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Volumn 26, Issue 1, 2012, Pages 137-150

Drug design for ever, from hype to hope

Author keywords

Drug design; G protein coupled receptors; Protein modeling; QSAR; Review; Translational research

Indexed keywords

COMPUTATIONAL CHEMISTRY; GENETIC ALGORITHMS; INDUSTRIAL RESEARCH; PROTEINS;

EID: 84857456514     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9519-9     Document Type: Review
Times cited : (36)

References (225)
  • 1
    • 34547619148 scopus 로고    scopus 로고
    • Accessed 6 Dec 2011
    • Life expectancy (2011) http://en.wikipedia.org/wiki/Life-expectancy. Accessed 6 Dec 2011
    • (2011) Life Expectancy
  • 2
    • 85053097521 scopus 로고    scopus 로고
    • Accessed 6 Dec 2011
    • World War I casualties (2011) http://en.wikipedia.org/wiki/World-War-I- casualties. Accessed 6 Dec 2011
    • (2011) World War i Casualties
  • 3
    • 84857457215 scopus 로고    scopus 로고
    • Medecine and World War II (2011) http://www.historylearningsite.co.uk/ medicine-and-world-war-two.htm. Accessed 16 Feb 2011
    • (2011) Medecine and World War II
  • 4
    • 0022421903 scopus 로고
    • How many medicines are there?
    • 1:STN:280:DyaL2M7itlOisg%3D%3D
    • ES Snell JP Griffin 1985 How many medicines are there? Br Med J 290 773 774 1:STN:280:DyaL2M7itlOisg%3D%3D
    • (1985) Br Med J , vol.290 , pp. 773-774
    • Snell, E.S.1    Griffin, J.P.2
  • 7
    • 73449101512 scopus 로고    scopus 로고
    • Lessons from 60 years of pharmaceutical innovation
    • doi: 10.1038/nrd2961
    • Munos B (2009) Lessons from 60 years of pharmaceutical innovation. Nat Rev Drug Discov. doi: 10.1038/nrd2961
    • (2009) Nat Rev Drug Discov.
    • Munos, B.1
  • 8
    • 84857456551 scopus 로고    scopus 로고
    • Troubled Asset Relief Program Accessed 6 Dec 2011
    • Troubled Asset Relief Program (2011) http://en.wikipedia.org/wiki/ Troubled-Asset-Relief-Program. Accessed 6 Dec 2011
    • (2011)
  • 9
    • 82455167799 scopus 로고    scopus 로고
    • Lessons from 54 years of pharmaceutical research
    • doi: 10.1038/nrd2961-c1
    • Firestone RA (2011) Lessons from 54 years of pharmaceutical research Nat Rev Drug Discov. doi: 10.1038/nrd2961-c1
    • (2011) Nat Rev Drug Discov.
    • Firestone, R.A.1
  • 11
    • 0345548661 scopus 로고    scopus 로고
    • Comparison of support vector machine and artificial neural network systems for drug/nondrug classification
    • 1:CAS:528:DC%2BD3sXns1Wmt74%3D
    • E Byvatov U Fechner J Sadowski G Schneider 2003 Comparison of support vector machine and artificial neural network systems for drug/nondrug classification J Chem Inf Comput Sci 43 1882 1889 1:CAS:528:DC%2BD3sXns1Wmt74%3D
    • (2003) J Chem Inf Comput Sci , vol.43 , pp. 1882-1889
    • Byvatov, E.1    Fechner, U.2    Sadowski, J.3    Schneider, G.4
  • 12
    • 38949213691 scopus 로고    scopus 로고
    • The cost of pushing pills: A new estimate of pharmaceutical promotion expenditures in the United States
    • DOI 10.1371/journal.pmed.0050001
    • Gagnon MA, Lexchin J (2008) The cost of pushing pills: a new estimate of pharmaceutical promotion expenditures in the United States. PLoS Med. doi: 10.1371/journal.pmed.0050001 (Pubitemid 351216978)
    • (2008) PLoS Medicine , vol.5 , Issue.1 , pp. 0029-0033
    • Gagnon, M.-A.1    Lexchin, J.2
  • 13
    • 0022785324 scopus 로고
    • Protein crystallography and computer graphics - Toward rational drug design
    • DOI 10.1002/anie.198607673
    • WGJ Hol 1986 Protein crystallography and computer-graphics toward rational drug design Angew Chem Int Ed Engl 25 767 778 (Pubitemid 17188759)
    • (1986) Angewandte Chemie - International Edition in English , vol.25 , Issue.9 , pp. 767-778
    • Hol, W.G.J.1
  • 14
    • 0020442184 scopus 로고
    • Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 Aθ resolution. II. Environment of bound NADPH and implications for catalysis
    • JT Bolin DJ Filman DA Matthews RC Hamlin J Kraut 1982 Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate J Biol Chem 257 13663 13672 (Pubitemid 13187128)
    • (1982) Journal of Biological Chemistry , vol.257 , Issue.22 , pp. 13663-13672
    • Filman, D.J.1    Bolin, J.T.2    Matthews, D.A.3    Kraut, J.4
  • 16
    • 0027581690 scopus 로고
    • QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues
    • 1:CAS:528:DyaK3sXlslemu7w%3D
    • J Ruiz M López J Milà E Lozoya JJ Lozano R Pouplana 1993 QSAR and conformational analysis of the antiinflammatory agent amfenac and analogues J Comput Aided Mol Des 7 183 198 1:CAS:528:DyaK3sXlslemu7w%3D
    • (1993) J Comput Aided Mol des , vol.7 , pp. 183-198
    • Ruiz, J.1    López, M.2    Milà, J.3    Lozoya, E.4    Lozano, J.J.5    Pouplana, R.6
  • 17
    • 0027581780 scopus 로고
    • SCF-MO study of the polyglycine II structure
    • 1:CAS:528:DyaK3sXmtVersb0%3D
    • C Aleman JJ Perez 1993 SCF-MO study of the polyglycine II structure J Comput Aided Mol Des 7 2 241 250 1:CAS:528:DyaK3sXmtVersb0%3D
    • (1993) J Comput Aided Mol des , vol.7 , Issue.2 , pp. 241-250
    • Aleman, C.1    Perez, J.J.2
  • 18
    • 0029283555 scopus 로고
    • Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide
    • 1:CAS:528:DyaK2MXltF2kt70%3D
    • H Oyasu I Nakanishi A Tanaka K Murano M Matsuo 1995 Conformational studies on the four stereoisomers of the novel anticholinergic 4-(dimethylamino)-2-phenyl-2-(2-pyridyl)pentanamide J Comput Aided Mol Des 9 171 180 1:CAS:528:DyaK2MXltF2kt70%3D
    • (1995) J Comput Aided Mol des , vol.9 , pp. 171-180
    • Oyasu, H.1    Nakanishi, I.2    Tanaka, A.3    Murano, K.4    Matsuo, M.5
  • 19
    • 0033963034 scopus 로고    scopus 로고
    • Molden: A pre- and post-processing program for molecular and electronic structures
    • DOI 10.1023/A:1008193805436
    • G Schaftenaar JH Noordik 2000 Molden: a pre- and post-processing program for molecular and electronic structures J Comput Aided Mol Des 14 123 134 1:CAS:528:DC%2BD3cXhslant7c%3D (Pubitemid 30110670)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.2 , pp. 123-134
    • Schaftenaar, G.1    Noordik, J.H.2
  • 20
    • 0346888553 scopus 로고    scopus 로고
    • Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10
    • DOI 10.1023/B:JCAM.0000005765.13637.38
    • S Manzetti DR McCulloch AC Herington D van der Spoel 2003 Modeling of enzyme-substrate complexes for the metalloproteases MMP-3, ADAM-9 and ADAM-10 J Comput Aided Mol Des 17 551 565 1:CAS:528:DC%2BD3sXptlGltbg%3D (Pubitemid 38008784)
    • (2003) Journal of Computer-Aided Molecular Design , vol.17 , Issue.9 , pp. 551-565
    • Manzetti, S.1    McCulloch, D.R.2    Herington, A.C.3    Van Der Spoel, D.4
  • 21
    • 4344700440 scopus 로고    scopus 로고
    • Solvent effect on the synthesis of clarithromycin: A molecular dynamics study
    • DOI 10.1023/B:jcam.0000030037.67742.cb
    • D Duran V Aviyente C Baysa 2004 Solvent effect on the synthesis of clarithromycin: a molecular dynamics study J Comput Aided Mol Des 18 145 154 1:CAS:528:DC%2BD2cXmtFGrt74%3D (Pubitemid 39137452)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.2 , pp. 145-154
    • Duran, D.1    Aviyente, V.2    Baysal, C.3
  • 22
    • 22144485942 scopus 로고    scopus 로고
    • Enhancing the accuracy of virtual screening: Molecular dynamics with quantum-refined force fields
    • DOI 10.1007/s10822-004-7881-6
    • A Curioni T Mordasini W Andreoni 2004 Enhancing the accuracy of virtual screening: molecular dynamics with quantum-refined force fields J Comput Aided Mol Des 18 773 784 1:CAS:528:DC%2BD2MXls1Smtro%3D (Pubitemid 40973866)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.12 , pp. 773-784
    • Curioni, A.1    Mordasini, T.2    Andreoni, W.3
  • 23
    • 20344385304 scopus 로고    scopus 로고
    • Protonation-induced stereoisomerism in nicotine: Conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics
    • DOI 10.1007/s10822-005-0096-7
    • PS Hammond Y Wu R Harris TJ Minehardt R Car JD Schmitt 2005 Protonation-induced stereoisomerism in nicotine: conformational studies using classical (AMBER) and ab initio (Car-Parrinello) molecular dynamics J Comput Aided Mol Des 19 1 15 1:CAS:528:DC%2BD2MXkt1Ons7k%3D (Pubitemid 40778799)
    • (2005) Journal of Computer-Aided Molecular Design , vol.19 , Issue.1 , pp. 1-15
    • Hammond, P.S.1    Wu, Y.2    Harris, R.3    Minehardt, T.J.4    Car, R.5    Schmitt, J.D.6
  • 25
    • 33644532518 scopus 로고    scopus 로고
    • Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
    • 1:CAS:528:DC%2BD28XhslWnsbY%3D
    • C Chipot X Rozanska SB Dixit 2005 Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein J Comput Aided Mol Des 19 765 770 1:CAS:528:DC%2BD28XhslWnsbY%3D
    • (2005) J Comput Aided Mol des , vol.19 , pp. 765-770
    • Chipot, C.1    Rozanska, X.2    Dixit, S.B.3
  • 26
    • 35748983934 scopus 로고    scopus 로고
    • Inactive and active states and supramolecular organization of GPCRs: Insights from computational modeling
    • DOI 10.1007/s10822-006-9064-0
    • F Fanelli PG De Benedetti 2006 Inactive and active states and supramolecular organization of GPCRs: insights from computational modeling J Comput Aided Mol Des 20 449 461 1:CAS:528:DC%2BD28Xht1erurnL (Pubitemid 44823883)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.7-8 , pp. 449-461
    • Fanelli, F.1    Benedetti, P.G.2
  • 27
    • 56049097649 scopus 로고    scopus 로고
    • Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling
    • 1:CAS:528:DC%2BD1cXhtlags7nF
    • K Bharatham N Bharatham YJ Kwon KW Lee 2008 Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling J Comput Aided Mol Des 22 925 933 1:CAS:528: DC%2BD1cXhtlags7nF
    • (2008) J Comput Aided Mol des , vol.22 , pp. 925-933
    • Bharatham, K.1    Bharatham, N.2    Kwon, Y.J.3    Lee, K.W.4
  • 28
    • 58149333699 scopus 로고    scopus 로고
    • What induces pocket openings on protein surface patches involved in protein-protein interactions?
