메뉴 건너뛰기




Volumn 16, Issue 9, 2016, Pages 901-916

Advances in computational structure-based drug design and application in drug discovery

Author keywords

Antibacterial drugs; Anticancer drugs; De novo design; Inhibitors of GPCRs; Structure based drug design; Virtual screening

Indexed keywords

ANTIINFECTIVE AGENT; ANTINEOPLASTIC AGENT; G PROTEIN COUPLED RECEPTOR;

EID: 84959548116     PISSN: 15680266     EISSN: 18734294     Source Type: Journal    
DOI: 10.2174/1568026615666150825142002     Document Type: Article
Times cited : (46)

References (163)
  • 1
    • 39449103059 scopus 로고    scopus 로고
    • The epidemic of antibiotic- resistant infections: A call to action for the medical community from the Infectious Diseases Society of America
    • Spellberg, B.; Guidos, R.; Gilbert, D.; Bradley, J.; Boucher, H. W.; Scheld, W. M.; Bartlett, J. G.; Edwards, J. The epidemic of antibiotic- resistant infections: a call to action for the medical community from the Infectious Diseases Society of America. Clin. Infect. Dis., 2008, 46 (2), 155-164.
    • (2008) Clin. Infect. Dis. , vol.46 , Issue.2 , pp. 155-164
    • Spellberg, B.1    Guidos, R.2    Gilbert, D.3    Bradley, J.4    Boucher, H.W.5    Scheld, W.M.6    Bartlett, J.G.7    Edwards, J.8
  • 3
    • 84908072433 scopus 로고    scopus 로고
    • Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections
    • Team, W. H. O. E. R. Ebola virus disease in West Africa--the first 9 months of the epidemic and forward projections. N. Engl. J. Med., 2014, 371 (16), 1481-1495.
    • (2014) N. Engl. J. Med. , vol.371 , Issue.16 , pp. 1481-1495
  • 4
    • 84862762587 scopus 로고    scopus 로고
    • 25 Years of AIDS: Recording progress and future challenges
    • Levy, J. A.; Autran, B.; Coutinho, R. A.; Phair, J. P. 25 Years of AIDS: recording progress and future challenges. AIDS, 2012, 26 (10), 1187-1189.
    • (2012) AIDS , vol.26 , Issue.10 , pp. 1187-1189
    • Levy, J.A.1    Autran, B.2    Coutinho, R.A.3    Phair, J.P.4
  • 6
    • 84876368637 scopus 로고    scopus 로고
    • Less talk, more action
    • Anonymous. Less talk, more action.Nat. Rev. Microbiol., 2013, 11 (5), 295-295.
    • (2013) Nat. Rev. Microbiol. , vol.11 , Issue.5
  • 7
    • 79955754627 scopus 로고    scopus 로고
    • The global need for effective antibiotics—a summary of plenary presentations
    • Alvan, G.; Edlund, C.; Heddini, A. The global need for effective antibiotics—a summary of plenary presentations. Drug Resist. Update., 2011, 14 (2), 70-76.
    • (2011) Drug Resist. Update. , vol.14 , Issue.2 , pp. 70-76
    • Alvan, G.1    Edlund, C.2    Heddini, A.3
  • 8
    • 84857195282 scopus 로고    scopus 로고
    • The crisis of no new antibiotics—what is the way forward? Lancet
    • Piddock, L. J. The crisis of no new antibiotics—what is the way forward? Lancet. Infect. Dis., 2012, 12 (3), 249-253.
    • (2012) Infect. Dis. , vol.12 , Issue.3 , pp. 249-253
    • Piddock, L.J.1
  • 10
    • 67650436176 scopus 로고    scopus 로고
    • Drug discovery and natural products: End of an era or an endless frontier?
    • Li, J. W.; Vederas, J. C. Drug discovery and natural products: end of an era or an endless frontier? Science 2009, 325(5937), 161-165.
    • (2009) Science , vol.325 , Issue.5937 , pp. 161-165
    • Li, J.W.1    Vederas, J.C.2
  • 11
    • 0034677966 scopus 로고    scopus 로고
    • Drug discovery: A historical perspective
    • Drews, J. Drug discovery: a historical perspective. Science 2000, 287(5460), 1960-1964.
