+ K+ Be2+ Mg2+ and Ca2
    • Rao, J. S.; Dinadayalane, T. C.; Leszczynski, J.; Sastry, G. N. A comprehensive study on the solvation of mono and di valent metal ions: Li+, Na+, K+, Be2+, Mg2+ and Ca2. J. Phys. Chem. A., 2008, 112, 12944-12953.
    • (2008) J. Phys. Chem. A. , vol.112 , pp. 12944-12953
    • Rao, J.S.1    Dinadayalane, T.C.2    Leszczynski, J.3    Sastry, G.N.4
  • 56
    • 79959777816 scopus 로고    scopus 로고
    • Hydrogen bonding in water clusters and their ionized counterparts
    • Neela, Y. I.; Mahadevi, A. S.; Sastry, G. N. Hydrogen bonding in water clusters and their ionized counterparts. J. Phys. Chem. B, 2010, 114, 17162-17171.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 17162-17171
    • Neela, Y.I.1    Mahadevi, A.S.2    Sastry, G.N.3
  • 57
    • 0000437635 scopus 로고    scopus 로고
    • Water: From clusters to the bulk
    • Ludwig, R. Water: From Clusters to the Bulk. Angew. Chem. Int. Ed. Engl., 2001, 113, 1856-1876
    • (2001) Angew. Chem. Int. Ed. Engl. , vol.113 , pp. 1856-1876
    • Ludwig, R.1
  • 58
    • 9644258919 scopus 로고
    • The cost of conformational order: Entropy changes in molecular associations
    • Searle, M. S.; Williams, D. H. The cost of conformational order: entropy changes in molecular associations. J. Am. Chem. Soc., 1992, 114, 10690-10697.
    • (1992) J. Am. Chem. Soc. , vol.114 , pp. 10690-10697
    • Searle, M.S.1    Williams, D.H.2
  • 60
    • 0000525863 scopus 로고
    • Solvent reorganization and thermodynamic enthalpy-entropy compensation
    • Grunwald, E.; Steel, C. Solvent Reorganization and Thermodynamic Enthalpy-Entropy Compensation. J. Am. Chem. Soc., 1995, 117, 5687-5692.
    • (1995) J. Am. Chem. Soc. , vol.117 , pp. 5687-5692
    • Grunwald, E.1    Steel, C.2
  • 61
    • 0031831627 scopus 로고    scopus 로고
    • Approaches to virtual drug design
    • Drie, J. H. V.; Lajiness, M. S. Approaches to virtual drug design. Drug Discov. Today, 1998, 3, 274-283.
    • (1998) Drug Discov. Today , vol.3 , pp. 274-283
    • Drie, J.H.V.1    Lajiness, M.S.2
  • 62
    • 0000058893 scopus 로고
    • Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm
    • Weber, L.; Wallbaum, S.; Broger, C.; Gubernator, K. Optimization of the biological activity of combinatorial compound libraries by a genetic algorithm. Angew. Chem. Int. Ed. Engl., 1995, 107, 2452-2454.
    • (1995) Angew. Chem. Int. Ed. Engl. , vol.107 , pp. 2452-2454
    • Weber, L.1    Wallbaum, S.2    Broger, C.3    Gubernator, K.4
  • 63
    • 77953631827 scopus 로고    scopus 로고
    • A medicinal chemist's guide to molecular interactions
    • Bissantz, C.; Kuhn, B.; Stahl, M. A Medicinal Chemist's Guide to Molecular Interactions. J. Med. Chem., 2010, 53, 5061-5084.
    • (2010) J. Med. Chem. , vol.53 , pp. 5061-5084
    • Bissantz, C.1    Kuhn, B.2    Stahl, M.3
  • 64
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands
    • Gohlke, H.; Klebe, G. Approaches to the description and prediction of the binding affinity of small-molecule ligands. Angew. Chem. Int. Ed. Engl., 2002, 41, 2644-2676.
    • (2002) Angew. Chem. Int. Ed. Engl. , vol.41 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 65
    • 40349087133 scopus 로고    scopus 로고
    • Towards the development of universal, fast and highly accurate docking/scoring methods: A long way to go
    • DOI 10.1038/sj.bjp.0707515, PII 0707515
    • Moitessier, N.; Englebienne, P.; Lee, D.; Lawandi, J.; Corbeil, C. R. Towards the development of universal, fast and highly accurate docking/scoring methods: a long way to go. Br. J. Clin. Pharmacol., 2008, 153, S7-S26. (Pubitemid 351340987)
    • (2008) British Journal of Pharmacology , vol.153 , Issue.SUPPL. 1
    • Moitessier, N.1    Englebienne, P.2    Lee, D.3    Lawandi, J.4    Corbeil, C.R.5
  • 66
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations
    • Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J. Chem. Inf. Model., 2011, 51, 69-82.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 67
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • DOI 10.1126/science.1096361
    • Jorgensen, W. L. The many roles of computation in drug discovery. Science, 2004, 303, 1813-1818. (Pubitemid 38374866)
    • (2004) Science , vol.303 , Issue.5665 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 68
    • 67649225348 scopus 로고    scopus 로고
    • Efficient drug lead discovery and optimization
    • Jorgensen, W. L. Efficient drug lead discovery and optimization. Acc. Chem. Res., 2009, 42, 724-33.
    • (2009) Acc. Chem. Res. , vol.42 , pp. 724-33
    • Jorgensen, W.L.1
  • 69
    • 77949345617 scopus 로고    scopus 로고
    • Quantum mechanical methods for drug design
    • Zhou, T.; Huang, D.; Caflisch, A. Quantum mechanical methods for drug design. Curr. Top. Med. Chem., 2010, 10, 33-45.