    • 1:CAS:528:DC%2BD1MXmtFGm
    • S Eyrisch V Helms 2009 What induces pocket openings on protein surface patches involved in protein-protein interactions? J Comput Aided Mol Des 23 73 86 1:CAS:528:DC%2BD1MXmtFGm
    • (2009) J Comput Aided Mol des , vol.23 , pp. 73-86
    • Eyrisch, S.1    Helms, V.2
  • 29
    • 0023380976 scopus 로고
    • Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry
    • WF van Gunsteren HJ Berendsen 1987 Thermodynamic cycle integration by computer simulation as a tool for obtaining free energy differences in molecular chemistry J Comput Aided Mol Des 1 171 176
    • (1987) J Comput Aided Mol des , vol.1 , pp. 171-176
    • Van Gunsteren, W.F.1    Berendsen, H.J.2
  • 30
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • T Hansson J Marelius J Aqvist 1998 Ligand binding affinity prediction by linear interaction energy methods J Comput Aided Mol Des 12 27 35 1:CAS:528:DyaK1cXisl2qsbc%3D (Pubitemid 128513811)
    • (1998) Journal of Computer-Aided Molecular Design , vol.12 , Issue.1 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 31
    • 0023824994 scopus 로고
    • Symposium overview. Minnesota conference on supercomputing in biology: Proteins, nucleic acids, and water
    • 1:STN:280:DyaL1M%2FlsFahsA%3D%3D
    • GL Wilcox FA Quiocho C Levinthal SC Harvey GM Maggiora JA McCammon 1988 Symposium overview. Minnesota conference on supercomputing in biology: proteins, nucleic acids, and water J Comput Aided Mol Des 1 271 281 1:STN:280: DyaL1M%2FlsFahsA%3D%3D
    • (1988) J Comput Aided Mol des , vol.1 , pp. 271-281
    • Wilcox, G.L.1    Quiocho, F.A.2    Levinthal, C.3    Harvey, S.C.4    Maggiora, G.M.5    McCammon, J.A.6
  • 32
    • 0023825016 scopus 로고
    • Future in biomolecular computation
    • 1:CAS:528:DyaL1cXksFWjsrs%3D
    • E Wimmer 1988 Future in biomolecular computation J Comput Aided Mol Des 1 283 290 1:CAS:528:DyaL1cXksFWjsrs%3D
    • (1988) J Comput Aided Mol des , vol.1 , pp. 283-290
    • Wimmer, E.1
  • 33
    • 3042988525 scopus 로고
    • Conformational-analysis. 130. Mm2-hydrocarbon force-field utilizing V1 and V2 torsional terms
    • 1:CAS:528:DyaE1cXmtVOm
    • NL Allinger 1977 Conformational-analysis. 130. Mm2-hydrocarbon force-field utilizing V1 and V2 torsional terms J Am Chem Soc 99 8127 8134 1:CAS:528:DyaE1cXmtVOm
    • (1977) J Am Chem Soc , vol.99 , pp. 8127-8134
    • Allinger, N.L.1
  • 34
    • 0025390935 scopus 로고
    • Special issue-Mopac - A semiempirical molecular-orbital program
    • JJP Stewart 1990 Special issue-Mopac-a semiempirical molecular-orbital program J Comput Aided Mol Des 4 1 45
    • (1990) J Comput Aided Mol des , vol.4 , pp. 1-45
    • Stewart, J.J.P.1
  • 35
    • 0030158210 scopus 로고    scopus 로고
    • Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques
    • FH Allen SE Harris R Taylor 1996 Comparison of conformer distributions in the crystalline state with conformational energies calculated by ab initio techniques J Comput Aided Mol Des 10 247 254 1:CAS:528:DyaK28XjvFGktbs%3D (Pubitemid 126712819)
    • (1996) Journal of Computer-Aided Molecular Design , vol.10 , Issue.3 , pp. 247-254
    • Allen, F.H.1
  • 36
    • 0028522365 scopus 로고
    • A fast and efficient method to generate biologically relevant conformations
    • 1:CAS:528:DyaK2MXitlSju7g%3D
    • G Klebe T Mietzner 1994 A fast and efficient method to generate biologically relevant conformations J Comput Aided Mol Des 8 583 606 1:CAS:528:DyaK2MXitlSju7g%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 583-606
    • Klebe, G.1    Mietzner, T.2
  • 38
    • 0023326161 scopus 로고
    • A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies
    • 1:CAS:528:DyaL2sXmtFCisL4%3D
    • D Mayer CB Naylor I Motoc GR Marshall 1987 A unique geometry of the active site of angiotensin-converting enzyme consistent with structure-activity studies J Comput Aided Mol Des 1 3 16 1:CAS:528:DyaL2sXmtFCisL4%3D
    • (1987) J Comput Aided Mol des , vol.1 , pp. 3-16
    • Mayer, D.1    Naylor, C.B.2    Motoc, I.3    Marshall, G.R.4
  • 39
    • 0023325045 scopus 로고
    • Conformation-activity relationships of opiate analgesics
    • 1:CAS:528:DyaL2sXmt1yntr4%3D
    • J Martin P Andrews 1987 Conformation-activity relationships of opiate analgesics J Comput Aided Mol Des 1 53 72 1:CAS:528:DyaL2sXmt1yntr4%3D
    • (1987) J Comput Aided Mol des , vol.1 , pp. 53-72
    • Martin, J.1    Andrews, P.2
  • 40
    • 0027548454 scopus 로고
    • A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists
    • 1:CAS:528:DyaK3sXksVSht7s%3D
    • YC Martin MG Bures EA Danaher J DeLazzer I Lico PA Pavlik 1993 A fast new approach to pharmacophore mapping and its application to dopaminergic and benzodiazepine agonists J Comput Aided Mol Des 7 83 102 1:CAS:528: DyaK3sXksVSht7s%3D
    • (1993) J Comput Aided Mol des , vol.7 , pp. 83-102
    • Martin, Y.C.1    Bures, M.G.2    Danaher, E.A.3    Delazzer, J.4    Lico, I.5    Pavlik, P.A.6
  • 41
    • 0042891852 scopus 로고    scopus 로고
    • Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: Taxol (case study)
    • doi: 10.1186/1472-6769-1-2
    • Lakdawala A, Wang M, Nevins N, Liotta D, Rusinska-Roszak D, Lozynski M, Snyder JP (2001) Calculated conformer energies for organic molecules with multiple polar functionalities are method dependent: taxol (case study). BMC Chem Biol. doi: 10.1186/1472-6769-1-2
    • (2001) BMC Chem Biol.
    • Lakdawala, A.1    Wang, M.2    Nevins, N.3    Liotta, D.4    Rusinska-Roszak, D.5    Lozynski, M.6    Snyder, J.P.7
  • 42
    • 0032197018 scopus 로고    scopus 로고
    • Do active site conformations of small ligands correspond to low free-energy solution structures?
    • Vieth M, Hirst JD, Brooks CL (1998) Do active site conformations of small ligands correspond to low free-energy solution structures? J Comput Aided Mol Des 12:563-572 (Pubitemid 128512192)
    • (1998) Journal of Computer-Aided Molecular Design , vol.12 , Issue.6 , pp. 563-572
    • Vieth, M.1    Hirst, J.D.2    Brooks III, C.L.3
  • 43
    • 0002659224 scopus 로고
    • Toward a more efficient handling of conformational flexibility in computer-assisted modelling of drug molecules
    • 1:CAS:528:DyaK2MXhtVSlsr%2FM
    • G Klebe 1995 Toward a more efficient handling of conformational flexibility in computer-assisted modelling of drug molecules Perspect Drug Discov Des 3 85 105 1:CAS:528:DyaK2MXhtVSlsr%2FM
    • (1995) Perspect Drug Discov des , vol.3 , pp. 85-105
    • Klebe, G.1
  • 44
    • 0035976749 scopus 로고    scopus 로고
    • Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement
    • DOI 10.1006/jmbi.2001.5147
    • N Ota DA Agard 2001 Binding mode prediction for a flexible ligand in a flexible pocket using multi-conformation simulated annealing pseudo crystallographic refinement J Mol Biol 314 607 617 1:CAS:528: DC%2BD38XivFGrtA%3D%3D (Pubitemid 33131860)
    • (2001) Journal of Molecular Biology , vol.314 , Issue.3 , pp. 607-617
    • Ota, N.1    Agard, D.A.2
  • 45
    • 0036022976 scopus 로고    scopus 로고
    • Can we separate active from inactive conformations?
    • DOI 10.1023/A:1016320106741
    • DJ Diller KM Merz Jr 2002 Can we separate active from inactive conformations? J Comput Aided Mol Des 16 105 112 1:CAS:528:DC%2BD38XltlSqsLo%3D (Pubitemid 34855037)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.2 , pp. 105-112
    • Diller, D.J.1    Merz Jr., K.M.2
  • 46
    • 0037013143 scopus 로고    scopus 로고
    • The conformational plasticity of protein kinases
    • DOI 10.1016/S0092-8674(02)00741-9
    • M Huse J Kuriyan 2003 The conformational plasticity of protein kinases Cell 109 275 282 (Pubitemid 34606870)
    • (2002) Cell , vol.109 , Issue.3 , pp. 275-282
    • Huse, M.1    Kuriyan, J.2
  • 47
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • SJ Teague 2003 Implications of protein flexibility for drug discovery Nat Rev Drug Discov 2 527 541 1:CAS:528:DC%2BD3sXltVaktrs%3D (Pubitemid 37361745)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.7 , pp. 527-541
    • Teague, S.J.1
  • 48
    • 79952436419 scopus 로고    scopus 로고
    • Structural biology: Breaking the protein rules
    • T Chouard 2005 Structural biology: breaking the protein rules Nature 471 151 153
    • (2005) Nature , vol.471 , pp. 151-153
    • Chouard, T.1
  • 49
    • 14644435825 scopus 로고    scopus 로고
    • Intrinsically unstructured proteins and their functions
    • DOI 10.1038/nrm1589
    • HJ Dyson PE Wright 2005 Intrinsically unstructured proteins and their functions Natl Rev Mol Cell Biol 6 197 208 1:CAS:528:DC%2BD2MXhslSlsLo%3D (Pubitemid 40314921)
    • (2005) Nature Reviews Molecular Cell Biology , vol.6 , Issue.3 , pp. 197-208
    • Dyson, H.J.1    Wright, P.E.2
  • 50
    • 77949916296 scopus 로고    scopus 로고
    • Understanding protein non-folding
    • 1:CAS:528:DC%2BC3cXjvFygtLk%3D
    • VN Uversky AK Dunker 2010 Understanding protein non-folding Biochim Biophys Acta 1804 1231 1264 1:CAS:528:DC%2BC3cXjvFygtLk%3D
    • (2010) Biochim Biophys Acta , vol.1804 , pp. 1231-1264
    • Uversky, V.N.1    Dunker, A.K.2
  • 51
    • 0020491251 scopus 로고
    • A geometric approach to macromolecule-ligand interactions
    • 1:CAS:528:DyaL38XmtFajsbw%3D
    • ID Kuntz JM Blaney SJ Oatley R Langridge TE Ferrin 1982 A geometric approach to macromolecule-ligand interactions J Mol Biol 161 269 288 1:CAS:528:DyaL38XmtFajsbw%3D
    • (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
  • 52
    • 0028454828 scopus 로고
    • The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure
    • 1:STN:280:DyaK2M%2FlsVahtQ%3D%3D
    • HJ Bohm 1994 The development of a simple empirical scoring function to estimate the binding constant for a protein-ligand complex of known three-dimensional structure J Comput Aided Mol Des 8 243 256 1:STN:280:DyaK2M%2FlsVahtQ%3D%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 243-256
    • Bohm, H.J.1
  • 53
    • 0028455325 scopus 로고
    • Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities
    • 1:CAS:528:DyaK2cXmslKjsLc%3D
    • EC Meng ID Kuntz DJ Abraham GE Kellogg 1994 Evaluating docked complexes with the HINT exponential function and empirical atomic hydrophobicities J Comput Aided Mol Des 8 299 306 1:CAS:528:DyaK2cXmslKjsLc%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 299-306