    • (2000) Science , vol.287 , Issue.5460 , pp. 1960-1964
    • Drews, J.1
  • 12
    • 79959929769 scopus 로고    scopus 로고
    • How were new medicines discovered?
    • Swinney, D.C.; Anthony, J. How were new medicines discovered? Nat.Rev. Drug Discov., 2011, 10(7), 507-519.
    • (2011) Nat.Rev. Drug Discov. , vol.10 , Issue.7 , pp. 507-519
    • Swinney, D.C.1    Anthony, J.2
  • 13
    • 0034082239 scopus 로고    scopus 로고
    • The influence of natural products upon drug discovery
    • Newman, D. J.; Cragg, G. M.; Snader, K. M. The influence of natural products upon drug discovery. Nat. Prod. Rep., 2000, 17(3), 215-234.
    • (2000) Nat. Prod. Rep. , vol.17 , Issue.3 , pp. 215-234
    • Newman, D.J.1    Cragg, G.M.2    Snader, K.M.3
  • 14
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • Shoichet, B. K. Virtual screening of chemical libraries. Nature 2004, 432(7019), 862-865.
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 15
    • 84862795414 scopus 로고    scopus 로고
    • Structurebased virtual screening for drug discovery: A problem-centric review
    • Cheng, T.; Li, Q.; Zhou, Z.; Wang, Y.; Bryant, S. H. Structurebased virtual screening for drug discovery: a problem-centric review. AAPS J., 2012, 14(1), 133-141.
    • (2012) AAPS J. , vol.14 , Issue.1 , pp. 133-141
    • Cheng, T.1    Li, Q.2    Zhou, Z.3    Wang, Y.4    Bryant, S.H.5
  • 17
    • 79955563790 scopus 로고    scopus 로고
    • Organic synthesis toward small-molecule probes and drugs
    • Schreiber, S. L. Organic synthesis toward small-molecule probes and drugs. Proc. Natl. Acad. Sci. U S A., 2011, 108(17), 6699-6702.
    • (2011) Proc. Natl. Acad. Sci. U S A. , vol.108 , Issue.17 , pp. 6699-6702
    • Schreiber, S.L.1
  • 18
    • 84856134589 scopus 로고    scopus 로고
    • Lead- Oriented Synthesis: A New Opportunity for Synthetic Chemistry
    • Nadin, A.; Hattotuwagama, C.; Churcher, I. Lead- Oriented Synthesis: A New Opportunity for Synthetic Chemistry. Angew. Chem. Int. Ed. Engl., 2012, 51(5), 1114-1122.
    • (2012) Angew. Chem. Int. Ed. Engl. , vol.51 , Issue.5 , pp. 1114-1122
    • Nadin, A.1    Hattotuwagama, C.2    Churcher, I.3
  • 20
    • 84911401229 scopus 로고    scopus 로고
    • Structurebased virtual screening for drug discovery: Principles, applications and recent advances
    • Lionta, E.; Spyrou, G.; Vassilatis, D. K.; Cournia, Z. Structurebased virtual screening for drug discovery: Principles, applications and recent advances. Curr. Top. Med. Chem., 2014, 14(16), 1923.
    • (2014) Curr. Top. Med. Chem. , vol.14 , Issue.16 , pp. 1923
    • Lionta, E.1    Spyrou, G.2    Vassilatis, D.K.3    Cournia, Z.4
  • 21
    • 84959545363 scopus 로고    scopus 로고
    • Structure-based drug design
    • Agrawal, P. Structure-based drug design. J. Pharmacovigil., 2013, 01(04)doi:10.4172/2329-6887.1000e1 11.
    • (2013) J. Pharmacovigil. , vol.1 , Issue.4 , pp. 11
    • Agrawal, P.1
  • 22
    • 77953605369 scopus 로고    scopus 로고
    • Structure-based discovery of antibacterial drugs
    • Simmons, K. J.; Chopra, I.; Fishwick, C. W. Structure-based discovery of antibacterial drugs. Nat. Rev. Microbio., 2010, 8 (7), 501-510.
    • (2010) Nat. Rev. Microbio. , vol.8 , Issue.7 , pp. 501-510
    • Simmons, K.J.1    Chopra, I.2    Fishwick, C.W.3
  • 23
    • 77954228177 scopus 로고    scopus 로고
    • Drug discovery: Pulled from a protein's embrace
    • Jorgensen, W. L. Drug discovery: Pulled from a protein's embrace. Nature 2010, 466(7302), 42-43.