    • (2010) Curr. Top. Med. Chem. , vol.10 , pp. 33-45
    • Zhou, T.1    Huang, D.2    Caflisch, A.3
  • 70
  • 71
    • 34547670476 scopus 로고    scopus 로고
    • Evaluations of molecular docking programs for virtual screening
    • DOI 10.1021/ci7000378
    • Onodera, K.; Satou, K.; Hirota H. evaluations of molecular docking programs for virtual screening. J. Chem. Inf. Model., 2007, 47, 1609-1618. (Pubitemid 47210064)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.4 , pp. 1609-1618
    • Onodera, K.1    Satou, K.2    Hirota, H.3
  • 73
    • 67650097331 scopus 로고    scopus 로고
    • 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. Comparison of several molecular docking programs: pose prediction and virtual screening accuracy. J. Chem. Inf. Model. 2009, 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
  • 74
    • 33748667774 scopus 로고    scopus 로고
    • Consensus scoring for protein-ligand interactions
    • DOI 10.1016/j.drudis.2006.03.009, PII S1359644606000523
    • M. Feher. Consensus scoring for protein-ligand interactions. Drug Discovery Today, 2006, 11, 421-428. (Pubitemid 44382521)
    • (2006) Drug Discovery Today , vol.11 , Issue.9-10 , pp. 421-428
    • Feher, M.1
  • 75
    • 0035966871 scopus 로고    scopus 로고
    • Detailed analysis of scoring functions for virtual screening
    • DOI 10.1021/jm0003992
    • Stahl, M.; Rarey, M. Detailed analysis of scoring functions for virtual screening. J. Med. Chem., 2001, 44, 1035-1042. (Pubitemid 32852130)
    • (2001) Journal of Medicinal Chemistry , vol.44 , Issue.7 , pp. 1035-1042
    • Stahl, M.1    Rarey, M.2
  • 77
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol., 1996, 261, 470-489. (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 78
    • 0036137713 scopus 로고    scopus 로고
    • Automated docking to multiple target structures: Incorporation of protein mobility and structural water heterogeneity in autodock
    • DOI 10.1002/prot.10028
    • Osterberg, F.; Morris, G. M.; Sanner, M. F.; Olson, A. J.; Goodsell, D. S. Automated docking to multiple target structures: incorporation of protein mobility and structural water heterogeneity in AutoDock. Proteins: Struct. Funct. Genet., 2002, 46, 34-40. (Pubitemid 34033574)
    • (2002) Proteins: Structure, Function and Genetics , vol.46 , Issue.1 , pp. 34-40
    • Osterberg, F.1    Morris, G.M.2    Sanner, M.F.3    Olson, A.J.4    Goodsell, D.S.5
  • 79
    • 33846000313 scopus 로고    scopus 로고
    • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking
    • DOI 10.1002/prot.21214
    • Huang, S. Y.; Zou, X. Ensemble docking of multiple protein structures: considering protein structural variations in molecular docking. Proteins: Struct., Funct., Bioinf., 2007, 66, 399-421. (Pubitemid 46053470)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.2 , pp. 399-421
    • Huang, S.-Y.1    Zou, X.2
  • 80
    • 73949141783 scopus 로고    scopus 로고
    • An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics. J
    • Armen, R. S.; Chen, J.; Brooks, C. L. An evaluation of explicit receptor flexibility in molecular docking using molecular dynamics and torsion angle molecular dynamics. J. Chem. Theory Comput., 2009, 13, 2909-2923.
    • (2009) Chem. Theory Comput. , vol.13 , pp. 2909-2923
    • Armen, R.S.1    Chen, J.2    Brooks, C.L.3
  • 82
    • 18344382014 scopus 로고    scopus 로고
    • Comparative analysis of protein-bound ligand conformations with respect to catalyst's conformational space subsampling algorithms
    • DOI 10.1021/ci0497531
    • Kirchmair, J.; Laggner, C.; Wolber, G.; Langer, T. Comparative analysis of protein-bound ligand conformations with respect to Catalyst's conformational space subsampling algorithms. J. Chem. Inf. Model., 2005, 45, 422-430. (Pubitemid 40635351)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.2 , pp. 422-430
    • Kirchmair, J.1    Laggner, C.2    Wolber, G.3    Langer, T.4
  • 84
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • DOI 10.1006/jmbi.1996.0897
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and validation of a genetic algorithm for flexible docking. J. Mol. Biol., 1997, 267, 727-748. (Pubitemid 27170693)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.3 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 85
    • 84986522918 scopus 로고
    • 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. ICM - a new method for protein modeling and design: applications to docking and structure prediction from the distorted native conformation. J. Comput. Chem., 1994, 15, 488-506.
    • (1994) J. Comput. Chem. , vol.15 , pp. 488-506
    • Abagyan, R.1    Totrov, M.2    Kuznetsov, D.3
  • 86
    • 0035438402 scopus 로고    scopus 로고
    • How does consensus scoring work for virtual library screening? An idealized computer experiment
    • Wang, R.X.; Wang, S.M. How does consensus scoring work for virtual library screening? An idealized computer experiment. J. Chem. Inf. Comput. Sci., 2001, 41, 1422-1426.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1422-1426
    • Wang, R.X.1    Wang, S.M.2
  • 87
    • 0032226476 scopus 로고    scopus 로고
    • Development of filter functions for protein-ligand docking
    • DOI 10.1016/S1093-3263(98)00018-7, PII S1093326398000187
    • Stahl, M.; Bohm, H. J. Development of filter functions for proteinligand docking. J. Mol. Graph. Model., 1998, 16, 121-132. (Pubitemid 32250262)
    • (1998) Journal of Molecular Graphics and Modelling , vol.16 , Issue.3 , pp. 121-132
    • Stahl, M.1    Bohm, H.-J.2
  • 88
    • 0038282311 scopus 로고    scopus 로고
    • The role of absorption, distribution, metabolism, excretion and toxicity in drug discovery
    • Lin, J.; Sahakian, D. C.; Morais, S. M.; Xu, J. J.; Polzer, R. J.; Winter, S. M. The role of absorption, distribution, metabolism, excretion and toxicity in drug discovery. Curr. Top. Med. Chem., 2003, 3, 1125-1154.
    • (2003) Curr. Top. Med. Chem. , vol.3 , pp. 1125-1154
    • Lin, J.1    Sahakian, D.C.2    Morais, S.M.3    Xu, J.J.4    Polzer, R.J.5    Winter, S.M.6
  • 89
    • 0037364162 scopus 로고    scopus 로고
    • ADMET in silico modelling: Towards prediction paradise?
    • DOI 10.1038/nrd1032
    • Waterbeemd, H.; Gifford, E. ADMET in silico modelling: towards prediction paradise? Nat. Rev. Drug Discov., 2003, 2,192-204. (Pubitemid 37361664)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.3 , pp. 192-204
    • Van De Waterbeemd, H.1    Gifford, E.2
  • 91
    • 12244291911 scopus 로고    scopus 로고
    • Towards a new age of virtual ADME/TOX and multidimensional drug discovery
    • Ekins, S.; Boulanger, B.; Swaan, P. W.; Hupcey, M. A. Towards a new age of virtual ADME/TOX and multidimensional drug discovery. Mol. Divers. 2002, 5, 255-275.
    • (2002) Mol. Divers. , vol.5 , pp. 255-275
    • Ekins, S.1    Boulanger, B.2    Swaan, P.W.3    Hupcey, M.A.4
  • 92
    • 0036234783 scopus 로고    scopus 로고
    • High-throughput and in silico techniques in drug metabolism and pharmacokinetics
    • Waterbeemd, H. High throughput and in silico techniques in drug metabolism and pharmacokinetics. Curr. Opin. Drug Discov. Devel., 2002, 5, 33-43. (Pubitemid 34453240)
    • (2002) Current Opinion in Drug Discovery and Development , vol.5 , Issue.1 , pp. 33-43
    • Van De Waterbeemd, H.1
  • 93
    • 0141675105 scopus 로고    scopus 로고
    • Studies of the relative stability of TFA adducts vs non-TFA analogues for combinatorial chemistry library members in DMSO in a repository compound collection
    • Hochlowski, J.; Cheng, X.; Sauer, D.; Djuric, S. Studies of the relative stability of TFA adducts vs non-TFA analogues for combinatorial chemistry library members in DMSO in a repository compound collection. J. Comb. Chem., 2003, 5, 345-350.
    • (2003) J. Comb. Chem. , vol.5 , pp. 345-350
    • Hochlowski, J.1    Cheng, X.2    Sauer, D.3    Djuric, S.4
  • 95
    • 0031024171 scopus 로고    scopus 로고
    • Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings
    • DOI 10.1016/S0169-409X(96)00423-1, PII S0169409X96004231
    • 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. Deliv. Rev., 1997, 23, 3-25. (Pubitemid 27046991)
    • (1997) Advanced Drug Delivery Reviews , vol.23 , Issue.1-3 , pp. 3-25
    • Lipinski, C.A.1    Lombardo, F.2    Dominy, B.W.3    Feeney, P.J.4
  • 96
    • 33744796586 scopus 로고    scopus 로고
    • Active-site acidic residues and structural analysis of human aromatase: Molecular modeling study based on mammalian CYP 2 C
    • Murthy, J. N.; Nagaraju, M.; Sastry, G. M.; Rao, A. R.; Sastry, G. N. Active-site acidic residues and structural analysis of human aromatase: Molecular modeling study based on mammalian CYP 2 C. J. Comp. Mol. Design., 2005, 19, 857-870.