    • Meng, E.C.1    Kuntz, I.D.2    Abraham, D.J.3    Kellogg, G.E.4
  • 54
    • 0030255303 scopus 로고    scopus 로고
    • Scoring noncovalent protein-ligand interactions: A continuous differentiable function tuned to compute binding affinities
    • AN Jain 1996 Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities J Comput Aided Mol Des 10 427 440 1:CAS:528:DyaK28XntV2ms7o%3D (Pubitemid 126712439)
    • (1996) Journal of Computer-Aided Molecular Design , vol.10 , Issue.5 , pp. 427-440
    • Jain, A.N.1
  • 55
    • 0036022960 scopus 로고    scopus 로고
    • Further development and validation of empirical scoring functions for structure-based binding affinity prediction
    • DOI 10.1023/A:1016357811882
    • R Wang L Lai S Wang 2002 Further development and validation of empirical scoring functions for structure-based binding affinity prediction J Comput Aided Mol Des 16 11 26 1:CAS:528:DC%2BD38XltlSqs7k%3D (Pubitemid 34855041)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.1 , pp. 11-26
    • Wang, R.1    Lai, L.2    Wang, S.3
  • 56
    • 0344465830 scopus 로고    scopus 로고
    • A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein
    • DOI 10.1023/A:1027346709963
    • MD Kelly RL Mancera 2003 A new method for estimating the importance of hydrogen-bonding groups in the binding site of a protein J Comput Aided Mol Des 17 401 414 1:CAS:528:DC%2BD3sXos1amt7k%3D (Pubitemid 37483677)
    • (2003) Journal of Computer-Aided Molecular Design , vol.17 , Issue.7 , pp. 401-414
    • Kelly, M.D.1    Mancera, R.L.2
  • 58
    • 4043058000 scopus 로고    scopus 로고
    • Validation of an empirical RNA-ligand scoring function for fast flexible docking using RiboDock®
    • DOI 10.1023/B:JCAM.0000035199.48747.1e
    • SD Morley M Afshar 2004 Validation of an empirical RNA-ligand scoring function for fast flexible docking using Ribodock J Comput Aided Mol Des 18 189 208 1:CAS:528:DC%2BD2cXlsl2qtrk%3D (Pubitemid 39069414)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.3 , pp. 189-208
    • Morley, S.D.1    Afshar, M.2
  • 59
    • 27744469829 scopus 로고    scopus 로고
    • Scoring functions - The first 100 years
    • DOI 10.1007/s10822-005-8483-7
    • JR Tame 2005 Scoring functions-the first 100 years J Comput Aided Mol Des 19 445 451 1:CAS:528:DC%2BD2MXhtFaht77E (Pubitemid 41600174)
    • (2005) Journal of Computer-Aided Molecular Design , vol.19 , Issue.6 , pp. 445-451
    • Tame, J.R.H.1
  • 60
    • 34247343346 scopus 로고    scopus 로고
    • Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search
    • DOI 10.1007/s10822-007-9114-2
    • AN Jain 2009 Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search J Comput Aided Mol Des 21 281 306 (Pubitemid 46630055)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.5 , pp. 281-306
    • Jain, A.N.1
  • 61
    • 59649101321 scopus 로고    scopus 로고
    • An improved scoring function for suboptimal polar ligand complexes
    • 1:CAS:528:DC%2BD1MXhtF2nt7g%3D
    • G Cincilla D Vidal M Pons 2009 An improved scoring function for suboptimal polar ligand complexes J Comput Aided Mol Des 23 143 152 1:CAS:528:DC%2BD1MXhtF2nt7g%3D
    • (2009) J Comput Aided Mol des , vol.23 , pp. 143-152
    • Cincilla, G.1    Vidal, D.2    Pons, M.3
  • 62
    • 79955395664 scopus 로고    scopus 로고
    • Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors
    • P Dobeš J Fanfrlík J Rezáč M Otyepka P Hobza 2011 Transferable scoring function based on semiempirical quantum mechanical PM6-DH2 method: CDK2 with 15 structurally diverse inhibitors J Comput Aided Mol Des 25 3 223 235
    • (2011) J Comput Aided Mol des , vol.25 , Issue.3 , pp. 223-235
    • Dobeš, P.1    Fanfrlík, J.2    Rezáč, J.3    Otyepka, M.4    Hobza, P.5
  • 63
    • 33747706795 scopus 로고    scopus 로고
    • Protein Alpha Shape (PAS) Dock: A new gaussian-based score function suitable for docking in homology modelled protein structures
    • DOI 10.1007/s10822-006-9041-7
    • K Tondel E Anderssen F Drablos 2006 Protein alpha shape (PAS) dock: a new gaussian-based score function suitable for docking in homology modelled protein structures J Comput Aided Mol Des 20 131 144 1:CAS:528:DC%2BD28XosVOnsbs%3D (Pubitemid 44269784)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.3 , pp. 131-144
    • Tondel, K.1    Anderssen, E.2    Drablos, F.3
  • 64
    • 0028412035 scopus 로고
    • FLOG: A system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure
    • 1:CAS:528:DyaK2cXltVOmsL8%3D
    • MD Miller SK Kearsley DJ Underwood RP Sheridan 1994 FLOG: a system to select 'quasi-flexible' ligands complementary to a receptor of known three-dimensional structure J Comput Aided Mol Des 8 153 174 1:CAS:528:DyaK2cXltVOmsL8%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 153-174
    • Miller, M.D.1    Kearsley, S.K.2    Underwood, D.J.3    Sheridan, R.P.4
  • 66
    • 0029283717 scopus 로고
    • Flexible ligand docking using a genetic algorithm
    • 1:CAS:528:DyaK2MXltF2ktrY%3D
    • CM Oshiro ID Kuntz JS Dixon 1995 Flexible ligand docking using a genetic algorithm J Comput Aided Mol Des 9 113 130 1:CAS:528:DyaK2MXltF2ktrY%3D
    • (1995) J Comput Aided Mol des , vol.9 , pp. 113-130
    • Oshiro, C.M.1    Kuntz, I.D.2    Dixon, J.S.3
  • 67
    • 0033065220 scopus 로고    scopus 로고
    • Grootenhuis PD Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors
    • Knegtel RM, Bayada DM, Engh RA, von der Saal W, van Geerestein VJ, Grootenhuis PD Comparison of two implementations of the incremental construction algorithm in flexible docking of thrombin inhibitors. J Comput Aided Mol Des 13:167-183
    • J Comput Aided Mol des , vol.13 , pp. 167-183
    • Knegtel, R.M.1    Bayada, D.M.2    Engh, R.A.3    Von Der Saal, W.4    Van Geerestein, V.J.5
  • 68
    • 0032840569 scopus 로고    scopus 로고
    • DREAM++: Flexible docking program for virtual combinatorial libraries
    • DOI 10.1023/A:1008066310669
    • S Makino TJ Ewing ID Kuntz 1999 DREAM++: flexible docking program for virtual combinatorial libraries J Comput Aided Mol Des 13 513 532 1:CAS:528:DyaK1MXmtVSku70%3D (Pubitemid 29395565)
    • (1999) Journal of Computer-Aided Molecular Design , vol.13 , Issue.5 , pp. 513-532
    • Makino, S.1    Ewing, T.J.A.2    Kuntz, I.D.3
  • 69
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • DOI 10.1023/A:1011115820450
    • TJ Ewing S Makino AG Skillman ID Kuntz 2001 DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases J Comput Aided Mol Des 15 411 428 1:CAS:528:DC%2BD3MXktVSlsbc%3D (Pubitemid 32452109)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.5 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 71
    • 0037837201 scopus 로고    scopus 로고
    • On the molecular interaction between lactoferrin and the dye Red HE-3B. A novel approach for docking a charged and highly flexible molecule to protein surfaces
    • DOI 10.1023/A:1023868309253
    • M Grasselli O Cascone F Birger Anspach JM Delfino 2002 On the molecular interaction between lactoferrin and the dye Red HE-3b. A novel approach for docking a charged and highly flexible molecule to protein surfaces J Comput Aided Mol Des 16 917 934 1:CAS:528:DC%2BD3sXjvFyjtLg%3D (Pubitemid 36701526)
    • (2002) Journal of Computer-Aided Molecular Design , vol.16 , Issue.12 , pp. 917-934
    • Grasselli, M.1    Cascone, O.2    Anspach, F.B.3    Delfino, J.M.4
  • 73
    • 47249102090 scopus 로고    scopus 로고
    • A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    • 1:CAS:528:DC%2BD1cXksVKksL4%3D
    • G Bottegoni I Kufareva M Totrov R Abagyan 2008 A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) J Comput Aided Mol Des 22 311 325 1:CAS:528:DC%2BD1cXksVKksL4%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 311-325
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 74
    • 50249132694 scopus 로고    scopus 로고
    • Protein-ligand docking with multiple flexible side chains
    • 1:CAS:528:DC%2BD1cXhtFCqur7L
    • Y Zhao MF Sanner 2008 Protein-ligand docking with multiple flexible side chains J Comput Aided Mol Des 22 673 679 1:CAS:528:DC%2BD1cXhtFCqur7L
    • (2008) J Comput Aided Mol des , vol.22 , pp. 673-679
    • Zhao, Y.1    Sanner, M.F.2
  • 75
    • 58049221176 scopus 로고    scopus 로고
    • An improved adaptive genetic algorithm for protein-ligand docking
    • 1:CAS:528:DC%2BD1cXhsVOgtbrM
    • L Kang H Li H Jiang X Wang 2009 An improved adaptive genetic algorithm for protein-ligand docking J Comput Aided Mol Des 23 1 12 1:CAS:528: DC%2BD1cXhsVOgtbrM
    • (2009) J Comput Aided Mol des , vol.23 , pp. 1-12
    • Kang, L.1    Li, H.2    Jiang, H.3    Wang, X.4
  • 76
    • 67349261359 scopus 로고    scopus 로고
    • Effects of protein conformation in docking: Improved pose prediction through protein pocket adaptation
    • 1:CAS:528:DC%2BD1MXmtF2rurs%3D
    • AN Jain 2009 Effects of protein conformation in docking: improved pose prediction through protein pocket adaptation J Comput Aided Mol Des 23 355 374 1:CAS:528:DC%2BD1MXmtF2rurs%3D
    • (2009) J Comput Aided Mol des , vol.23 , pp. 355-374
    • Jain, A.N.1
  • 77
    • 77950917551 scopus 로고    scopus 로고
    • Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function
    • 1:CAS:528:DC%2BC3cXjt1Cjtr4%3D
    • DP Garden BS Zhorov 2010 Docking flexible ligands in proteins with a solvent exposure- and distance-dependent dielectric function J Comput Aided Mol Des 24 91 105 1:CAS:528:DC%2BC3cXjt1Cjtr4%3D
    • (2010) J Comput Aided Mol des , vol.24 , pp. 91-105
    • Garden, D.P.1    Zhorov, B.S.2
  • 78
    • 41949132916 scopus 로고    scopus 로고
    • Flexible ligand docking to multiple receptor conformations: A practical alternative
    • 1:CAS:528:DC%2BD1cXkvFClsrY%3D
    • M Totrov R Abagyan 2008 Flexible ligand docking to multiple receptor conformations: a practical alternative Curr Opin Struct Biol 18 178 184 1:CAS:528:DC%2BD1cXkvFClsrY%3D
    • (2008) Curr Opin Struct Biol , vol.18 , pp. 178-184
    • Totrov, M.1    Abagyan, R.2
  • 79
    • 0030474049 scopus 로고    scopus 로고
    • What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs?