    • (2010) Nature , vol.466 , Issue.7302 , pp. 42-43
    • Jorgensen, W.L.1
  • 24
    • 0002716825 scopus 로고    scopus 로고
    • Combinatorial and computational approaches in structure- based drug design
    • Kubinyi, H. Combinatorial and computational approaches in structure- based drug design. Curr. Opin. Drug Discov. Dev, 1998, 1, 16-27.
    • (1998) Curr. Opin. Drug Discov. Dev , vol.1 , pp. 16-27
    • Kubinyi, H.1
  • 25
    • 61649109015 scopus 로고    scopus 로고
    • The influence of lead discovery strategies on the properties of drug candidates
    • Keseru, G. M.; Makara, G. M. The influence of lead discovery strategies on the properties of drug candidates. Nat. Rev. Drug. Discov., 2009, 8(3), 203-212.
    • (2009) Nat. Rev. Drug. Discov. , vol.8 , Issue.3 , pp. 203-212
    • Keseru, G.M.1    Makara, G.M.2
  • 26
    • 33846502057 scopus 로고    scopus 로고
    • Hit and lead identification: Integrated technology- based approaches. Drug Discov
    • Goodnow Jr, R. A., Hit and lead identification: Integrated technology- based approaches. Drug Discov. Today: Technol., 2007, 3, (4), 367-375.
    • (2007) Today: Technol. , vol.3 , Issue.4 , pp. 367-375
    • Goodnow, R.A.1
  • 27
    • 61649109015 scopus 로고    scopus 로고
    • The influence of lead discovery strategies on the properties of drug candidates
    • Keseru, G. M.; Makara, G. M. The influence of lead discovery strategies on the properties of drug candidates. Nat. Rev. Drug. Discov., 2009, 8(3), 203-212.
    • (2009) Nat. Rev. Drug. Discov. , vol.8 , Issue.3 , pp. 203-212
    • Keseru, G.M.1    Makara, G.M.2
  • 28
    • 84874431865 scopus 로고    scopus 로고
    • Cyclophilin A inhibition: Targeting transition-state-bound enzyme conformations for structure-based drug design
    • Nagaraju, M.; McGowan, L. C.; Hamelberg, D. Cyclophilin A inhibition: targeting transition-state-bound enzyme conformations for structure-based drug design. J. Chem. Inf. Model., 2013, 53(2), 403-410.
    • (2013) J. Chem. Inf. Model. , vol.53 , Issue.2 , pp. 403-410
    • Nagaraju, M.1    McGowan, L.C.2    Hamelberg, D.3
  • 31
    • 73949094934 scopus 로고    scopus 로고
    • Structure- based drug design identifies novel LPA3 antagonists
    • Fells, J. I.; Tsukahara, R.; Liu, J.; Tigyi, G.; Parrill, A. L., Structure- based drug design identifies novel LPA3 antagonists. Bioorg. Med. Chem., 2009, 17(21), 7457-7464.
    • (2009) Bioorg. Med. Chem. , vol.17 , Issue.21 , pp. 7457-7464
    • Fells, J.I.1    Tsukahara, R.2    Liu, J.3    Tigyi, G.4    Parrill, A.L.5
  • 33
    • 84865209497 scopus 로고    scopus 로고
    • Structure and ligand based drug design strategies in the development of novel 5-LOX inhibitors
    • Aparoy, P.; Reddy, K. K.; Reddanna, P. Structure and ligand based drug design strategies in the development of novel 5-LOX inhibitors. Curr. Med. Chem., 2012, 19(22), 3763-3778.
    • (2012) Curr. Med. Chem. , vol.19 , Issue.22 , pp. 3763-3778
    • Aparoy, P.1    Reddy, K.K.2    Reddanna, P.3
  • 34
    • 80053615320 scopus 로고    scopus 로고
    • The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol
    • Salon, J. A.; Lodowski, D. T.; Palczewski, K. The significance of G protein-coupled receptor crystallography for drug discovery. Pharmacol. Rev., 2011, 63(4), 901-937.