    • (2005) J. Comp. Mol. Design. , vol.19 , pp. 857-870
    • Murthy, J.N.1    Nagaraju, M.2    Sastry, G.M.3    Rao, A.R.4    Sastry, G.N.5
  • 98
    • 2942744554 scopus 로고    scopus 로고
    • Characterization of calcium and magnesium binding domains of human5- Lipoxygenase
    • Bindu, P. H.; Sastry, G. M.; Sastry, G. N. Characterization of calcium and magnesium binding domains of human5- Lipoxygenase. Biophysic. Biochem. Res. Commun., 2004, 320, 461-467.
    • (2004) Biophysic. Biochem. Res. Commun. , vol.320 , pp. 461-467
    • Bindu, P.H.1    Sastry, G.M.2    Sastry, G.N.3
  • 99
    • 27544493521 scopus 로고    scopus 로고
    • Structural and active site analysis of plasmepsins of Plasmodium falciparum: Potential anti-malarial targets
    • DOI 10.1016/j.ijbiomac.2005.08.006, PII S0141813005001820
    • Bhargavi, R.; Sastry, G. M.; Murty, U. S. N.; Sastry, G. N. Structural and active site analysis of plasmepsins of plasmodium falciiparum; Potential anti-malarial targets. Int. J. Biol. Macromol., 2005, 37, 73-84. (Pubitemid 41539677)
    • (2005) International Journal of Biological Macromolecules , vol.37 , Issue.1-2 , pp. 73-84
    • Bhargavi, R.1    Sastry, G.M.2    Murty, U.S.3    Sastry, G.N.4
  • 100
    • 2642531012 scopus 로고    scopus 로고
    • +-ATPase: A comparative protein modeling study
    • DOI 10.1016/j.bbrc.2004.05.006, PII S0006291X0400960X
    • Bindu, P. H.; Sastry, G. M.; Murty, U. S. N.; Sastry, G. N. Structural and Conformational Changes Concomitant with the E1- E2 transition in H+K+-ATPase: A comparative protein modeling study. Biophysic. Biochem. Res. Commun., 2004, 319, 312-320. (Pubitemid 38725948)
    • (2004) Biochemical and Biophysical Research Communications , vol.319 , Issue.2 , pp. 312-320
    • Bindu, P.H.1    Sastry, G.M.2    Murty, U.S.3    Sastry, G.N.4
  • 101
    • 79953177054 scopus 로고    scopus 로고
    • Comparison of computational methods to model DNA minor groove binders
    • Srivastava, H. K.; Chourasia, M.; Kumar, D.; Sastry, G. N. Comparison of computational methods to model DNA minor groove binders. J. Chem. Inf. Model., 2011, 51, 558-571.
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 558-571
    • Srivastava, H.K.1    Chourasia, M.2    Kumar, D.3    Sastry, G.N.4
  • 102
    • 33750330064 scopus 로고    scopus 로고
    • 2D and 3D quantitative structure-activity relationship studies on a series of bis-pyridinium compounds as choline kinase inhibitors
    • DOI 10.1002/qsar.200530199
    • Janardhan, S.; Srivani, P.; Sastry, G. N. 2D and 3D quantitative structure-activity relationship studies on a series of bis-pyridinium compounds as choline kinase inhibitors. QSAR & Comb. Sci., 2006, 25, 860-872. (Pubitemid 44621663)
    • (2006) QSAR and Combinatorial Science , vol.25 , Issue.10 , pp. 860-872
    • Janardhan, S.1    Srivani, P.2    Sastry, G.N.3
  • 103
    • 33645962844 scopus 로고    scopus 로고
    • Choline kinase: An important target for cancer
    • Janardhan, S.; Srivani, P.; Sastry, G. N. Choline kinase: An important target for cancer. Curr. Med Chem., 2006, 13, 1169-1186.
    • (2006) Curr. Med Chem. , vol.13 , pp. 1169-1186
    • Janardhan, S.1    Srivani, P.2    Sastry, G.N.3
  • 104
    • 0037032835 scopus 로고    scopus 로고
    • The protein kinase complement of the human genome
    • DOI 10.1126/science.1075762
    • Mannig, G.; Whyte, D. B.; Martinez, R.; Hunter, T.; Sudarsanam, S. The protein kinase complement of the human genome. Science, 2002, 298, 1912-1934. (Pubitemid 35425239)
    • (2002) Science , vol.298 , Issue.5600 , pp. 1912-1934
    • Manning, G.1    Whyte, D.B.2    Martinez, R.3    Hunter, T.4    Sudarsanam, S.5
  • 105
    • 1642323740 scopus 로고    scopus 로고
    • Protein kinase inhibitors: Insights into drug design from structure
    • DOI 10.1126/science.1095920
    • Noble, M. E. M.; Endicott, J.; Johnson, L. K. Protein kinase inhibitors: Insights into drug design from structure. Science, 2004, 303, 1800-1805. (Pubitemid 38374863)
    • (2004) Science , vol.303 , Issue.5665 , pp. 1800-1805
    • Noble, M.E.M.1    Endicott, J.A.2    Johnson, L.N.3
  • 106
    • 77649204688 scopus 로고    scopus 로고
    • Selectively nonselective kinase inhibition: Striking the right balance
    • Morphy, R. Selectively nonselective kinase inhibition: striking the right balance. J. Med. Chem., 2010, 53, 1413-1437.
    • (2010) J. Med. Chem. , vol.53 , pp. 1413-1437
    • Morphy, R.1
  • 107
    • 77949464598 scopus 로고    scopus 로고
    • Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro
    • Hendriks, B. S.; Seidl, K. M.; Chabot, J. R. Two additive mechanisms impair the differentiation of 'substrate-selective' p38 inhibitors from classical p38 inhibitors in vitro. BMC Syst. Biol., 2010, 4, 23.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 23
    • Hendriks, B.S.1    Seidl, K.M.2    Chabot, J.R.3
  • 108
    • 63749101636 scopus 로고    scopus 로고
    • Structural biology contributions to tyrosine kinase drug discovery
    • Cowan, J. S. W.; Meobitz, H.; Fabbro, D. Structural biology contributions to tyrosine kinase drug discovery. Curr. Opin. Cell Biol., 2009, 21, 280-287.