    • HJ Bohm G Klebe 1996 What can we learn from molecular recognition in protein-ligand complexes for the design of new drugs? Angew Chem Int Ed Engl 35 2589 2614
    • (1996) Angew Chem Int Ed Engl , vol.35 , pp. 2589-2614
    • Bohm, H.J.1    Klebe, G.2
  • 80
    • 0032939345 scopus 로고    scopus 로고
    • Ligand solvation in molecular docking
    • DOI 10.1002/(SICI)1097-0134(1999 0101)34:1<4::AID-PR OT2>3.0.CO;2-6
    • BK Shoichet AR Leach ID Kuntz 1999 Ligand solvation in molecular docking Protein Sruct Funct Genet 34 4 16 1:CAS:528:DyaK1MXjtFartQ%3D%3D (Pubitemid 29019528)
    • (1999) Proteins: Structure, Function and Genetics , vol.34 , Issue.1 , pp. 4-16
    • Shoichet, B.K.1    Leach, A.R.2    Kuntz, I.D.3
  • 81
    • 0037008160 scopus 로고    scopus 로고
    • Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors
    • 1:CAS:528:DC%2BD38Xmt1entbw%3D
    • H Gohlke G Klebe 2002 Approaches to the description and prediction of the binding affinity of small-molecule ligands to macromolecular receptors Angew Chem Int Ed 41 2644 2676 1:CAS:528:DC%2BD38Xmt1entbw%3D
    • (2002) Angew Chem Int Ed , vol.41 , pp. 2644-2676
    • Gohlke, H.1    Klebe, G.2
  • 82
    • 33748593093 scopus 로고    scopus 로고
    • as of ionizable groups in proteins
    • E Demchuk RC Wade 1996 Improving the continuum dielectric approach to calculating pK(a)s of ionizable groups in proteins J Phys Chem 100 17373 17387 1:CAS:528:DyaK28XlvF2ju7k%3D (Pubitemid 126790125)
    • (1996) Journal of Physical Chemistry , vol.100 , Issue.43 , pp. 17373-17387
    • Demchuk, E.1    Wade, R.C.2
  • 83
    • 0035370422 scopus 로고    scopus 로고
    • a calculations
    • DOI 10.1002/prot.1053
    • JE Nielsen G Vriend 2001 Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations Protein Stuct Funct Genet 43 403 412 1:STN:280:DC%2BD3MvosVemug%3D%3D (Pubitemid 32476436)
    • (2001) Proteins: Structure, Function and Genetics , vol.43 , Issue.4 , pp. 403-412
    • Nielsen, J.E.1    Vriend, G.2
  • 84
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • M Rarey B Kramer T Lengauer G Klebe 1996 A fast flexible docking method using an incremental construction algorithm J Mol Biol 261 470 489 1:CAS:528:DyaK28XltlKisLo%3D (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
  • 85
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AutoDock
    • DS Goodsell GM Morris AJ Olson 1996 Automated docking of flexible ligands: applications of AutoDock J Mol Recognit 9 1 5 1:CAS:528: DyaK28Xis1SqtrY%3D (Pubitemid 126565462)
    • (1996) Journal of Molecular Recognition , vol.9 , Issue.1 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 87
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • DOI 10.1006/jmbi.1996.0897
    • G Jones P Willett RC Glen AR Leach R Taylor 1997 Development and validation of a genetic algorithm for flexible docking J Mol Biol 267 727 748 1:CAS:528:DyaK2sXis1KntLo%3D (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
  • 88
    • 59849126340 scopus 로고    scopus 로고
    • Docking and scoring with alternative side-chain conformations
    • 1:CAS:528:DC%2BD1MXhtFOhtLw%3D
    • C Hartmann I Antes T Lengauer 2009 Docking and scoring with alternative side-chain conformations Proteins 74 712 726 1:CAS:528:DC%2BD1MXhtFOhtLw%3D
    • (2009) Proteins , vol.74 , pp. 712-726
    • Hartmann, C.1    Antes, I.2    Lengauer, T.3
  • 89
    • 0042282803 scopus 로고    scopus 로고
    • FDS: Flexible ligand and receptor docking with a continuum solvent model and soft-core energy function
    • 1:CAS:528:DC%2BD3sXntFentL8%3D
    • RD Taylor PJ Jewsbury JW Essex 2003 FDS: flexible ligand and receptor docking with a continuum solvent model and soft-core energy function J Comput Chem 24 1637 1656 1:CAS:528:DC%2BD3sXntFentL8%3D
    • (2003) J Comput Chem , vol.24 , pp. 1637-1656
    • Taylor, R.D.1    Jewsbury, P.J.2    Essex, J.W.3
  • 90
    • 33749242403 scopus 로고    scopus 로고
    • PMF scoring revisited
    • DOI 10.1021/jm050038s
    • I Muegge 2006 PMF scoring revisited J Med Chem 49 5895 5902 1:CAS:528:DC%2BD2MXmtlGmtb0%3D (Pubitemid 44484936)
    • (2006) Journal of Medicinal Chemistry , vol.49 , Issue.20 , pp. 5895-5902
    • Muegge, I.1
  • 91
    • 67650077384 scopus 로고    scopus 로고
    • Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?
    • 1:CAS:528:DC%2BD1MXlvFCku7w%3D
    • P Englebienne N Moitessier 2009 Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins? J Chem Inf Model 49 1568 1580 1:CAS:528:DC%2BD1MXlvFCku7w%3D
    • (2009) J Chem Inf Model , vol.49 , pp. 1568-1580
    • Englebienne, P.1    Moitessier, N.2
  • 92
    • 33244478322 scopus 로고    scopus 로고
    • Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes
    • DOI 10.1021/ci050283k
    • A Oda K Tsuchida T Takakura N Yamaotsu S Hirono 2006 Comparison of consensus scoring strategies for evaluating computational models of protein-ligand complexes J Chem Inf Model 46 380 391 1:CAS:528: DC%2BD2MXht1Gju7zK (Pubitemid 43282129)
    • (2006) Journal of Chemical Information and Modeling , vol.46 , Issue.1 , pp. 380-391
    • Oda, A.1    Tsuchida, K.2    Takakura, T.3    Yamaotsu, N.4    Hirono, S.5
  • 93
    • 33845335781 scopus 로고    scopus 로고
    • Towards predictive ligand design with free-energy based computational methods?
    • DOI 10.2174/092986706779026165
    • N Foloppe R Hubbard 2006 Towards predictive ligand design with free-energy based computational methods? Curr Med Chem 13 3583 3608 1:CAS:528:DC%2BD28Xht1aksL7K (Pubitemid 44873749)
    • (2006) Current Medicinal Chemistry , vol.13 , Issue.29 , pp. 3583-3608
    • Foloppe, N.1    Hubbard, R.2    Foloppe, N.3
  • 94
    • 33749513370 scopus 로고    scopus 로고
    • Scoring functions for protein-ligand docking
    • DOI 10.2174/138920306778559395
    • AN Jain 2006 Scoring functions for protein-ligand docking Curr Protein Pept Sci 7 407 420 1:CAS:528:DC%2BD28XhtVamsLrE (Pubitemid 44524490)
    • (2006) Current Protein and Peptide Science , vol.7 , Issue.5 , pp. 407-420
    • Jain, A.N.1
  • 95
    • 33845976703 scopus 로고    scopus 로고
    • An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure
    • DOI 10.1002/prot.21162
    • TA Robertson G Varani 2007 An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure Proteins 66 359 374 1:CAS:528:DC%2BD2sXms1Sjsg%3D%3D (Pubitemid 46053467)
    • (2007) Proteins: Structure, Function and Genetics , vol.66 , Issue.2 , pp. 359-374
    • Robertson, T.A.1    Varani, G.2
  • 96
    • 34249278087 scopus 로고    scopus 로고
    • Ranking poses in structure-based lead discovery and optimization: Current trends in scoring function development
    • R Rajamani AC Good 2007 Ranking poses in structure-based lead discovery and optimization: current trends in scoring function development Curr Opin Drug Discov Devel 10 308 315 1:CAS:528:DC%2BD2sXmtVWls74%3D (Pubitemid 46804927)
    • (2007) Current Opinion in Drug Discovery and Development , vol.10 , Issue.3 , pp. 308-315
    • Rajamani, R.1    Good, A.C.2
  • 98
    • 0026047763 scopus 로고
    • Determination of the relative binding free-energies of peptide inhibitors to the Hiv-1 protease
    • 1:CAS:528:DyaK3MXkvVCru78%3D
    • DM Ferguson RJ Radmer PA Kollman 1991 Determination of the relative binding free-energies of peptide inhibitors to the Hiv-1 protease J Med Chem 34 2654 2659 1:CAS:528:DyaK3MXkvVCru78%3D
    • (1991) J Med Chem , vol.34 , pp. 2654-2659
    • Ferguson, D.M.1    Radmer, R.J.2    Kollman, P.A.3
  • 99
    • 0023751431 scopus 로고
    • Comparative molecular-field analysis (Comfa).1. Effect of shape on binding of steroids to carrier proteins
    • 1:CAS:528:DyaL1cXltVCqsbs%3D
    • RD Cramer DE Patterson JD Bunce 1988 Comparative molecular-field analysis (Comfa).1. Effect of shape on binding of steroids to carrier proteins J Am Chem Soc 110 5959 5967 1:CAS:528:DyaL1cXltVCqsbs%3D
    • (1988) J Am Chem Soc , vol.110 , pp. 5959-5967
    • Cramer, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 100
    • 0025617054 scopus 로고
    • Experimental design based 3-D QSAR analysis of steroid-protein interactions: Application to human CBG complexes
    • 1:CAS:528:DyaK3MXmt1ektLw%3D
    • U Norinder 1990 Experimental design based 3-D QSAR analysis of steroid-protein interactions: application to human CBG complexes J Comput Aided Mol Des 4 381 389 1:CAS:528:DyaK3MXmt1ektLw%3D
    • (1990) J Comput Aided Mol des , vol.4 , pp. 381-389
    • Norinder, U.1
  • 101
    • 0033004250 scopus 로고    scopus 로고
    • Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes
    • DOI 10.1023/A:1008010016362
    • R Bursi PD Grootenhuis 1999 Comparative molecular field analysis and energy interaction studies of thrombin-inhibitor complexes J Comput Aided Mol Des 13 221 232 1:CAS:528:DyaK1MXitlehsLg%3D (Pubitemid 29145096)
    • (1999) Journal of Computer-Aided Molecular Design , vol.13 , Issue.3 , pp. 221-232
    • Bursi, R.1    Grootenhuis, P.D.J.2
  • 102
    • 34047092770 scopus 로고    scopus 로고
    • 3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach
    • DOI 10.1007/s10822-006-9090-y
    • Z Zhang L An W Hu Y Xiang 2007 3D-QSAR study of hallucinogenic phenylalkylamines by using CoMFA approach J Comput Aided Mol Des 21 145 153 1:CAS:528:DC%2BD2sXjs1ekt78%3D (Pubitemid 46510840)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.4 , pp. 145-153
    • Zhang, Z.1    An, L.2    Hu, W.3    Xiang, Y.4
  • 104
    • 0026935503 scopus 로고
    • QSAR of conformationally flexible molecules: Comparative molecular field analysis of protein-tyrosine kinase inhibitors
    • 1:CAS:528:DyaK3sXlvFyhu74%3D
    • MC Nicklaus GW Milne TR Burke Jr 1992 QSAR of conformationally flexible molecules: comparative molecular field analysis of protein-tyrosine kinase inhibitors J Comput Aided Mol Des 6 487 504 1:CAS:528:DyaK3sXlvFyhu74%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 487-504
    • Nicklaus, M.C.1    Milne, G.W.2    Burke Jr., T.R.3
  • 105
    • 0027026407 scopus 로고
    • Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands
    • 1:CAS:528:DyaK3sXitVCks74%3D
    • S Rault R Bureau JC Pilo M Robba 1992 Comparative molecular field analysis of CCK-A antagonists using field-fit as an alignment technique. A convenient guide to design new CCK-A ligands J Comput Aided Mol Des 6 553 568 1:CAS:528:DyaK3sXitVCks74%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 553-568
    • Rault, S.1    Bureau, R.2    Pilo, J.C.3    Robba, M.4
  • 106
    • 0027551098 scopus 로고
    • CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively
    • 1:CAS:528:DyaK3sXkvVyrtrk%3D
    • JA Calder JA Wyatt DA Frenkel JE Casida 1993 CoMFA validation of the superposition of six classes of compounds which block GABA receptors non-competitively J Comput Aided Mol Des 7 45 60 1:CAS:528:DyaK3sXkvVyrtrk%3D
    • (1993) J Comput Aided Mol des , vol.7 , pp. 45-60
    • Calder, J.A.1    Wyatt, J.A.2    Frenkel, D.A.3    Casida, J.E.4
  • 107
    • 0029382594 scopus 로고
    • A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors
    • 1:CAS:528:DyaK2MXpslehsrs%3D
    • RT Kroemer P Hecht 1995 A new procedure for improving the predictiveness of CoMFA models and its application to a set of dihydrofolate reductase inhibitors J Comput Aided Mol Des 9 396 406 1:CAS:528:DyaK2MXpslehsrs%3D
    • (1995) J Comput Aided Mol des , vol.9 , pp. 396-406
    • Kroemer, R.T.1    Hecht, P.2
  • 108
    • 0034028576 scopus 로고    scopus 로고
    • A CoMFA analysis with conformational propensity: An attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method
    • DOI 10.1023/A:1008193217627
    • K Gohda I Mori D Ohta T Kikuchi 2000 A CoMFA analysis with conformational propensity: an attempt to analyze the SAR of a set of molecules with different conformational flexibility using a 3D-QSAR method J Comput Aided Mol Des 14 265 275 1:CAS:528:DC%2BD3cXitlCktrY%3D (Pubitemid 30175945)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.3 , pp. 265-275
    • Gohda, K.1    Mori, I.2    Ohta, D.3    Kikuchi, T.4
  • 109
    • 67650046977 scopus 로고    scopus 로고
    • CAUTION: Popular "benchmark" data sets do not distinguish the merits of 3D QSAR methods
    • 1:CAS:528:DC%2BD1MXlvVWmtbY%3D
    • J Manchester R Czermiński 2009 CAUTION: popular "Benchmark" data sets do not distinguish the merits of 3D QSAR methods J Chem Inf Model 49 1449 1454 1:CAS:528:DC%2BD1MXlvVWmtbY%3D
    • (2009) J Chem Inf Model , vol.49 , pp. 1449-1454
    • Manchester, J.1    Czermiński, R.2
  • 110
    • 38649105515 scopus 로고    scopus 로고
    • Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors
    • 1:CAS:528:DC%2BD1cXps1agsA%3D%3D
    • PS Kharkar ME Reith AK Dutta 2008 Three-dimensional quantitative structure-activity relationship (3D QSAR) and pharmacophore elucidation of tetrahydropyran derivatives as serotonin and norepinephrine transporter inhibitors J Comput Aided Mol Des 22 1 17 1:CAS:528:DC%2BD1cXps1agsA%3D%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 1-17
    • Kharkar, P.S.1    Reith, M.E.2    Dutta, A.K.3
  • 111
    • 11244279997 scopus 로고    scopus 로고
    • Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors
    • DOI 10.1007/s10822-004-2283-3
    • H Park S Lee 2004 Homology modeling, force field design, and free energy simulation studies to optimize the activities of histone deacetylase inhibitors J Comput Aided Mol Des 18 375 388 1:CAS:528:DC%2BD2cXhtFWqsb3I (Pubitemid 40069136)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.6 , pp. 375-388
    • Park, H.1    Lee, S.2
  • 112
    • 22144477181 scopus 로고    scopus 로고
    • Homology modeling and molecular interaction field studies of α-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors
    • DOI 10.1007/s10822-005-1486-6
    • CH Tomich P da Silva I Carvalho CA Taft 2005 Homology modeling and molecular interaction field studies of alpha-glucosidases as a guide to structure-based design of novel proposed anti-HIV inhibitors J Comput Aided Mol Des 19 83 92 1:STN:280:DC%2BD2MvgtFWrsw%3D%3D (Pubitemid 40974009)
    • (2005) Journal of Computer-Aided Molecular Design , vol.19 , Issue.2 , pp. 83-92
    • Da Silva, C.H.T.1    Da Silva, P.2    Carvalho, I.3    Taft, C.A.4
  • 113
    • 22144457954 scopus 로고    scopus 로고
    • Understanding and modulating cyclin-dependent kinase inhibitor specificity: Molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors
    • DOI 10.1007/s10822-005-1778-x
    • KA Rossi JA Markwalder SP Seitz CH Chang S Cox MD Boisclair L Brizuela SL Brenner PF Stouten 2005 Understanding and modulating cyclin-dependent kinase inhibitor specificity: molecular modeling and biochemical evaluation of pyrazolopyrimidinones as CDK2/cyclin A and CDK4/cyclin D1 inhibitors J Comput Aided Mol Des 19 111 122 1:CAS:528:DC%2BD2MXls1Smsr8%3D (Pubitemid 40974011)
    • (2005) Journal of Computer-Aided Molecular Design , vol.19 , Issue.2 , pp. 111-122
    • Rossi, K.A.1    Markwalder, J.A.2    Seitz, S.P.3    Chang, C.-H.4    Cox, S.5    Boisclair, M.D.6    Brizuela, L.7    Brenner, S.L.8    Stouten, P.F.W.9
  • 115
    • 36949007602 scopus 로고    scopus 로고
    • Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches
    • DOI 10.1007/s10822-007-9138-7
    • V Katritch CM Byrd V Tseitin D Dai E Raush M Totrov R Abagyan R Jordan DE Hruby 2007 Discovery of small molecule inhibitors of ubiquitin-like poxvirus proteinase I7L using homology modeling and covalent docking approaches J Comput Aided Mol Des 21 549 558 1:CAS:528:DC%2BD2sXhtlyrsrnJ (Pubitemid 350238547)
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.10-11 , pp. 549-558
    • Katritch, V.1    Byrd, C.M.2    Tseitin, V.3    Dai, D.4    Raush, E.5    Totrov, M.6    Abagyan, R.7    Jordan, R.8    Hruby, D.E.9
  • 116
    • 78651281188 scopus 로고    scopus 로고
    • Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach
    • 1:CAS:528:DC%2BC3cXhsVektbvN
    • MA Neves S Simoes ML Sa e Melo 2010 Ligand-guided optimization of CXCR4 homology models for virtual screening using a multiple chemotype approach J Comput Aided Mol Des 24 1023 1033 1:CAS:528:DC%2BC3cXhsVektbvN
    • (2010) J Comput Aided Mol des , vol.24 , pp. 1023-1033
    • Neves, M.A.1    Simoes, S.2    Sa E Melo, M.L.3
  • 118
    • 80055071653 scopus 로고    scopus 로고
    • In silico identification of new ligands for GPR17: A promising therapeutic target for neurodegenerative diseases
    • 1:CAS:528:DC%2BC3MXhtF2rtrfN
    • I Eberini S Daniele C Parravicini C Sensi ML Trincavelli C Martini MP Abbracchio 2011 In silico identification of new ligands for GPR17: a promising therapeutic target for neurodegenerative diseases J Comput Aided Mol Des 25 743 752 1:CAS:528:DC%2BC3MXhtF2rtrfN
    • (2011) J Comput Aided Mol des , vol.25 , pp. 743-752
    • Eberini, I.1    Daniele, S.2    Parravicini, C.3    Sensi, C.4    Trincavelli, M.L.5    Martini, C.6    Abbracchio, M.P.7
  • 119
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • DOI 10.1006/jmbi.1993.1626
    • A Sali TL Blundell 1993 Comparative protein modelling by statisfaction of spatial restraints J Mol Biol 234 779 815 1:CAS:528:DyaK2cXnt1ylug%3D%3D (Pubitemid 24007801)
    • (1993) Journal of Molecular Biology , vol.234 , Issue.3 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 120
    • 0025398721 scopus 로고
    • WHAT IF. A molecular modeling and drug design program
    • DOI 10.1016/0263-7855(90)80070-V
    • Vriend G (1990) WHAT IF: a molecular modeling and drug design program. J Mol Graph 8:52-56 (Pubitemid 20717037)
    • (1990) Journal of Molecular Graphics , vol.8 , Issue.1 , pp. 52-56
    • Vriend, G.1
  • 121
    • 16344375771 scopus 로고    scopus 로고
    • BRAGI: Linking and visualization of database information in a 3D viewer and modeling tool
    • DOI 10.1093/bioinformatics/bti138
    • Reichelt J, Dieterich G, Kvesic M, Schomburg D, Heinz DW (2005) BRAGI: linking and visualization of database information in a 3D viewer and modeling tool. Bioinformatics 21:1291-1293 (Pubitemid 40467965)
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1291-1293
    • Reichelt, J.1    Dieterich, G.2    Kvesic, M.3    Schomburg, D.4    Heinz, D.W.5
  • 122
    • 74249090260 scopus 로고    scopus 로고
    • Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: Four approaches that performed well in CASP8
    • E Krieger K Joo J Lee J Lee S Raman J Thompson M Tyka D Baker K Karplus 2009 Improving physical realism, stereochemistry, and side-chain accuracy in homology modeling: four approaches that performed well in CASP8 Proteins 9 114 122
    • (2009) Proteins , vol.9 , pp. 114-122
    • Krieger, E.1    Joo, K.2    Lee, J.3    Lee, J.4    Raman, S.5    Thompson, J.6    Tyka, M.7    Baker, D.8    Karplus, K.9
  • 123
    • 79960078022 scopus 로고    scopus 로고
    • Incorporation of evolutionary information into Rosetta comparative modeling
    • 1:CAS:528:DC%2BC3MXosFajtLw%3D
    • J Thompson D Baker 2011 Incorporation of evolutionary information into Rosetta comparative modeling Protein Struct Func Bioinfo 79 2380 2388 1:CAS:528:DC%2BC3MXosFajtLw%3D
    • (2011) Protein Struct Func Bioinfo , vol.79 , pp. 2380-2388
    • Thompson, J.1    Baker, D.2
  • 124
    • 0029176077 scopus 로고
    • CASP1 proceedings
    • CASP1 proceedings 1995 Protein Struct Funct Genet 23 295 460
    • (1995) Protein Struct Funct Genet , vol.23 , pp. 295-460
  • 125
    • 0027658134 scopus 로고
    • PLIM: A protein-ligand interaction modeller
    • 1:CAS:528:DyaK2cXlsVyqu78%3D
    • MR Harris M Kihlen RP Bywater 1993 PLIM: a protein-ligand interaction modeller J Mol Recognit 6 111 115 1:CAS:528:DyaK2cXlsVyqu78%3D
    • (1993) J Mol Recognit , vol.6 , pp. 111-115
    • Harris, M.R.1    Kihlen, M.2    Bywater, R.P.3
  • 127
    • 80051521545 scopus 로고    scopus 로고
    • GPCR Dock 2010 participants Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment
    • Kufareva I, Rueda M, Vsevolod K, Stevens RC, Abagyan R, GPCR Dock 2010 participants Status of GPCR modeling and docking as reflected by community wide GPCR Dock 2010 assessment. Structure 19:1108-1126
    • Structure , vol.19 , pp. 1108-1126
    • Kufareva, I.1    Rueda, M.2    Vsevolod, K.3    Stevens, R.C.4    Abagyan, R.5
  • 128
    • 12144291706 scopus 로고    scopus 로고
    • Molecular modelling studies on the ORL1-receptor and ORL1-agonists
    • DOI 10.1023/B:JCAM.0000017491.97244.69
    • BM Broer M Gurrath HD Holtje 2003 Molecular modelling studies on the ORL1-receptor and ORL1-agonists J Comput Aided Mol Des 17 739 754 (Pubitemid 38418286)
    • (2003) Journal of Computer-Aided Molecular Design , vol.17 , Issue.11 , pp. 739-754
    • Broer, B.M.1    Gurrath, M.2    Holtje, H.-D.3
  • 129
    • 33745125766 scopus 로고    scopus 로고
    • Comparison of a homology model and the crystallographic structure of human 11β-hydroxysteroid dehydrogenase type 1 (11βHSD1) in a structure-based identification of inhibitors
    • DOI 10.1007/s10822-006-9037-3