    • (2011) Rev. , vol.63 , Issue.4 , pp. 901-937
    • Salon, J.A.1    Lodowski, D.T.2    Palczewski, K.3
  • 35
    • 58549117672 scopus 로고    scopus 로고
    • Discovery and optimization of highly ligand-efficient oxytocin receptor antagonists using structure-based drug design
    • Bellenie, B. R.; Barton, N. P.; Emmons, A. J.; Heer, J. P.; Salvagno, C. Discovery and optimization of highly ligand-efficient oxytocin receptor antagonists using structure-based drug design. Bioorg. Med. Chem. Lett., 2009, 19(3), 990-994.
    • (2009) Bioorg. Med. Chem. Lett. , vol.19 , Issue.3 , pp. 990-994
    • Bellenie, B.R.1    Barton, N.P.2    Emmons, A.J.3    Heer, J.P.4    Salvagno, C.5
  • 36
    • 85026964878 scopus 로고    scopus 로고
    • Discovery of novel α-amylase inhibitors using structure-based drug design
    • Al-Asri, J.; Wolber, G. Discovery of novel α-amylase inhibitors using structure-based drug design. J. Cheminformatics, 2014, 6(Suppl 1), P50.
    • (2014) J. Cheminformatics , vol.6
    • Al-Asri, J.1    Wolber, G.2
  • 38
    • 71249140665 scopus 로고    scopus 로고
    • Protein structure prediction in structure-based ligand design and virtual screening
    • Grant, M. A. Protein structure prediction in structure-based ligand design and virtual screening. Comb. Chem. High Throughput. Screen., 2009, 12(10), 940-960.
    • (2009) Comb. Chem. High Throughput. Screen. , vol.12 , Issue.10 , pp. 940-960
    • Grant, M.A.1
  • 40
    • 0030448994 scopus 로고    scopus 로고
    • Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV- 1 capsid
    • Gamble, T. R.; Vajdos, F. F.; Yoo, S.; Worthylake, D. K.; Houseweart, M.; Sundquist, W. I.; Hill, C. P. Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV- 1 capsid. Cell, 1996, 87(7), 1285-1294.
    • (1996) Cell , vol.87 , Issue.7 , pp. 1285-1294
    • Gamble, T.R.1    Vajdos, F.F.2    Yoo, S.3    Worthylake, D.K.4    Houseweart, M.5    Sundquist, W.I.6    Hill, C.P.7
  • 41
    • 0027207885 scopus 로고
    • Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B
    • Luban, J.; Bossolt, K. L.; Franke, E. K.; Kalpana, G. V.; Goff, S. P. Human immunodeficiency virus type 1 Gag protein binds to cyclophilins A and B. Cell, 1993, 73(6), 1067-1078.
    • (1993) Cell , vol.73 , Issue.6 , pp. 1067-1078
    • Luban, J.1    Bossolt, K.L.2    Franke, E.K.3    Kalpana, G.V.4    Goff, S.P.5
  • 44
    • 33846104376 scopus 로고    scopus 로고
    • All-atom ab initio folding of a diverse set of proteins
    • Yang, J. S.; Chen, W. W.; Skolnick, J.; Shakhnovich, E. I. All-atom ab initio folding of a diverse set of proteins. Structure, 2007, 15(1), 53-63.
    • (2007) Structure , vol.15 , Issue.1 , pp. 53-63
    • Yang, J.S.1    Chen, W.W.2    Skolnick, J.3    Shakhnovich, E.I.4
  • 45
    • 84858119090 scopus 로고    scopus 로고
    • Comparison of common homology modeling algorithms: Application of user-defined alignments
    • Dolan, M. A.; Noah, J. W.; Hurt, D. Comparison of common homology modeling algorithms: application of user-defined alignments. Methods Mol. Biol., 2012, 857, 399-414.
    • (2012) Methods Mol. Biol. , vol.857 , pp. 399-414
    • Dolan, M.A.1    Noah, J.W.2    Hurt, D.3
  • 48
    • 84858126537 scopus 로고    scopus 로고
    • Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal
    • Bordoli, L.; Schwede, T. Automated protein structure modeling with SWISS-MODEL workspace and the protein model portal. Methods Mol. Biol., 2012, 857, 107-136.
    • (2012) Methods Mol. Biol. , vol.857 , pp. 107-136
    • Bordoli, L.1    Schwede, T.2
  • 49
    • 32144432437 scopus 로고    scopus 로고
    • The SWISSMODEL workspace: A web-based environment for protein structure homology modelling
    • Arnold, K.; Bordoli, L.; Kopp, J.; Schwede, T. The SWISSMODEL workspace: a web-based environment for protein structure homology modelling. Bioinformatics 2006, 22(2), 195-201.