    • (2009) Curr. Opin. Cell Biol. , vol.21 , pp. 280-287
    • Cowan, J.S.W.1    Meobitz, H.2    Fabbro, D.3
  • 109
    • 5044236233 scopus 로고    scopus 로고
    • Sequence and structural analysis of kinase ATP pocket residues
    • DOI 10.1016/j.farmac.2004.05.010, PII S0014827X04001405
    • Vulpetti, A.; Bosotti, R. Sequence and structural analysis of kinase ATP pocket residues. Farmaco, 2004, 59, 759-765. (Pubitemid 39335946)
    • (2004) Farmaco , vol.59 , Issue.10 , pp. 759-765
    • Vulpetti, A.1    Bosotti, R.2
  • 110
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • DOI 10.1016/S0092-8674(02)00741-9
    • Huse, M.; Kuriyan, J. The conformational plasticity of protein kinases. Cell, 2002, 109, 275-282. (Pubitemid 34606870)
    • (2002) Cell , vol.109 , Issue.3 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 111
    • 0033026444 scopus 로고    scopus 로고
    • Strategies toward the design of novel and selective protein tyrosine kinase inhibitors
    • DOI 10.1016/S0163-7258(98)00044-8, PII S0163725898000448
    • Traxler, P.; Furet, P. Strategies toward the design of novel and selective protein tyrosine kinase inhibitors. Pharmacol. Ther. 1999, 82, 195-206. (Pubitemid 29255915)
    • (1999) Pharmacology and Therapeutics , vol.82 , Issue.2-3 , pp. 195-206
    • Traxler, P.1    Furet, P.2
  • 114
    • 33745740053 scopus 로고    scopus 로고
    • Novel targets for antiinflammatory and anti-arthritic agents
    • Ravindra, G. K.; Achaiah, G.; Sastry, G. N. Novel targets for antiinflammatory and anti-arthritic agents. Curr. Pharm. Design., 2006, 12, 2437-2454.
    • (2006) Curr. Pharm. Design. , vol.12 , pp. 2437-2454
    • Ravindra, G.K.1    Achaiah, G.2    Sastry, G.N.3
  • 115
    • 41249089027 scopus 로고    scopus 로고
    • Molecular modeling studies of phenoxypyrimidinyl imidazoles as p38 kinase inhibitors using QSAR and docking
    • DOI 10.1016/j.ejmech.2007.06.009, PII S0223523407002589
    • Ravindra, G. K.; Achaiah, G.; Sastry, G. N. Molecular modeling studies of phenoxypyrimidinyl imidazoles as p38 kinase inhibitors using QSAR and docking. Eur. J. Med. Chem., 2008, 43, 830-838. (Pubitemid 351446153)
    • (2008) European Journal of Medicinal Chemistry , vol.43 , Issue.4 , pp. 830-838
    • Ravindra, G.K.1    Achaiah, G.2    Sastry, G.N.3
  • 116
    • 77950573400 scopus 로고    scopus 로고
    • Through the "Gatekeeper door": Exploiting the active kinase conformation
    • Zuccotto, F.; Ardini, E.; Casale, E.; Angiolini, M. Through the "Gatekeeper door": exploiting the active kinase conformation. J. Med. Chem., 2010, 53, 2681-2694.
    • (2010) J. Med. Chem. , vol.53 , pp. 2681-2694
    • Zuccotto, F.1    Ardini, E.2    Casale, E.3    Angiolini, M.4
  • 126
    • 0036401042 scopus 로고    scopus 로고
    • Design and discovery of small molecules targeting Raf-1 kinase
    • DOI 10.2174/1381612023393125
    • Lowinger, T.B., Riedl, B., Dumas, J. & Smith, R.A. Design and discovery of small molecules targeting raf-1 kinase. Curr. Pharm. Des., 2002, 8, 2269-2278. (Pubitemid 35189900)
    • (2002) Current Pharmaceutical Design , vol.8 , Issue.25 , pp. 2269-2278
    • Lowinger, T.B.1    Riedl, B.2    Dumas, J.3    Smith, R.A.4
  • 127
    • 4644289313 scopus 로고    scopus 로고
    • A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): Relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells
    • DOI 10.1158/0008-5472.CAN-04-1168
    • Wood, E. R.; Truesdale, A. T.; McDonald, O. B.; Yuan, D.; Hassell, A.; Dickerson, S. H.; Ellis, B.; Pennisi, C.; Horne, E.; Lackey, K.; Alligood, K. J.; Rusnak, D. W.; Gilmer, T. M.; Shewchuk, L. A unique structure for epidermal growth factor receptor bound to GW572016 (Lapatinib): relationships among protein conformation, inhibitor off-rate, and receptor activity in tumor cells. Cancer Res., 2004, 64, 6652-6659. (Pubitemid 39297926)
    • (2004) Cancer Research , vol.64 , Issue.18 , pp. 6652-6659
    • Wood, E.R.1    Truesdale, A.T.2    McDonald, O.B.3    Yuan, D.4    Hassell, A.5    Dickerson, S.H.6    Ellis, B.7    Pennisi, C.8    Horne, E.9    Lackey, K.10    Alligood, K.J.11    Rusnak, D.W.12    Gilmer, T.M.13    Shewchuk, L.14
  • 128
    • 79952593846 scopus 로고    scopus 로고
    • Sequence structure, and active site analyses of p38 MAP kinase: Exploiting DFG-out conformation as a strategy to design new type II leads
    • Badrinarayan, P.; Sastry, G. N. Sequence, structure, and active site analyses of p38 MAP kinase: Exploiting DFG-out conformation as a strategy to design new type II leads. J. Chem. Inf. Model., 2010, 51, 115-129.
    • (2010) J. Chem. Inf. Model. , vol.51 , pp. 115-129
    • Badrinarayan, P.1    Sastry, G.N.2
  • 129
    • 0001074646 scopus 로고    scopus 로고
    • Subtypes of the type 4 cAMP phosphodiesterases: Structure, regulation and selective inhibition
    • DOI 10.1016/0165-6147(96)10035-3
    • Muller, T.; Engels, P.; Fozard, J. R. Subtypes of the type4 cAMP phosphodiesterase: Structure, regulation and selective inhibition. Trends Pharmacol. Sci., 1996, 17, 294-298. (Pubitemid 26261894)
    • (1996) Trends in Pharmacological Sciences , vol.17 , Issue.8 , pp. 294-298
    • Muller, T.1    Engels, P.2    Fozard, J.R.3
  • 131
    • 0036891154 scopus 로고    scopus 로고
    • 4D or not 4D - The emetogenic basis of PDE4 inhibitors uncovered?
    • Giembycz, M. A. 4D or not 4D the emetogenic basis of PDE4 inhibitors uncovered? Trends Pharmacol. Sci., 2002, 23, 548. (Pubitemid 35375796)
    • (2002) Trends in Pharmacological Sciences , vol.23 , Issue.12 , pp. 548
    • Giembycz, M.A.1
  • 132
    • 0001559662 scopus 로고
    • Fractionation and characterization of a cyclic adenine ribonucleotide formed by tissue particles
    • Sutherland, E. W.; Rall, T. W. Fractionation and characterization of a cyclic adenine ribonucleotide formed by tissue particles. J. Biol. Chem. 1958, 232, 1077-1091.
    • (1958) J. Biol. Chem. , vol.232 , pp. 1077-1091
    • Sutherland, E.W.1    Rall, T.W.2
  • 133
    • 33749059769 scopus 로고    scopus 로고
    • Profiling human phosphodiesterase genes and splice isoforms
    • Jonathan, B.; Sucha, S.; Subha, S. Profiling human phosphodiesterase genes and splice isoforms. Biochem. Biophys. Res. Comm., 2006, 350, 25-32.