    • L Miguet Z Zhang M Barbier MG Grigorov 2006 Comparison of a homology model and the crystallographic structure of human 11beta-hydroxysteroid dehydrogenase type 1 (11betaHSD1) in a structure-based identification of inhibitors J Comput Aided Mol Des 20 67 81 1:CAS:528:DC%2BD28XlvVGru7o%3D (Pubitemid 43899118)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.2 , pp. 67-81
    • Miguet, L.1    Zhang, Z.2    Barbier, M.3    Grigorov, M.G.4
  • 132
    • 22144432626 scopus 로고    scopus 로고
    • The de novo design of median molecules within a property range of interest
    • DOI 10.1007/s10822-004-6986-2
    • N Brown B McKay J Gasteiger 2004 The de novo design of median molecules within a property range of interest J Comput Aided Mol Des 18 761 771 1:CAS:528:DC%2BD2MXls1Smtrg%3D (Pubitemid 40973865)
    • (2004) Journal of Computer-Aided Molecular Design , vol.18 , Issue.12 , pp. 761-771
    • Brown, N.1    McKay, B.2    Gasteiger, J.3
  • 133
    • 31444443422 scopus 로고    scopus 로고
    • ENPDA: An evolutionary structure-based de novo peptide design algorithm
    • Belda I, Madurga S, Llorà X, Martinell M, Tarragó T, Piqueras MG, Nicolás E, Giralt E (2005) ENPDA: an evolutionary structure-based de novo peptide design algorithm. J Comput Aided Mol Des 19:585-601
    • (2005) J Comput Aided Mol des , vol.19 , pp. 585-601
    • Belda I, M.1
  • 134
    • 67650945012 scopus 로고    scopus 로고
    • Second-generation de novo design: A view from a medicinal chemist perspective
    • Zaliani A et al (2009) Second-generation de novo design: a view from a medicinal chemist perspective. J Comput Aided Mol Des
    • (2009) J Comput Aided Mol des
    • Zaliani, A.1
  • 135
    • 0021871375 scopus 로고
    • A computational procedure for determining energetically favorable binding sites on biologically important macromolecules
    • DOI 10.1021/jm00145a002
    • PJ Goodford 1985 A computational-procedure for determining energetically favorable binding-sites on biologically important macromolecules J Med Chem 28 849 857 1:CAS:528:DyaL2MXktVeit7c%3D (Pubitemid 15012490)
    • (1985) Journal of Medicinal Chemistry , vol.28 , Issue.7 , pp. 849-857
    • Goodford, P.J.1
  • 136
    • 0027439587 scopus 로고
    • Further development of hydrogen bond functions for use in determining energetically favorable binding sites on molecules of known structure. 1. Ligand probe groups with the ability to form two hydrogen bonds
    • DOI 10.1021/jm00053a018
    • RC Wade KJ Clark PJ Goodford 1993 Further development of hydrogen-bond functions for use in determining energetically favorable binding-sites on molecules of known structure.1. Ligand probe groups with the ability to form 2 hydrogen-bonds J Med Chem 36 140 147 1:CAS:528:DyaK3sXltFymsA%3D%3D (Pubitemid 23040155)
    • (1993) Journal of Medicinal Chemistry , vol.36 , Issue.1 , pp. 140-147
    • Wade, R.C.1    Clark, K.J.2    Goodford, P.J.3
  • 137
    • 0027193713 scopus 로고
    • GroupBuild: A fragment-based method for de novo drug design
    • SH Rotstein MA Murcko 1993 GroupBuild: a fragment-based method for de novo drug design J Med Chem 36 1700 1710 1:CAS:528:DyaK3sXktVSitbk%3D (Pubitemid 23191297)
    • (1993) Journal of Medicinal Chemistry , vol.36 , Issue.12 , pp. 1700-1710
    • Rotstein, S.H.1    Murcko, M.A.2
  • 138
    • 0028863971 scopus 로고
    • Genetic algorithms in molecular recognition and design
    • 1:CAS:528:DyaK2MXpslansbs%3D
    • P Willett 1995 Genetic algorithms in molecular recognition and design Trends Biotechnol 13 516 521 1:CAS:528:DyaK2MXpslansbs%3D
    • (1995) Trends Biotechnol , vol.13 , pp. 516-521
    • Willett, P.1
  • 139
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • 1:STN:280:DyaK383mtVarsw%3D%3D
    • HJ Bohm 1992 The computer program LUDI: a new method for the de novo design of enzyme inhibitors J Comput Aided Mol Des 6 61 78 1:STN:280: DyaK383mtVarsw%3D%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 61-78
    • Bohm, H.J.1
  • 140
    • 0027027467 scopus 로고
    • LUDI: Rule-based automatic design of new substituents for enzyme inhibitor leads
    • 1:STN:280:DyaK3s7nvF2jtg%3D%3D
    • HJ Bohm 1992 LUDI: rule-based automatic design of new substituents for enzyme inhibitor leads J Comput Aided Mol Des 6 593 606 1:STN:280: DyaK3s7nvF2jtg%3D%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 593-606
    • Bohm, H.J.1
  • 143
    • 0030076041 scopus 로고    scopus 로고
    • Placement of medium-sized molecular fragments into active sites of proteins
    • M Rarey S Wefing T Lengauer 1996 Placement of medium-sized molecular fragments into active sites of proteins J Comput Aided Mol Des 10 41 54 1:CAS:528:DyaK28Xhs1arsrY%3D (Pubitemid 126712801)
    • (1996) Journal of Computer-Aided Molecular Design , vol.10 , Issue.1 , pp. 41-54
    • Rarey, M.1    Wefing, S.2    Lengauer, T.3
  • 144
    • 0029348176 scopus 로고
    • The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties
    • 1:CAS:528:DyaK2MXotV2itb0%3D
    • MT Barakat PM Dean 1995 The atom assignment problem in automated de novo drug design. 1. Transferability of molecular fragment properties J Comput Aided Mol Des 9 341 350 1:CAS:528:DyaK2MXotV2itb0%3D
    • (1995) J Comput Aided Mol des , vol.9 , pp. 341-350
    • Barakat, M.T.1    Dean, P.M.2
  • 145
    • 0027550408 scopus 로고
    • GenStar: A method for de novo drug design
    • 1:CAS:528:DyaK3sXktVShur4%3D
    • SH Rotstein MA Murcko 1993 GenStar: a method for de novo drug design J Comput Aided Mol Des 7 23 43 1:CAS:528:DyaK3sXktVShur4%3D
    • (1993) J Comput Aided Mol des , vol.7 , pp. 23-43
    • Rotstein, S.H.1    Murcko, M.A.2
  • 146
    • 0029320812 scopus 로고
    • BUILDER v.2: Improving the chemistry of a de novo design strategy
    • 1:CAS:528:DyaK2MXntFGksrk%3D
    • DC Roe ID Kuntz 1995 BUILDER v.2: improving the chemistry of a de novo design strategy J Comput Aided Mol Des 9 269 282 1:CAS:528:DyaK2MXntFGksrk%3D
    • (1995) J Comput Aided Mol des , vol.9 , pp. 269-282
    • Roe, D.C.1    Kuntz, I.D.2
  • 147
    • 0028457010 scopus 로고
    • Automated molecular design: A new fragment-joining algorithm
    • 1:CAS:528:DyaK2cXmt1GktbY%3D
    • AR Leach SR Kilvington 1994 Automated molecular design: a new fragment-joining algorithm J Comput Aided Mol Des 8 283 298 1:CAS:528: DyaK2cXmt1GktbY%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 283-298
    • Leach, A.R.1    Kilvington, S.R.2
  • 149
    • 0031088353 scopus 로고    scopus 로고
    • Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design
    • NP Todorov PM Dean 1997 Evaluation of a method for controlling molecular scaffold diversity in de novo ligand design J Comput Aided Mol Des 11 175 192 1:CAS:528:DyaK2sXis1Kjt7Y%3D (Pubitemid 127508828)
    • (1997) Journal of Computer-Aided Molecular Design , vol.11 , Issue.2 , pp. 175-192
    • Todorov, N.P.1    Dean, P.M.2
  • 150
    • 0034130399 scopus 로고    scopus 로고
    • De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks
    • DOI 10.1023/A:1008184403558
    • G Schneider ML Lee M Stahl P Schneider 2000 De novo design of molecular architectures by evolutionary assembly of drug-derived building blocks J Comput Aided Mol Des 14 487 494 1:CAS:528:DC%2BD3cXktl2ju7c%3D (Pubitemid 30386823)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.5 , pp. 487-494
    • Schneider, G.1    Lee, M.-L.2    Stahl, M.3    Schneider, P.4
  • 151
    • 67649619336 scopus 로고    scopus 로고
    • 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13
    • 1:CAS:528:DC%2BD1MXmvFWru7k%3D
    • LC Blum JL Reymond 2009 970 million druglike small molecules for virtual screening in the chemical universe database GDB-13 J Am Chem Soc 131 8732 8733 1:CAS:528:DC%2BD1MXmvFWru7k%3D
    • (2009) J Am Chem Soc , vol.131 , pp. 8732-8733
    • Blum, L.C.1    Reymond, J.L.2
  • 152
    • 34848905491 scopus 로고
    • HTS technologies-IBC informa conference
    • H Kubinyi 1992 HTS technologies-IBC informa conference IDrugs 4 168 173
    • (1992) IDrugs , vol.4 , pp. 168-173
    • Kubinyi, H.1
  • 153
    • 0026875036 scopus 로고
    • An approach to computer-aided inhibitor design: Application to cathepsin L
    • 1:CAS:528:DyaK3sXisFSgtr4%3D
    • S Sudarsanam GD Virca CJ March S Srinivasan 1992 An approach to computer-aided inhibitor design: application to cathepsin L J Comput Aided Mol Des 6 223 233 1:CAS:528:DyaK3sXisFSgtr4%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 223-233
    • Sudarsanam, S.1    Virca, G.D.2    March, C.J.3    Srinivasan, S.4
  • 154
    • 0040541621 scopus 로고    scopus 로고
    • Combinatorial docking and combinatorial chemistry: Design of potent non- peptide thrombin inhibitors
    • DOI 10.1023/A:1008040531766
    • HJ Bohm DW Banner L Weber 1999 Combinatorial docking and combinatorial chemistry: design of potent non-peptide thrombin inhibitors J Comput Aided Mol Des 13 51 56 1:CAS:528:DyaK1MXisVKrs7k%3D (Pubitemid 29098942)
    • (1999) Journal of Computer-Aided Molecular Design , vol.13 , Issue.1 , pp. 51-56
    • Bohm, H.-J.1    Banner, D.W.2    Weber, L.3
  • 156
    • 0035015532 scopus 로고    scopus 로고
    • Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching
    • DOI 10.1023/A:1011128510728
    • P Furet T Meyer P Mittl H Fretz 2001 Identification of cylin-dependent kinase 1 inhibitors of a new chemical type by structure-based design and database searching J Comput Aided Mol Des 15 489 495 1:CAS:528: DC%2BD3MXktVSltro%3D (Pubitemid 32452113)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.5 , pp. 489-495
    • Furet, P.1    Meyer, T.2    Mittl, P.3    Fretz, H.4
  • 157
    • 33745178511 scopus 로고    scopus 로고
    • Investigation of substituent effect of 1-(3,3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques
    • DOI 10.1007/s10822-006-9038-2
    • A Afantitis G Melagraki H Sarimveis PA Koutentis J Markopoulos O Igglessi-Markopoulou 2006 Investigation of substituent effect of 1-(3, 3-diphenylpropyl)-piperidinyl phenylacetamides on CCR5 binding affinity using QSAR and virtual screening techniques J Comput Aided Mol Des 20 83 95 1:CAS:528:DC%2BD28XlvVGru7s%3D (Pubitemid 43899119)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.2 , pp. 83-95
    • Afantitis, A.1    Melagraki, G.2    Sarimveis, H.3    Koutentis, P.A.4    Markopoulos, J.5    Igglessi-Markopoulou, O.6
  • 158
    • 33947581421 scopus 로고    scopus 로고
    • Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors
    • DOI 10.1007/s10822-006-9077-8, Advances in Phatmacophores and 3-D Screening
    • S Kortagere WJ Welsh 2006 Development and application of hybrid structure based method for efficient screening of ligands binding to G-protein coupled receptors J Comput Aided Mol Des 20 789 802 1:CAS:528:DC%2BD2sXhsVyrtbw%3D (Pubitemid 46476947)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.12 , pp. 789-802