    • (2006) Bioinformatics , vol.22 , Issue.2 , pp. 195-201
    • Arnold, K.1    Bordoli, L.2    Kopp, J.3    Schwede, T.4
  • 51
    • 0035703311 scopus 로고    scopus 로고
    • Analysis and assessment of comparative modeling predictions in CASP4
    • Tramontano, A.; Leplae, R.; Morea, V. Analysis and assessment of comparative modeling predictions in CASP4. Proteins, 2001, 45(S5), 22-38.
    • (2001) Proteins , vol.45 , Issue.S5 , pp. 22-38
    • Tramontano, A.1    Leplae, R.2    Morea, V.3
  • 52
    • 66149114339 scopus 로고    scopus 로고
    • Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening
    • Perez-Nueno, V. I.; Pettersson, S.; Ritchie, D. W.; Borrell, J. I.; Teixido, J. Discovery of novel HIV entry inhibitors for the CXCR4 receptor by prospective virtual screening. J. Chem. Inf. Model., 2009, 49(4), 810-823.
    • (2009) J. Chem. Inf. Model. , vol.49 , Issue.4 , pp. 810-823
    • Perez-Nueno, V.I.1    Pettersson, S.2    Ritchie, D.W.3    Borrell, J.I.4    Teixido, J.5
  • 53
    • 53349142711 scopus 로고    scopus 로고
    • Enhancing drug discovery through in silico screening: Strategies to increase true positives retrieval rates
    • Kirchmair, J.; Distinto, S.; Schuster, D.; Spitzer, G.; Langer, T.; Wolber, G. Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates. Curr. med. chem., 2008, 15(20), 2040-2053.
    • (2008) Curr. Med. Chem. , vol.15 , Issue.20 , pp. 2040-2053
    • Kirchmair, J.1    Distinto, S.2    Schuster, D.3    Spitzer, G.4    Langer, T.5    Wolber, G.6
  • 54
    • 34547566446 scopus 로고    scopus 로고
    • ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins
    • Wiederstein, M.; Sippl, M. J. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res., 2007, 35, 407-410.
    • (2007) Nucleic Acids Res. , vol.35 , pp. 407-410
    • Wiederstein, M.1    Sippl, M.J.2
  • 55
    • 55549141879 scopus 로고    scopus 로고
    • How well can the accuracy of comparative protein structure models be predicted?
    • Eramian, D.; Eswar, N.; Shen, M. Y.; Sali, A. How well can the accuracy of comparative protein structure models be predicted? Protein Sci., 2008, 17(11), 1881-1893.
    • (2008) Protein Sci. , vol.17 , Issue.11 , pp. 1881-1893
    • Eramian, D.1    Eswar, N.2    Shen, M.Y.3    Sali, A.4
  • 56
    • 66149156968 scopus 로고    scopus 로고
    • Evaluating the absolute quality of a single protein model using structural features and support vector machines
    • Wang, Z.; Tegge, A. N.; Cheng, J. Evaluating the absolute quality of a single protein model using structural features and support vector machines. Proteins, 2009, 75(3), 638-647.
    • (2009) Proteins , vol.75 , Issue.3 , pp. 638-647
    • Wang, Z.1    Tegge, A.N.2    Cheng, J.3
  • 57
    • 79551613290 scopus 로고    scopus 로고
    • Toward the estimation of the absolute quality of individual protein structure models
    • Benkert, P.; Biasini, M.; Schwede, T. Toward the estimation of the absolute quality of individual protein structure models. Bioinformatics, 2011, 27(3), 343-350.
    • (2011) Bioinformatics , vol.27 , Issue.3 , pp. 343-350
    • Benkert, P.1    Biasini, M.2    Schwede, T.3
  • 58
    • 84883780190 scopus 로고    scopus 로고
    • Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system
    • Giri, R.; Morrone, A.; Toto, A.; Brunori, M.; Gianni, S. Structure of the transition state for the binding of c-Myb and KIX highlights an unexpected order for a disordered system. Proc. Natl. Acad. Sci. USA., 2013, 110(37), 14942-14947.