    • (2006) Biochem. Biophys. Res. Comm. , vol.350 , pp. 25-32
    • Jonathan, B.1    Sucha, S.2    Subha, S.3
  • 134
    • 0028802726 scopus 로고
    • Cyclic nucleotide phosphodiesterases: Functional implications of multiple isoforms
    • Beavo, J. A. Cyclic nucleotide phosphodiesterases: functional implications of multiple isoforms. Physiol. Rev., 1995, 75, 725-48.
    • (1995) Physiol. Rev. , vol.75 , pp. 725-48
    • Beavo, J.A.1
  • 137
    • 33646924049 scopus 로고    scopus 로고
    • Are phosphodiesterase 4 inhibitors just more theophylline?
    • DOI 10.1016/j.jaci.2006.02.045, PII S0091674906006348
    • Boswell, S. V.; Cazzola, M.; Page, C. P. Are phosphodiesterase 4 inhibitors just more theophylline? J. Allergy Clin. Immunol., 2006, 117, 1237-43. (Pubitemid 43795733)
    • (2006) Journal of Allergy and Clinical Immunology , vol.117 , Issue.6 , pp. 1237-1243
    • Boswell-Smith, V.1    Cazzola, M.2    Page, C.P.3
  • 138
    • 0000203434 scopus 로고    scopus 로고
    • Phosphodiesterase 4 inhibitors, structurally unrelated to Rolipram, as promising agents for the treatment of asthma and other pathologies
    • DOI 10.1016/S0223-5234(00)00179-3
    • Piaz, D. V.; Giovannoni, M. P. Phosphodiesterase 4 inhibitors, structurally unrelated to rolipram, as promising agents for the treatment of asthma and other pathologies. Eur. J. Med. Chem., 2000, 35, 463-480. (Pubitemid 30395096)
    • (2000) European Journal of Medicinal Chemistry , vol.35 , Issue.5 , pp. 463-480
    • Dal Piaz, V.1    Giovannoni, M.P.2
  • 139
    • 0036265607 scopus 로고    scopus 로고
    • Recent advances in PDE4 inhibitors as immunoregulators and anti-inflammatory drugs
    • DOI 10.2174/1381612023394665
    • Burnouf, C.; Pruniaux, M. P. Recent advances in PDE4 inhibitors as immunoregulators and anti-inflammatory drugs. Curr. Pharm. Design, 2002, 8, 1255-1296. (Pubitemid 34594253)
    • (2002) Current Pharmaceutical Design , vol.8 , Issue.14 , pp. 1255-1296
    • Burnouf, C.1    Pruniaux, M.-P.2
  • 141
    • 0030925148 scopus 로고    scopus 로고
    • Proposal for pharmacologically distinct conformers of PDE4 cyclic AMP phosphodiesterases
    • DOI 10.1016/S0898-6568(96)00173-8, PII S0898656896001738
    • Souness, J. E.; Rao, S. Proposal for pharmacologically distinct conformers of PDE4 cyclic AMP phosphodiesterases. Cell Signal., 1997, 9, 227-236. (Pubitemid 27271642)
    • (1997) Cellular Signalling , vol.9 , Issue.3-4 , pp. 227-236
    • Souness, J.E.1    Rao, S.2
  • 144
    • 33646542713 scopus 로고    scopus 로고
    • Antidepressant-like effects of PDE4 inhibitors mediated by the high-affinity rolipram binding state (HARBS) of the phosphodiesterase-4 enzyme (PDE4) in rats
    • DOI 10.1007/s00213-006-0369-4
    • Zhang, H. T.; Zhao, Y.; Huang, Y.; Deng, C.; Hopper, A. T.; Vivo, M. D.; Rose, G. M.; O'Donnell, J. M. Antidepressant-like effects of PDE4 inhibitors mediated by the high-affinity rolipram binding state (HARBS) of the phosphodiesterase-4 enzyme (PDE4) in rats. Psychopharmacology, 2006, 186, 209-217. (Pubitemid 43727338)
    • (2006) Psychopharmacology , vol.186 , Issue.2 , pp. 209-217
    • Zhang, H.-T.1    Zhao, Y.2    Huang, Y.3    Deng, C.4    Hopper, A.T.5    De Vivo, M.6    Rose, G.M.7    O'Donnell, J.M.8
  • 145
    • 4444330207 scopus 로고    scopus 로고
    • The potential of PDE4 inhibitors in respiratory disease
    • Spina, D. The potential of PDE4 inhibitors in respiratory disease. Curr. Drug Targ. Inflamm. Allergy, 2004, 3, 231-246.
    • (2004) Curr. Drug Targ. Inflamm. Allergy , vol.3 , pp. 231-246
    • Spina, D.1
  • 147
    • 33644811309 scopus 로고    scopus 로고
    • Phosphodiesterase inhibitors in airways disease
    • Chung, K. F. Phosphodiesterase inhibitors in airways disease. Eur. J. Pharm., 2006, 533, 110-117.
    • (2006) Eur. J. Pharm. , vol.533 , pp. 110-117
    • Chung, K.F.1
  • 148
    • 33748620914 scopus 로고    scopus 로고
    • Effects of ciclamilast, a new PDE 4 PDE4 inhibitor, on airway hyperresponsiveness, PDE4D expression and airway inflammation in a murine model of asthma
    • DOI 10.1016/j.ejphar.2006.07.002, PII S001429990600700X
    • Deng, Y.; Qiang-min, X.; Hui-fang, T.; Jian-gang, S.; Jun-fang, D.; Ji-qiang, C.; Zhejiang, Y. S. Effects of ciclamilast, a new PDE4 inhibitor, on airway hyperresponsiveness, PDE4D expression and airway inflammation in a murine model of asthma. Eur. J. Pharm., 2006, 547, 125-135. (Pubitemid 44376758)
    • (2006) European Journal of Pharmacology , vol.547 , Issue.1-3 , pp. 125-135
    • Deng, Y.-m.1    Xie, Q.-m.2    Tang, H.-f.3    Sun, J.-g.4    Deng, J.-f.5    Chen, J.-q.6    Yang, S.-y.7
  • 149
  • 150
    • 0027454556 scopus 로고
    • A family of human phosphodiesterases homologous to the dunce learning and memory gene product of Drosophila melanogaster are potential targets for antidepressant drugs
    • Bolger, G.; Michaeli, T.; Martins, T.; St. John, T.; Steiner, B.; Rodgers, L.; Riggs, M.; Wigler, M.; Ferguson, K. A family of human phosphodiesterases homologous to the dunce learning and memory gene product of Drosophila melanogaster is potential targets for antidepressant drugs. Mol. Cell. Biol., 1993, 13, 6558-6571. (Pubitemid 23292650)
    • (1993) Molecular and Cellular Biology , vol.13 , Issue.10 , pp. 6558-6571
    • Bolger, G.1    Michaeli, T.2    Martins, T.3    St. John, T.4    Steiner, B.5    Rodgers, L.6    Riggs, M.7    Wigler, M.8    Ferguson, K.9
  • 152
    • 0030665303 scopus 로고    scopus 로고
    • Characterization of five different proteins produced by alternatively spliced mRNAs from the human cAMP-specific phosphodiesterase PDE4D gene
    • Bolger, G. B.; Erdogan, S.; Jones, R. E.; Loughney, K.; Scotland, G.; Hoffmann, R.; Wilkinson, I.; Farrell, C.; Houslay, M. D. Characterization of five different proteins produced by alternatively spliced mRNAs from the human cAMP-specific phosphodiesterase PDE4D gene. Biochem. J., 1997, 328, 539-548. (Pubitemid 27515598)
    • (1997) Biochemical Journal , vol.328 , Issue.2 , pp. 539-548
    • Bolger, G.B.1    Erdogan, S.2    Jones, R.E.3    Loughney, K.4    Scotland, G.5    Hoffmann, R.6    Wilkinson, I.7    Farrell, C.8    Houslay, M.D.9