    • Kortagere, S.1    Welsh, W.J.2
  • 159
    • 35748950717 scopus 로고    scopus 로고
    • A successful virtual screening application: Prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and propylparaben
    • DOI 10.1007/s10822-007-9136-9
    • A Talevi CL Bellera EA Castro LE Bruno-Blanch 2007 A successful virtual screening application: prediction of anticonvulsant activity in MES test of widely used pharmaceutical and food preservatives methylparaben and
    • (2007) Journal of Computer-Aided Molecular Design , vol.21 , Issue.9 , pp. 527-538
    • Talevi, A.1    Bellera, C.L.2    Castro, E.A.3    Bruno-Blanch, L.E.4
  • 160
    • 41449114598 scopus 로고    scopus 로고
    • Community benchmarks for virtual screening
    • 1:CAS:528:DC%2BD1cXjsFOnsb8%3D
    • JJ Irwin 2008 Community benchmarks for virtual screening J Comput Aided Mol Des 22 193 199 1:CAS:528:DC%2BD1cXjsFOnsb8%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 193-199
    • Irwin, J.J.1
  • 161
    • 76449114766 scopus 로고    scopus 로고
    • Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists
    • 1:CAS:528:DC%2BD1MXhsFGru7bN
    • BA Krueger T Weil G Schneider 2009 Comparative virtual screening and novelty detection for NMDA-GlycineB antagonists J Comput Aided Mol Des 23 869 881 1:CAS:528:DC%2BD1MXhsFGru7bN
    • (2009) J Comput Aided Mol des , vol.23 , pp. 869-881
    • Krueger, B.A.1    Weil, T.2    Schneider, G.3
  • 162
    • 78149413951 scopus 로고    scopus 로고
    • Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition
    • 1:CAS:528:DC%2BC3cXhtlSjt77K
    • R Didziapetris J Dapkunas A Sazonovas P Japertas 2010 Trainable structure-activity relationship model for virtual screening of CYP3A4 inhibition J Comput Aided Mol Des 24 891 906 1:CAS:528:DC%2BC3cXhtlSjt77K
    • (2010) J Comput Aided Mol des , vol.24 , pp. 891-906
    • Didziapetris, R.1    Dapkunas, J.2    Sazonovas, A.3    Japertas, P.4
  • 163
    • 0036212418 scopus 로고    scopus 로고
    • An overview of in silico design and screening: Toward efficient drug discovery
    • Joseph-McCarthy D (2002) An overview of in silico design and screening: toward efficient drug discovery. Curr Drug Discov 20-23
    • (2002) Curr Drug Discov , pp. 20-23
    • Joseph-Mccarthy, D.1
  • 164
    • 0036214750 scopus 로고    scopus 로고
    • Virtual screening in drug discovery: Methods, expectations and reality
    • J Bajorath 2002 Virtual screening: methods, expectations, and reality Curr Opin Drug Discov Dev 2 24 28 (Pubitemid 34269451)
    • (2002) Current Drug Discovery , Issue.MAR. , pp. 24-28
    • Bajorath, J.1
  • 165
    • 0034923575 scopus 로고    scopus 로고
    • Similarity searching in large combinatorial chemistry spaces
    • DOI 10.1023/A:1011144622059
    • M Rarey M Stahl 2001 Similarity searching in large combinatorial chemistry spaces J Comput Aided Mol Des 15 497 520 1:CAS:528: DC%2BD3MXls1Snsbc%3D (Pubitemid 32680852)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.6 , pp. 497-520
    • Rarey, M.1    Stahl, M.2
  • 166
    • 1942453243 scopus 로고    scopus 로고
    • Ligand efficiency: A useful metric for lead selection
    • DOI 10.1016/S1359-6446(04)03069-7, PII S1359644604030697
    • AL Hopkins CR Groom A Alex 2004 Ligand efficiency: a useful metric for lead selection Drug Discov Today 9 430 431 (Pubitemid 38510559)
    • (2004) Drug Discovery Today , vol.9 , Issue.10 , pp. 430-431
    • Hopkins, A.L.1    Groom, C.R.2    Alex, A.3
  • 167
    • 17044403086 scopus 로고    scopus 로고
    • Ligand efficiency indices as guideposts for drug discovery
    • C Abad-Zapatero JT Metz 2005 Ligand efficiency indices as guideposts for drug discovery Drug Discov Today 10 464 469
    • (2005) Drug Discov Today , vol.10 , pp. 464-469
    • Abad-Zapatero, C.1    Metz, J.T.2
  • 168
    • 0027930292 scopus 로고
    • Compass: Predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark
    • DOI 10.1021/jm00041a010
    • AN Jain K Koile D Chapman 1994 Compass: predicting biological activities from molecular surface properties. Performance comparisons on a steroid benchmark J Med Chem 37 2315 2327 1:CAS:528:DyaK2cXkslCjur4%3D (Pubitemid 24262320)
    • (1994) Journal of Medicinal Chemistry , vol.37 , Issue.15 , pp. 2315-2327
    • Jain, A.N.1    Koile, K.2    Chapman, D.3
  • 169
    • 0033824764 scopus 로고    scopus 로고
    • Steroid binding by antibodies and artificial receptors: Exploration of theoretical methods to determine the origins of binding affinities and specificities
    • 1:CAS:528:DC%2BD3cXmvFKhu7Y%3D
    • S Handschuh B Goldfuss J Chen J Gasteiger KN Houk 2000 Steroid binding by antibodies and artificial receptors: exploration of theoretical methods to determine the origins of binding affinities and specificities J Comput Aided Mol Des 14 611 629 1:CAS:528:DC%2BD3cXmvFKhu7Y%3D
    • (2000) J Comput Aided Mol des , vol.14 , pp. 611-629
    • Handschuh, S.1    Goldfuss, B.2    Chen, J.3    Gasteiger, J.4    Houk, K.N.5
  • 171
    • 0037204546 scopus 로고    scopus 로고
    • Prediction of 'drug-likeness'
    • 1:CAS:528:DC%2BD38Xitlartbo%3D
    • WP Walters MA Murcko 2002 Prediction of 'drug-likeness' Adv Drug Deliv Rev 54 255 271 1:CAS:528:DC%2BD38Xitlartbo%3D
    • (2002) Adv Drug Deliv Rev , vol.54 , pp. 255-271
    • Walters, W.P.1    Murcko, M.A.2
  • 173
    • 39149104296 scopus 로고    scopus 로고
    • Molecular docking studies on tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors
    • 1:CAS:528:DC%2BD1cXhs1yhu7s%3D
    • NS Sapre S Gupta N Pancholi N Sapre 2008 Molecular docking studies on tetrahydroimidazo-[4, 5, 1-jk][1, 4]-benzodiazepinone (TIBO) derivatives as HIV-1 NNRT inhibitors J Comput Aided Mol Des 22 69 80 1:CAS:528: DC%2BD1cXhs1yhu7s%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 69-80
    • Sapre, N.S.1    Gupta, S.2    Pancholi, N.3    Sapre, N.4
  • 174
    • 0028492113 scopus 로고
    • Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines
    • 1:CAS:528:DyaK2MXnsFyisQ%3D%3D
    • JD Hirst RD King MJ Sternberg 1994 Quantitative structure-activity relationships by neural networks and inductive logic programming. II. The inhibition of dihydrofolate reductase by triazines J Comput Aided Mol Des 8 421 432 1:CAS:528:DyaK2MXnsFyisQ%3D%3D
    • (1994) J Comput Aided Mol des , vol.8 , pp. 421-432
    • Hirst, J.D.1    King, R.D.2    Sternberg, M.J.3
  • 176
    • 39149129373 scopus 로고    scopus 로고
    • QSAR: Dead or alive?
    • 1:CAS:528:DC%2BD1cXhs1yhu7Y%3D
    • AM Doweyko 2008 QSAR: dead or alive? J Comput Aided Mol Des 22 81 89 1:CAS:528:DC%2BD1cXhs1yhu7Y%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 81-89
    • Doweyko, A.M.1
  • 177
    • 33745181229 scopus 로고    scopus 로고
    • Development of small molecules designed to modulate protein-protein interactions
    • DOI 10.1007/s10822-006-9040-8
    • Y Che BR Brooks GR Marshall 2006 Development of small molecules designed to modulate protein-protein interactions J Comput Aided Mol Des 20 109 130 1:CAS:528:DC%2BD28XlvVGru70%3D (Pubitemid 43899121)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.2 , pp. 109-130
    • Che, Y.1    Brooks, B.R.2    Marshall, G.R.3
  • 178
    • 0026873439 scopus 로고
    • PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors
    • 1:CAS:528:DyaK38XlsVartLc%3D
    • T Lotta J Taskinen R Bäckström E Nissinen 1992 PLS modelling of structure-activity relationships of catechol O-methyltransferase inhibitors J Comput Aided Mol Des 6 253 272 1:CAS:528:DyaK38XlsVartLc%3D
    • (1992) J Comput Aided Mol des , vol.6 , pp. 253-272
    • Lotta, T.1    Taskinen, J.2    Bäckström, R.3    Nissinen, E.4
  • 179
    • 59649129141 scopus 로고    scopus 로고
    • Computational study on the molecular inclusion of andrographolide by cyclodextrin
    • Zhou H, Lai WP, Zhang Z, Li WK, Cheung HY (2009) Computational study on the molecular inclusion of andrographolide by cyclodextrin. J Comput Aided Mol Des 23:153-162
    • (2009) J Comput Aided Mol des , vol.23 , pp. 153-162
    • Zhou, H.1    Lai, W.P.2    Zhang, Z.3    Li, W.K.4    Cheung, H.Y.5
  • 180
    • 67349173677 scopus 로고    scopus 로고
    • DFT-based QSAR and QSPR models of several cis-platinum complexes: Solvent effect
    • 1:CAS:528:DC%2BD1MXmtF2rur8%3D
    • P Sarmah RC Deka 2009 DFT-based QSAR and QSPR models of several cis-platinum complexes: solvent effect J Comput Aided Mol Des 23 343 354 1:CAS:528:DC%2BD1MXmtF2rur8%3D
    • (2009) J Comput Aided Mol des , vol.23 , pp. 343-354
    • Sarmah, P.1    Deka, R.C.2
  • 181
    • 34249277652 scopus 로고    scopus 로고
    • A combined ligand-based and target-based drug design approach for G-protein coupled receptors: Application to salvinorin A, a selective kappa opioid receptor agonist
    • DOI 10.1007/s10822-006-9067-x
    • N Singh G Chevé DM Ferguson CR McCurdy 2006 A combined ligand-based and target-based drug design approach for G-protein coupled receptors: application to salvinorin A, a selective kappa opioid receptor agonist J Comput Aided Mol Des 20 471 493 1:CAS:528:DC%2BD28Xht1erurnF (Pubitemid 44823885)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.7-8 , pp. 471-493
    • Singh, N.1    Cheve, G.2    Ferguson, D.M.3    McCurdy, C.R.4
  • 182
    • 35548943518 scopus 로고    scopus 로고
    • QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR
    • DOI 10.1007/s10822-006-9080-0
    • M Zheng K Yu H Liu X Luo K Chen W Zhu H Jiang 2006 QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR J Comput Aided Mol Des 20 549 566 1:CAS:528:DC%2BD28Xht1eru77N (Pubitemid 44823891)
    • (2006) Journal of Computer-Aided Molecular Design , vol.20 , Issue.9 , pp. 549-566
    • Zheng, M.1    Yu, K.2    Liu, H.3    Luo, X.4    Chen, K.5    Zhu, W.6    Jiang, H.7
  • 183
    • 44249128682 scopus 로고    scopus 로고
    • A ligand's-eye view of protein binding
    • 1:CAS:528:DC%2BD1cXmtVSnt7s%3D
    • RD Clark 2008 A ligand's-eye view of protein binding J Comput Aided Mol Des 22 507 521 1:CAS:528:DC%2BD1cXmtVSnt7s%3D
    • (2008) J Comput Aided Mol des , vol.22 , pp. 507-521
    • Clark, R.D.1
  • 184
    • 79956188006 scopus 로고    scopus 로고
    • Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-f][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2- fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors
    • 1:CAS:528:DC%2BC3MXlvFOhsL4%3D