    • (2013) Proc. Natl. Acad. Sci. USA. , vol.110 , Issue.37 , pp. 14942-14947
    • Giri, R.1    Morrone, A.2    Toto, A.3    Brunori, M.4    Gianni, S.5
  • 59
    • 84925114160 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in cellular signalling and regulation
    • Wright, P. E.; Dyson, H. J. Intrinsically disordered proteins in cellular signalling and regulation. Nat. Rev. Mol. Cell Biol., 2015, 16(1), 18-29.
    • (2015) Nat. Rev. Mol. Cell Biol. , vol.16 , Issue.1 , pp. 18-29
    • Wright, P.E.1    Dyson, H.J.2
  • 60
    • 48249097986 scopus 로고    scopus 로고
    • Intrinsically disordered proteins in human diseases: Introducing the D2 concept
    • Uversky, V. N.; Oldfield, C. J.; Dunker, A. K. Intrinsically disordered proteins in human diseases: introducing the D2 concept. Annu. Rev. Biophys. 2008, 37, 215-246.
    • (2008) Annu. Rev. Biophys , vol.37 , pp. 215-246
    • Uversky, V.N.1    Oldfield, C.J.2    Dunker, A.K.3
  • 61
    • 77955327536 scopus 로고    scopus 로고
    • Intrinsically disordered proteins are potential drug targets
    • Metallo, S. J. Intrinsically disordered proteins are potential drug targets. Curr. Opin. Chem. Biol., 2010, 14(4), 481-488.
    • (2010) Curr. Opin. Chem. Biol. , vol.14 , Issue.4 , pp. 481-488
    • Metallo, S.J.1
  • 62
    • 84860838201 scopus 로고    scopus 로고
    • Structure-based computational analysis of protein binding sites for function and druggability prediction
    • Nisius, B.; Sha, F.; Gohlke, H. Structure-based computational analysis of protein binding sites for function and druggability prediction. J.biotechnol., 2012, 159(3), 123-134.
    • (2012) J.Biotechnol. , vol.159 , Issue.3 , pp. 123-134
    • Nisius, B.1    Sha, F.2    Gohlke, H.3
  • 63
    • 54749109580 scopus 로고    scopus 로고
    • How to measure the similarity between protein ligand-binding sites
    • Kellenberger, E.; Schalon, C.; Rognan, D. How to measure the similarity between protein ligand-binding sites? Curr. Compu.-Aid Drug 2008, 4(3), 1-12.
    • (2008) Curr. Compu.-Aid Drug , vol.4 , Issue.3 , pp. 1-12
    • Kellenberger, E.1    Schalon, C.2    Rognan, D.3
  • 64
    • 0037661398 scopus 로고    scopus 로고
    • A new bioinformatic approach to detect common 3D sites in protein structures
    • Jambon, M.; Imberty, A.; Deleage, G.; Geourjon, C. A new bioinformatic approach to detect common 3D sites in protein structures. Proteins, 2003, 52(2), 137-145.
    • (2003) Proteins , vol.52 , Issue.2 , pp. 137-145
    • Jambon, M.1    Imberty, A.2    Deleage, G.3    Geourjon, C.4
  • 65
    • 0041620372 scopus 로고    scopus 로고
    • Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures
    • Stark, A.; Russell, R. B. Annotation in three dimensions. PINTS: Patterns in Non-homologous Tertiary Structures. Nucleic Acids Res., 2003, 31(13), 3341-3344.
    • (2003) Nucleic Acids Res. , vol.31 , Issue.13 , pp. 3341-3344
    • Stark, A.1    Russell, R.B.2
  • 66
    • 44349119204 scopus 로고    scopus 로고
    • A simple and fuzzy method to align and compare druggable ligand-binding sites
    • Schalon, C.; Surgand, J. S.; Kellenberger, E.; Rognan, D. A simple and fuzzy method to align and compare druggable ligand-binding sites. Proteins, 2008, 71(4), 1755-1778.
    • (2008) Proteins , vol.71 , Issue.4 , pp. 1755-1778
    • Schalon, C.1    Surgand, J.S.2    Kellenberger, E.3    Rognan, D.4
  • 67
    • 78650352933 scopus 로고    scopus 로고
    • Quo vadis, virtual screening? A comprehensive survey of prospective applications
    • Ripphausen, P.; Nisius, B.; Peltason, L.; Bajorath, J. Quo vadis, virtual screening? A comprehensive survey of prospective applications. J. Med. Chem., 2010, 53(24), 8461-8467.