  • 153
  • 154
    • 34249097646 scopus 로고    scopus 로고
    • The mechanism of cyclic nucleotide hydrolysis in the phosphodiesterase catalytic site
    • DOI 10.1021/jp066582
    • Salter, E. A.; Wierzbicki, A. The mechanism of cyclic nucleotide hydrolysis in the phosphodiesterase catalytic site. J. Phy. Chem. B., 2007, 111, 4547-4552. (Pubitemid 46787651)
    • (2007) Journal of Physical Chemistry B , vol.111 , Issue.17 , pp. 4547-4552
    • Salter, E.A.1    Wierzbicki, A.2
  • 156
    • 33748474414 scopus 로고    scopus 로고
    • Characterization of a catalytic ligand bridging metal ions in phosphodiesterases 4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations
    • DOI 10.1529/biophysj.106.086835
    • Xiong, Y.; Lu, H-T.; Li, Y.; Yang, G. F.; Zhan, C. G. Characterization of a catalytic ligand bridging metal ions in PDE4 and 5 by molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical calculations. Biophys. J., 2006, 91, 1858-1867. (Pubitemid 44352449)
    • (2006) Biophysical Journal , vol.91 , Issue.5 , pp. 1858-1867
    • Xiong, Y.1    Lu, H.-T.2    Li, Y.3    Yang, G.-F.4    Zhan, C.-G.5
  • 157
    • 33748534489 scopus 로고    scopus 로고
    • Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations
    • DOI 10.1080/08927020600717111, PII N0548742PW628535
    • Kang, N. S.; Chae, C. H.; Yoo, S. E. Study on the hydrolysis mechanism of phosphodiesterase 4 using molecular dynamics simulations. Mol. Simul., 2006, 32, 369-374. (Pubitemid 44371348)
    • (2006) Molecular Simulation , vol.32 , Issue.5 , pp. 369-374
    • Kang, N.S.1    Chae, C.H.2    Yoo, S.-E.3
  • 159
    • 61449112246 scopus 로고    scopus 로고
    • Subtype selectivity in phosphodiesterase 4 (PDE4): A bottleneck in rational drug design
    • Srivani, P.; Usharani, D.; Jemmis, E. D.; Sastry, G. N. Subtype selectivity in phosphodiesterase 4 (PDE4): a bottleneck in rational drug design. Curr. Pharma. Design, 2008, 14, 3854-3872.
    • (2008) Curr. Pharma. Design , vol.14 , pp. 3854-3872
    • Srivani, P.1    Usharani, D.2    Jemmis, E.D.3    Sastry, G.N.4
  • 160
    • 58149114921 scopus 로고    scopus 로고
    • A pH dependence of 310-helix versus turn in m-loop region of PDE4: Observations on PDB entries and an electronic structure study
    • Usharani, D.; Srivani, P.; Sastry, G. N.; Jemmis, E. D. A pH dependence of 310-helix versus turn in m-loop region of PDE4: Observations on PDB entries and an electronic structure study. J. Chem. Theory Comput., 2008, 4, 974-984.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 974-984
    • Usharani, D.1    Srivani, P.2    Sastry, G.N.3    Jemmis, E.D.4
  • 161
    • 33750898596 scopus 로고    scopus 로고
    • Comprehensive theoretical study towards the accurate proton affinity values of naturally occurring amino acids
    • DOI 10.1002/qua.21117
    • Dinadayalane, T. C.; Sastry, G. N.; Leszczynski, J. Comprehensive theoretical study towards the accurate proton affinity values of naturally occurring amino acids. Int. J. Quant. Chem., 2006, 106, 2920-2933. (Pubitemid 44726730)
    • (2006) International Journal of Quantum Chemistry , vol.106 , Issue.14 , pp. 2920-2933
    • Dinadayalane, T.C.1    Sastry, G.N.2    Leszczynski, J.3
  • 162
    • 79957944746 scopus 로고    scopus 로고
    • Design of 1- arylsulfamido-2-alkylpiperazine derivatives as secreted PLA2 inhibitors
    • DOI: 10.1007/s00894-010-0752-2
    • Badrinarayan, P.; Srivani, P.; Sastry, G. N. Design of 1- arylsulfamido-2-alkylpiperazine derivatives as secreted PLA2 inhibitors. J Mol. Model., 2010, DOI: 10.1007/s00894-010-0752-2.
    • (2010) J Mol. Model.
    • Badrinarayan, P.1    Srivani, P.2    Sastry, G.N.3
  • 164
    • 34047158651 scopus 로고    scopus 로고
    • Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: A molecular modeling study
    • DOI 10.1007/s10822-006-9092-9
    • Kulkarni, G. K.; Srivani, P.; Achiah, G.; Sastry, G. N. Strategies to design pyrazolyl urea derivatives for p38 kinase inhibition: A molecular modeling study. J. Comp. -Aided Mol. Des., 2007, 21, 155-166. (Pubitemid 46510841)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.4 , pp. 155-166
    • Kulkarni, R.G.1    Srivani, P.2    Achaiah, G.3    Sastry, G.N.4
  • 165
    • 34347257750 scopus 로고    scopus 로고
    • Molecular modeling studies of pyridopurinone derivatives-Potential phosphodiesterase 5 inhibitors
    • DOI 10.1016/j.jmgm.2007.01.007, PII S1093326307000083
    • Srivani, P.; Srinivas, E.; Raghu, R.; Sastry, G. N. Molecular modeling studies of pyridopurinone derivatives - Potential phosphodiesterase5 inhibitors. J. Mol. Graphics Modell., 2007, 26, 378-390. (Pubitemid 46992725)
    • (2007) Journal of Molecular Graphics and Modelling , vol.26 , Issue.1 , pp. 378-390
    • Srivani, P.1    Srinivas, E.2    Raghu, R.3    Sastry, G.N.4
  • 167
    • 0035800032 scopus 로고    scopus 로고
    • Advances in determination of a high-resolution three-dimensional structure of rhodopsin, a model of G-protein-coupled receptors (GPCRs)
    • DOI 10.1021/bi0155091
    • Teller, D. C.; Okada, T.; Behnke, C. A.; Palczewski, K.; Stenkamp, R. E. Advances in determination of a high-resolution threedimensional structure of rhodopsin, a model of G-proteincoupled receptors (GPCRs). Biochemistry, 2001, 40, 7761-7772. (Pubitemid 32622966)
    • (2001) Biochemistry , vol.40 , Issue.26 , pp. 7761-7772
    • Teller, D.C.1    Okada, T.2    Behnke, C.A.3    Palczewski, K.4    Stenkamp, R.E.5
  • 173
    • 47049130668 scopus 로고    scopus 로고
    • Crystal structure of the ligand-free G-protein-coupled receptor opsin
    • DOI 10.1038/nature07063, PII NATURE07063
    • Park, J. H.; Scheerer, P.; Hofmann, K. P.; Choe, H. W.; Ernst, O. P. Crystal structure of the ligand-free G-protein-coupled receptor opsin. Nature, 2008, 454, 183-187. (Pubitemid 351969893)
    • (2008) Nature , vol.454 , Issue.7201 , pp. 183-187
    • Park, J.H.1    Scheerer, P.2    Hofmann, K.P.3    Choe, H.-W.4    Ernst, O.P.5
  • 175
    • 0037235663 scopus 로고    scopus 로고
    • Protein-based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets?