    • J Caballero M Quiliano JH Alzate-Morales M Zimic E Deharo 2011 Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2, 1-f][1, 2, 4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H-pyrrolo[2, 3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2- fluorophenoxy)-2-pyridinylamine derivatives as c-Met kinase inhibitors J Comput Aided Mol Des 25 349 369 1:CAS:528:DC%2BC3MXlvFOhsL4%3D
    • (2011) J Comput Aided Mol des , vol.25 , pp. 349-369
    • Caballero, J.1    Quiliano, M.2    Alzate-Morales, J.H.3    Zimic, M.4    Deharo, E.5
  • 185
    • 80051544346 scopus 로고    scopus 로고
    • Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase
    • 1:CAS:528:DC%2BC3MXosFCgs78%3D
    • J Yoo JL Medina-Franco 2011 Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase J Comput Aided Mol Des 25 555 567 1:CAS:528:DC%2BC3MXosFCgs78%3D
    • (2011) J Comput Aided Mol des , vol.25 , pp. 555-567
    • Yoo, J.1    Medina-Franco, J.L.2
  • 186
    • 80052031934 scopus 로고    scopus 로고
    • Systems-biology approaches for predicting genomic evolution
    • 1:CAS:528:DC%2BC3MXhtVeiurrJ
    • B Papp RA Notebaart C Pál 2011 Systems-biology approaches for predicting genomic evolution Nat Rev Genet 12 591 602 1:CAS:528: DC%2BC3MXhtVeiurrJ
    • (2011) Nat Rev Genet , vol.12 , pp. 591-602
    • Papp, B.1    Notebaart, R.A.2    Pál, C.3
  • 187
    • 57149126216 scopus 로고    scopus 로고
    • PK/PD modelling and beyond: Impact on drug development
    • 1:CAS:528:DC%2BD1cXhsVeqsrfI
    • DD Breimer 2008 PK/PD modelling and beyond: impact on drug development Pharm Res 25 2720 2722 1:CAS:528:DC%2BD1cXhsVeqsrfI
    • (2008) Pharm Res , vol.25 , pp. 2720-2722
    • Breimer, D.D.1
  • 188
    • 84857456553 scopus 로고    scopus 로고
    • Swati Chaturvedi Outsourcing in Pharmaceutical Industry Accessed 6 Dec 2011
    • Swati Chaturvedi Outsourcing in Pharmaceutical Industry (2011) http://www.bionity.com/en/whitepapers/49803/outsourcing-in-pharmaceutical- industry.html. Accessed 6 Dec 2011
    • (2011)
  • 189
    • 84857448936 scopus 로고    scopus 로고
    • Protein Data Bank 2011 Accessed 6 Dec 2011
    • Protein Data Bank (2011) http://www.pdb.org. Accessed 6 Dec 2011
  • 192
    • 84857456550 scopus 로고    scopus 로고
    • PDB redo Accessed 29 Nov 2011
    • PDB redo (2011) http://www.cmbi.ru.nl/pdb-redo/. Accessed 29 Nov 2011
    • (2011)
  • 193
    • 34447498926 scopus 로고    scopus 로고
    • PDB improvement starts with data deposition [3]
    • DOI 10.1126/science.317.5835.195
    • RP Joosten G Vriend 2007 PDB improvement starts with data deposition Science 317 195 196 1:CAS:528:DC%2BD2sXnvVGruro%3D (Pubitemid 47076180)
    • (2007) Science , vol.317 , Issue.5835 , pp. 195-196
    • Joosten, R.P.1    Vriend, G.2
  • 194
    • 84857452557 scopus 로고    scopus 로고
    • Automatic rebuilding and optimization of crystallographic structures in the PDB
    • Epub ahead of print
    • Joosten RP, Joosten K, Cohen SX, Vriend G, Perrakis A (2011) Automatic rebuilding and optimization of crystallographic structures in the PDB. Bioinformatics Epub ahead of print
    • (2011) Bioinformatics
    • Joosten, R.P.1    Joosten, K.2    Cohen, S.X.3    Vriend, G.4    Perrakis, A.5
  • 197
    • 33750576990 scopus 로고    scopus 로고
    • The role of serendipity in drug discovery
    • TA Ban 2006 The role of serendipity in drug discovery Dialogues Clin Neurosci 8 244 335
    • (2006) Dialogues Clin Neurosci , vol.8 , pp. 244-335
    • Ban, T.A.1
  • 199
    • 0030910261 scopus 로고    scopus 로고
    • Study of the interaction between aryloxypropanolamines and Asn386 in helix VII of the human 5-hydroxytryptamine(1A) receptor
    • W Kuipers R Link PJ Standaar AR Stoit I Van Wijngaarden R Leurs AP Ijzerman 1997 Study of the interaction between aryloxypropanolamines and Asn386 in helix VII of the human 5-hydroxytryptamine1A receptor Mol Pharmacol 51 889 896 1:CAS:528:DyaK2sXjt1eht7c%3D (Pubitemid 27224695)
    • (1997) Molecular Pharmacology , vol.51 , Issue.5 , pp. 889-896
    • Kuipers, W.1    Link, R.2    Standaar, P.J.3    Stoit, A.R.4    Van Wijngaarden, I.5    Leurs, R.6    Ijzerman, A.P.7
  • 203
    • 0001228323 scopus 로고
    • A common motif in G-protein-coupled seven transmembrane helix receptors
    • 1:CAS:528:DyaK2cXlvFykt78%3D
    • L Oliveira ACM Paiva G Vriend 1993 A common motif in G-protein-coupled seven transmembrane helix receptors J Comp aided Mol Des 7 649 658 1:CAS:528:DyaK2cXlvFykt78%3D
    • (1993) J Comp Aided Mol des , vol.7 , pp. 649-658
    • Oliveira, L.1    Paiva, A.C.M.2    Vriend, G.3
  • 204
    • 0028276459 scopus 로고
    • A common step for signal transduction in G protein-coupled receptors
    • DOI 10.1016/0165-6147(94)90137-6
    • L Oliveira ACM Paiva C Sander G Vriend 1994 A common step for signal transduction in G protein-coupled receptors Trends Pharmacol Sci 15 170 172 1:CAS:528:DyaK2MXisFOksw%3D%3D (Pubitemid 24196173)
    • (1994) Trends in Pharmacological Sciences , vol.15 , Issue.6 , pp. 170-172
    • Oliveira, L.1    Paiva, A.C.M.2    Sander, C.3    Vriend, G.4
  • 205
    • 0033452126 scopus 로고    scopus 로고
    • A low resolution model for the interaction of G proteins with G protein-coupled receptors
    • L Oliveira ACM Paiva G Vriend 1999 A low resolution model for the interaction of G proteins with G protein-coupled receptors Protein Eng 12 1087 1095 1:CAS:528:DC%2BD3cXmt1ansQ%3D%3D (Pubitemid 30011484)
    • (1999) Protein Engineering , vol.12 , Issue.12 , pp. 1087-1095
    • Oliveira, L.1    Paiva, A.C.M.2    Vriend, G.3
  • 206
    • 77955779227 scopus 로고    scopus 로고
    • Conserved binding mode of human beta(2) adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography
    • 1:CAS:528:DC%2BC3cXpsV2mtLo%3D
    • D Wacker MA Brown G Fenalti V Katritch R Abagyan V Cherezov RC Stevens 2010 Conserved binding mode of human beta(2) adrenergic receptor inverse agonists and antagonist revealed by X-ray crystallography J Am Chem Soc 132 11443 11445 1:CAS:528:DC%2BC3cXpsV2mtLo%3D
    • (2010) J Am Chem Soc , vol.132 , pp. 11443-11445
    • Wacker, D.1    Brown, M.A.2    Fenalti, G.3    Katritch, V.4    Abagyan, R.5    Cherezov, V.6    Stevens, R.C.7
  • 214
    • 37348999191 scopus 로고    scopus 로고
    • Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method
    • DOI 10.1002/prot.21622
    • HJ Joosten Y Han W Niu J Vervoort D Dunaway-Mariano PJ Schaap 2008 Identification of fungal oxaloacetate hydrolyase within the isocitrate lyase/PEP mutase enzyme superfamily using a sequence marker-based method Proteins 70 157 166 1:CAS:528:DC%2BD1cXisValtg%3D%3D (Pubitemid 350293457)
    • (2008) Proteins: Structure, Function and Genetics , vol.70 , Issue.1 , pp. 157-166
    • Joosten, H.-J.1    Han, Y.2    Niu, W.3    Vervoort, J.4    Dunaway-Mariano, D.5    Schaap, P.J.6
  • 217
    • 77956287596 scopus 로고    scopus 로고
    • Novel tools for extraction and validation of disease-related mutations applied to Fabry disease
    • 1:CAS:528:DC%2BC3cXht1SqtL3F
    • R Kuipers T van den Bergh HJ Joosten RH Lekanne dit Deprez MM Mannens PJ Schaap 2010 Novel tools for extraction and validation of disease-related mutations applied to Fabry disease Hum Mutat 31 1026 1032 1:CAS:528: DC%2BC3cXht1SqtL3F
    • (2010) Hum Mutat , vol.31 , pp. 1026-1032
    • Kuipers, R.1    Van Den Bergh, T.2    Joosten, H.J.3    Lekanne Dit Deprez, R.H.4    Mannens, M.M.5    Schaap, P.J.6
  • 218
    • 80054902432 scopus 로고    scopus 로고
    • Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis
    • 1:CAS:528:DC%2BC3MXhtlGku7bK
    • A Cerdobbel K De Winter D Aerts R Kuipers HJ Joosten W Soetaert T Desmet 2011 Increasing the thermostability of sucrose phosphorylase by a combination of sequence- and structure-based mutagenesis Protein Eng Des Sel 24 829 834 1:CAS:528:DC%2BC3MXhtlGku7bK
    • (2011) Protein Eng des Sel , vol.24 , pp. 829-834
    • Cerdobbel, A.1    De Winter, K.2    Aerts, D.3    Kuipers, R.4    Joosten, H.J.5    Soetaert, W.6    Desmet, T.7
  • 219
    • 73149083488 scopus 로고    scopus 로고
    • Calling international rescue: Knowledge lost in literature and data landslide!
    • 1:CAS:528:DC%2BD1MXhsFCitbjI
    • TK Attwood DB Kell P McDermott J Marsh SR Pettifer D Thorne 2009 Calling international rescue: knowledge lost in literature and data landslide! Biochem J 424 317 333 1:CAS:528:DC%2BD1MXhsFCitbjI
    • (2009) Biochem J , vol.424 , pp. 317-333
    • Attwood, T.K.1    Kell, D.B.2    McDermott, P.3    Marsh, J.4    Pettifer, S.R.5    Thorne, D.6
  • 221
    • 1942532331 scopus 로고    scopus 로고
    • Heavier-than-air flying machines are impossible
    • DOI 10.1016/S0014-5793(04)00320-5, PII S0014579304003205
    • L Oliveira T Hulsen D Lutje Hulsik AC Paiva G Vriend 2004 Heavier-than-air flying machines are impossible FEBS Lett 564 269 273 1:CAS:528:DC%2BD2cXjsVemsLY%3D (Pubitemid 38520932)
    • (2004) FEBS Letters , vol.564 , Issue.3 , pp. 269-273
    • Oliveira, L.1    Hulsen, T.2    Lutje Hulsik, D.3    Paiva, A.C.M.4    Vriend, G.5
  • 222
    • 0033569709 scopus 로고    scopus 로고
    • Mutational analysis of the antagonist-binding site of the histamine H(1) receptor
    • 1:CAS:528:DyaK1MXmvVajtrY%3D
    • K Wieland AM ter Laak MJ Smit R Kühne H Timmerman R Leurs 1999 Mutational analysis of the antagonist-binding site of the histamine H(1) receptor J Biol Chem 274 29994 30000 1:CAS:528:DyaK1MXmvVajtrY%3D
    • (1999) J Biol Chem , vol.274 , pp. 29994-30000
    • Wieland, K.1    Ter Laak, A.M.2    Smit, M.J.3    Kühne, R.4    Timmerman, H.5    Leurs, R.6
  • 223
    • 84857448540 scopus 로고    scopus 로고
    • Accessed 9 Dec 2011
    • Nuclear Receptors 3DM (2011) https://fungen.wur.nl/?sfamid=NR&mode= alignment. Accessed 9 Dec 2011
    • (2011) Nuclear Receptors 3DM
  • 224
    • 79952278365 scopus 로고    scopus 로고
    • Prospects for the automated extraction of mutation data from the scientific literature
    • 1:CAS:528:DC%2BC3MXhvVeksrc%3D
    • PD Stenson DN Cooper 2010 Prospects for the automated extraction of mutation data from the scientific literature Hum Genomics 5 1 4 1:CAS:528:DC%2BC3MXhvVeksrc%3D
    • (2010) Hum Genomics , vol.5 , pp. 1-4
    • Stenson, P.D.1    Cooper, D.N.2
  • 225
    • 78049484011 scopus 로고    scopus 로고
    • Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces
    • H Venselaar TA Te Beek RK Kuipers ML Hekkelman G Vriend 2010 Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces BMC Bioinfo 11 548
    • (2010) BMC Bioinfo , vol.11 , pp. 548
    • Venselaar, H.1    Te Beek, T.A.2    Kuipers, R.K.3    Hekkelman, M.L.4    Vriend, G.5


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