    • (2010) J. Med. Chem. , vol.53 , Issue.24 , pp. 8461-8467
    • Ripphausen, P.1    Nisius, B.2    Peltason, L.3    Bajorath, J.4
  • 68
    • 48749127628 scopus 로고    scopus 로고
    • What has virtual screening ever done for drug discovery? Expert Opin
    • Clark, D. E. What has virtual screening ever done for drug discovery? Expert Opin. Drug Discov., 2008, 3(8):841-851.
    • (2008) Drug Discov. , vol.3 , Issue.8 , pp. 841-851
    • Clark, D.E.1
  • 69
    • 33846064318 scopus 로고    scopus 로고
    • Processing of small molecule databases for automated docking
    • Cummings, M. D.; Maxwell, A. C.; DesJarlais, R. L. Processing of small molecule databases for automated docking. Med. Chem., 2007, 3(1), 107-113.
    • (2007) Med. Chem. , vol.3 , Issue.1 , pp. 107-113
    • Cummings, M.D.1    Maxwell, A.C.2    Desjarlais, R.L.3
  • 70
    • 77950571108 scopus 로고    scopus 로고
    • New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays
    • Baell, J. B.; Holloway, G. A. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J.Med.Chem., 2010, 53(7), 2719-2740.
    • (2010) J.Med.Chem. , vol.53 , Issue.7 , pp. 2719-2740
    • Baell, J.B.1    Holloway, G.A.2
  • 71
    • 77952477596 scopus 로고    scopus 로고
    • Privileged scaffolds for library design and drug discovery
    • Welsch, M. E.; Snyder, S. A.; Stockwell, B. R. Privileged scaffolds for library design and drug discovery. Curr.Opin.Chem.Biol., 2010, 14(3), 347-361.
    • (2010) Curr.Opin.Chem.Biol. , vol.14 , Issue.3 , pp. 347-361
    • Welsch, M.E.1    Snyder, S.A.2    Stockwell, B.R.3
  • 72
    • 84921838527 scopus 로고    scopus 로고
    • Fragment-Based Drug Discovery and Molecular Docking in Drug Design
    • Wang, T.; Wu, M.; Chen, Z.; Lin, J.; Yang, L. Fragment-Based Drug Discovery and Molecular Docking in Drug Design. Curr. Pharm. Biotechnol., 2015, 16(1):11-25.
    • (2015) Curr. Pharm. Biotechnol. , vol.16 , Issue.1 , pp. 11-25
    • Wang, T.1    Wu, M.2    Chen, Z.3    Lin, J.4    Yang, L.5
  • 73
    • 76149120388 scopus 로고    scopus 로고
    • AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
    • Trott, O.; Olson, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. J.Comput.Chem., 2010, 31(2), 455-461.
    • (2010) J.Comput.Chem. , vol.31 , Issue.2 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 74
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J.Mol.Biol., 1996, 261(3), 470-489.
    • (1996) J.Mol.Biol. , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 75
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S. J. Implications of protein flexibility for drug discovery. Nat.Rev. Drug Discov., 2003, 2(7), 527-541.
    • (2003) Nat.Rev. Drug Discov. , vol.2 , Issue.7 , pp. 527-541
    • Teague, S.J.1
  • 77
    • 77953189302 scopus 로고    scopus 로고
    • A new Lamarckian genetic algorithm for flexible ligand-receptor docking
    • Fuhrmann, J.; Rurainski, A.; Lenhof, H. P.; Neumann, D. A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J. Comput. Chem., 2010, 31(9), 1911-1918.
    • (2010) J. Comput. Chem , vol.31 , Issue.9 , pp. 1911-1918
    • Fuhrmann, J.1    Rurainski, A.2    Lenhof, H.P.3    Neumann, D.4
  • 78
    • 47249102090 scopus 로고    scopus 로고
    • A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE)
    • Bottegoni, G.; Kufareva, I.; Totrov, M.; Abagyan, R. A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE). J.Comput-Aid Mol.Design 2008, 22(5), 311-325.
    • (2008) J.Comput-Aid Mol.Design , vol.22 , Issue.5 , pp. 311-325
    • Bottegoni, G.1    Kufareva, I.2    Totrov, M.3    Abagyan, R.4
  • 80
    • 79959224583 scopus 로고    scopus 로고
    • Molecular docking: A powerful approach for structure-based drug discovery
    • Meng, X.Y.; Zhang, H.X.; Mezei, M.; Cui, M. Molecular docking: a powerful approach for structure-based drug discovery. Curr.Comput-Aid Drug Des., 2011, 7(2), 146.