    • DOI 10.1002/prot.10237
    • Bissantz, C.; Bernard, P.; Hibert, M.; Rognan, D. Protein based virtual screening of chemical databases. II. Are homology models of G-protein coupled receptors suitable targets? Proteins, 2003, 50, 5-25. (Pubitemid 36090604)
    • (2003) Proteins: Structure, Function and Genetics , vol.50 , Issue.1 , pp. 5-25
    • Bissantz, C.1    Bernard, P.2    Hibert, M.3    Rognan, D.4
  • 176
    • 23944454816 scopus 로고    scopus 로고
    • Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols
    • DOI 10.1021/jm050090o
    • Evers, A.; Hessler, G.; Matter, H.; Klabunde, T. Virtual screening of biogenic amine-binding G-protein coupled receptors: Comparative evaluation of protein- and ligand-based virtual screening protocols. J. Med. Chem., 2005, 48, 5448-5465. (Pubitemid 41209243)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.17 , pp. 5448-5465
    • Evers, A.1    Hessler, G.2    Matter, H.3    Klabunde, T.4
  • 177
    • 33646526072 scopus 로고    scopus 로고
    • I want a new drug: G-protein-coupled receptors in drug development
    • Schlyer, S.; Horuk, R. I want a new drug: G-protein-coupled receptors in drug development. Drug Discov. Today, 2006, 11, 481-493.
    • (2006) Drug Discov. Today , vol.11 , pp. 481-493
    • Schlyer, S.1    Horuk, R.2
  • 178
    • 33744551693 scopus 로고    scopus 로고
    • Structure-based virtual screening of chemical libraries for drug discovery
    • DOI 10.1016/j.cbpa.2006.04.002, PII S1367593106000536
    • Ghosh, S.; Nie, A.; An, J.; Z. Huang. Structure-based virtual screening of chemical libraries for drug discovery. Curr. Opin. Chem. Biol., 2006, 10,194-202. (Pubitemid 43815778)
    • (2006) Current Opinion in Chemical Biology , vol.10 , Issue.3 , pp. 194-202
    • Ghosh, S.1    Nie, A.2    An, J.3    Huang, Z.4
  • 179
    • 33745199815 scopus 로고    scopus 로고
    • Virtual ligand screening: Strategies, perspectives and limitations
    • Klebe, G. Virtual ligand screening: Strategies, perspectives and limitations. Drug Discov. Today, 2006, 11, 580-594.
    • (2006) Drug Discov. Today , vol.11 , pp. 580-594
    • Klebe, G.1
  • 180
    • 51849091933 scopus 로고    scopus 로고
    • Modulating G-protein coupled receptor/G-protein signal transduction by small molecules suggested by virtual screening
    • Taylor, C. M.; Barda, Y.; Kisselev, O. G.; Marshall, G. R. Modulating G-protein coupled receptor/G-protein signal transduction by small molecules suggested by virtual screening. J. Med. Chem., 2008, 51, 5297-5303.
    • (2008) J. Med. Chem. , vol.51 , pp. 5297-5303
    • Taylor, C.M.1    Barda, Y.2    Kisselev, O.G.3    Marshall, G.R.4
  • 181
    • 84889844714 scopus 로고    scopus 로고
    • Success stories of computer-aided design
    • Ekins, S. Ed.; [Wiley Series in Drug Discovery and Development (Wang, B. Ed.)], Wiley-Interscience
    • Kubinyi, H. Success Stories of Computer-Aided Design, In: Computer Applications in Pharmaceutical Research and Development, Ekins, S. Ed.; [Wiley Series in Drug Discovery and Development (Wang, B. Ed.)], Wiley-Interscience, 2006, 377-424.
    • (2006) Computer Applications in Pharmaceutical Research and Development , pp. 377-424
    • Kubinyi, H.1
  • 182
    • 33645658325 scopus 로고    scopus 로고
    • Determination and mapping of activityspecific descriptor value ranges (MAD) for the identification of active compounds
    • Eckert, H.; Bajorath, J. Determination and mapping of activityspecific descriptor value ranges (MAD) for the identification of active compounds. J. Med. Chem., 2006, 49, 2284-2293.
    • (2006) J. Med. Chem. , vol.49 , pp. 2284-2293
    • Eckert, H.1    Bajorath, J.2
  • 183
    • 1842679452 scopus 로고    scopus 로고
    • Molecular similarity analysis and virtual screening in binarytransformed chemical descriptor spaces with variable dimensionality
    • Godden, J. W.; Furr, J. R.; Xue, L.; Stahura, F. L.; Bajorath, J. Molecular similarity analysis and virtual screening in binarytransformed chemical descriptor spaces with variable dimensionality. J. Chem. Inf. Comput. Sci., 2004, 44, 21-29.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 21-29
    • Godden, J.W.1    Furr, J.R.2    Xue, L.3    Stahura, F.L.4    Bajorath, J.5
  • 184
    • 7444270927 scopus 로고    scopus 로고
    • POT-DMC: A virtual screening method for the identification of potent hits
    • DOI 10.1021/jm049505g
    • Godden, J. W.; Furr, J. R.; Stahura, F. L.; Bajorath, J. POT-DMC: a virtual screening method for the identification of potent hits. J. Med. Chem., 2004, 47, 5608-5611. (Pubitemid 39447256)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.23 , pp. 5608-5611
    • Godden, J.W.1    Stahura, F.L.2    Bajorathj, J.3
  • 185
    • 33746883889 scopus 로고    scopus 로고
    • Mapping algorithms for molecular similarity analysis and ligand-based virtual screening: Design of DynaMAD and comparison with MAD and DMC
    • DOI 10.1021/ci060083o
    • Eckert, H.; Vogt, I.; Bajorath, J. Mapping algorithms for molecular similarity analysis and ligand-based virtual screening: design of DynaMAD and comparison with MAD and DMC. J. Chem. Inf. Model., 2006, 46, 1623-1634. (Pubitemid 44185689)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.4 , pp. 1623-1634
    • Eckert, H.1    Vogt, I.2    Bajorath, J.3
  • 186
    • 33745343573 scopus 로고    scopus 로고
    • A distance function for retrieval of active molecules from complex chemical space representations
    • DOI 10.1021/ci050510i
    • Godden, J.W.; Bajorath, J. A distance function for retrieval of active molecules from complex chemical space representations. J. Chem. Inf. Model.; 2006, 46, 1094-1097. (Pubitemid 43999154)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.3 , pp. 1094-1097
    • Godden, J.W.1    Bajorath, J.2
  • 187
    • 80054911315 scopus 로고    scopus 로고
    • Bayesian interpretation of a distance function for navigating high-dimensional descriptor spaces
    • Vogt, M.; Godden, J. W.; Bajorath, J. Bayesian interpretation of a distance function for navigating high-dimensional descriptor spaces. J. Chem. Inf. Model., 2007, 38, 1522-2667.
    • (2007) J. Chem. Inf. Model. , vol.38 , pp. 1522-2667
    • Vogt, M.1    Godden, J.W.2    Bajorath, J.3
  • 188
    • 21244468757 scopus 로고    scopus 로고
    • Searching techniques for databases of two- and three-dimensional chemical structures
    • DOI 10.1021/jm0582165
    • Willett, P. Searching techniques for databases of two- and threedimensional chemical structures. J. Med. Chem., 2005, 48, 4183-4199. (Pubitemid 40884919)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.13 , pp. 4183-4199
    • Willett, P.1
  • 190
    • 0035438388 scopus 로고    scopus 로고
    • Prediction of biological activity for high throughput screening using binary kernel discrimination
    • Harper, G.; Bradshaw, J.; Gittins, J. C.; Green, D. V.; Leach, A. R. Prediction of biological activity for high throughput screening using binary kernel discrimination. J. Chem. Inf. Comput. Sci., 2001, 41, 1295-1300.
    • (2001) J. Chem. Inf. Comput. Sci. , vol.41 , pp. 1295-1300
    • Harper, G.1    Bradshaw, J.2    Gittins, J.C.3    Green, D.V.4    Leach, A.R.5
  • 192
    • 20444410410 scopus 로고    scopus 로고
    • Virtual screening of molecular databases using a support vector machine
    • DOI 10.1021/ci049641u
    • Jorissen, R.N.; Gilson, M.K. Virtual screening of molecular databases using a support vector machine. J. Chem. Inf. Model., 2005, 45, 549-561. (Pubitemid 40795161)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.3 , pp. 549-561
    • Jorissen, R.N.1    Gilson, M.K.2
  • 194
    • 5544290537 scopus 로고    scopus 로고
    • Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): Evaluation of performance
    • Bender, A.; Mussa, H. Y.; Glen, R. C. Similarity searching of chemical databases using atom environment descriptors (MOLPRINT 2D): evaluation of performance. J. Chem. Inf. Comput. Sci., 2004, 44, 1708-1718.
    • (2004) J. Chem. Inf. Comput. Sci. , vol.44 , pp. 1708-1718
    • Bender, A.1    Mussa, H.Y.2    Glen, R.C.3
  • 195
    • 33845775349 scopus 로고    scopus 로고
    • Design and evaluation of a novel class-directed 2D fingerprint to search for structurally diverse active compounds
    • DOI 10.1021/ci600303b
    • Eckert, H.; Bajorath, J. Design and evaluation of a novel classdirected 2D fingerprint to search for structurally diverse active compounds. J. Chem. Inf. Model., 2006, 46, 2515-2526. (Pubitemid 46008123)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2515-2526
    • Eckert, H.1    Bajorath, J.2
  • 198
    • 33750986884 scopus 로고    scopus 로고
    • "Bayes affinity fingerprints" Improve retrieval rates in virtual screening and define orthogonal bioactivity space: When are multitarget drugs a feasible concept?
    • DOI 10.1021/ci600197y
    • Bender, A.; Jenkins, J. L.; Glick, M.; Deng, Z.; Nettles, J. H.; Davies, J. W. Bayes affinity fingerprints'' improve retrieval rates in virtual screening and define orthogonal bioactivity space: when are multitarget drugs a feasible concept? J. Chem. Inf. Model., 2006, 46, 2445-2456. (Pubitemid 46008117)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.6 , pp. 2445-2456
    • Bender, A.1    Jenkins, J.L.2    Glick, M.3    Zhan, D.4    Nettles, J.H.5    Davies, J.W.6
  • 200
    • 33750381015 scopus 로고    scopus 로고
    • Assessment of molecular similarity from the analysis of randomly generated structural fragment populations
    • DOI 10.1021/ci0601261
    • Batista, J.; Godden, J. W.; Bajorath J. Assessment of molecular similarity from the analysis of randomly generated structural fragment populations. J. Chem. Inf. Model., 2006, 46, 1937-1944. (Pubitemid 44625965)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.5 , pp. 1937-1944
    • Batista, J.1    Godden, J.W.2    Bajorath, J.3
  • 201
    • 33846881583 scopus 로고    scopus 로고
    • Chemical database mining through entropy-based molecular similarity assessment of randomly generated structural fragment populations
    • DOI 10.1021/ci600377m
    • Batista, J.; Bajorath, J. Chemical database mining through entropybased molecular similarity assessment of randomly generated structural fragment populations. J. Chem. Inf. Model., 2007, 47, 59-68. (Pubitemid 46225560)
    • (2007) Journal of Chemical Information and Modeling , vol.47 , Issue.1 , pp. 59-68
    • Batista, J.1    Bajorath, J.2
  • 203
    • 14944348527 scopus 로고    scopus 로고
    • A shape-based 3-D scaffold hopping method and its application to a bacterial protein-protein interaction
    • DOI 10.1021/jm040163o
    • Rush III, T. S.; Grant, J. A.; Mosyak, L.; Nicholls, A. A shapebased 3D scaffold hopping method and its application to a bacterial protein-protein interaction. J. Med. Chem., 2005, 48, 1489-1495. (Pubitemid 40364556)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.5 , pp. 1489-1495
    • Rush III, T.S.1    Grant, J.A.2    Mosyak, L.3    Nicholls, A.4
  • 204
    • 0346962971 scopus 로고    scopus 로고
    • Structural Interaction Fingerprint (SIFt): A Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions
    • DOI 10.1021/jm030331x
    • Deng, Z.; Chuaqui, C.; Singh, J. Structural interaction fingerprint (SIFt): A novel method for analyzing three-dimensional proteinligand binding interactions. J. Med. Chem., 2004, 47, 337-344. (Pubitemid 38057878)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.2 , pp. 337-344
    • Deng, Z.1    Chuaqui, C.2    Singh, J.3
  • 205
    • 66249123260 scopus 로고    scopus 로고
    • APIF: A new Interaction fingerprint based on atom pairs and its application to virtual screening
    • Prez-Nueno, V. I.; Rabal, O.; Borrell, J. I.; Teixid, J.APIF: A new Interaction fingerprint based on atom pairs and its application to virtual screening. J. Chem. Inf. Model., 2009, 49, 1245-1260.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1245-1260
    • Prez-Nueno, V.I.1    Rabal, O.2    Borrell, J.I.3    Teixid, J.4
  • 206
    • 75749126524 scopus 로고    scopus 로고
    • Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening
    • Sato, T.; Honma, T.; Yokoyama, S. Combining machine learning and pharmacophore-based interaction fingerprint for in silico screening. J. Chem. Inf. Model., 2010, 50, 170-185.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 170-185
    • Sato, T.1    Honma, T.2    Yokoyama, S.3
  • 207
    • 4544367743 scopus 로고    scopus 로고
    • Comparative evaluation of eight docking tools for docking and virtual screening accuracy
    • DOI 10.1002/prot.20149
    • Kellenberger, E.; Rodrigo, J.; Muller, P.; Rognan, D. Comparative evaluation of eight docking tools for docking and virtual screening accuracy. Proteins, 2004, 57, 225-242. (Pubitemid 39223729)
    • (2004) Proteins: Structure, Function and Genetics , vol.57 , Issue.2 , pp. 225-242
    • Kellenberger, E.1    Rodrigo, J.2    Muller, P.3    Rognan, D.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.