    • (2011) Curr.Comput-Aid Drug Des. , vol.7 , Issue.2 , pp. 146
    • Meng, X.Y.1    Zhang, H.X.2    Mezei, M.3    Cui, M.4
  • 81
    • 79952181220 scopus 로고    scopus 로고
    • Challenges and advances in computational docking: 2009 in review
    • Yuriev, E.; Agostino, M.; Ramsland, P. A. Challenges and advances in computational docking: 2009 in review. J.Mol. Recognit., 2011, 24(2), 149-164.
    • (2011) J.Mol. Recognit. , vol.24 , Issue.2 , pp. 149-164
    • Yuriev, E.1    Agostino, M.2    Ramsland, P.A.3
  • 82
    • 77953201731 scopus 로고    scopus 로고
    • 4SC-101, a novel immunosuppressive drug, inhibits IL-17 and attenuates colitis in two murine models of inflammatory bowel disease
    • Fitzpatrick, L. R.; Deml, L.; Hofmann, C.; Small, J. S.; Groeppel, M.; Hamm, S.; Lemstra, S.; Leban, J.; Ammendola, A. 4SC-101, a novel immunosuppressive drug, inhibits IL-17 and attenuates colitis in two murine models of inflammatory bowel disease. Inflamm. Bowel. Dis., 2010, 16(10), 1763-1777.
    • (2010) Inflamm. Bowel. Dis. , vol.16 , Issue.10 , pp. 1763-1777
    • Fitzpatrick, L.R.1    Deml, L.2    Hofmann, C.3    Small, J.S.4    Groeppel, M.5    Hamm, S.6    Lemstra, S.7    Leban, J.8    Ammendola, A.9
  • 86
    • 84858440068 scopus 로고    scopus 로고
    • Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint-and pharmacophore-based virtual screening approach
    • Distinto, S.; Esposito, F.; Kirchmair, J.; Cardia, M. C.; Gaspari, M.; Maccioni, E.; Alcaro, S.; Markt, P.; Wolber, G.; Zinzula, L. Identification of HIV-1 reverse transcriptase dual inhibitors by a combined shape-, 2D-fingerprint-and pharmacophore-based virtual screening approach. Euro.J.Med.Chem., 2012, 50, 216-229.
    • (2012) Euro.J.Med.Chem. , vol.50 , pp. 216-229
    • Distinto, S.1    Esposito, F.2    Kirchmair, J.3    Cardia, M.C.4    Gaspari, M.5    Maccioni, E.6    Alcaro, S.7    Markt, P.8    Wolber, G.9    Zinzula, L.10
  • 89
    • 80052858265 scopus 로고    scopus 로고
    • Structure-based drug design to augment hit discovery
    • Kalyaanamoorthy, S.; Chen, Y.P. P. Structure-based drug design to augment hit discovery. Drug Discov.Today, 2011, 16(17), 831-839.
    • (2011) Drug Discov.Today , vol.16 , Issue.17 , pp. 831-839
    • Kalyaanamoorthy, S.1    Chen, Y.P.P.2
  • 90
    • 77955982439 scopus 로고    scopus 로고
    • Structural biology in fragmentbased drug design
    • Murray, C. W.; Blundell, T. L. Structural biology in fragmentbased drug design. Curr.Opin.Struc.Biol., 2010, 20(4), 497-507.
    • (2010) Curr.Opin.Struc.Biol. , vol.20 , Issue.4 , pp. 497-507
    • Murray, C.W.1    Blundell, T.L.2
  • 91
    • 23844449940 scopus 로고    scopus 로고
    • Computer-based de novo design of drug-like molecules
    • Schneider, G.; Fechner, U., Computer-based de novo design of drug-like molecules. Nat. Rev. Drug Discov., 2005, 4(8), 649-663.
    • (2005) Nat. Rev. Drug Discov. , vol.4 , Issue.8 , pp. 649-663
    • Schneider, G.1    Fechner, U.2
  • 92
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Bohm, H. J., The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J. Comput-Aid Mol.Des., 1992, 6(1), 61-78.
    • (1992) J. Comput-Aid Mol.Des. , vol.6 , Issue.1 , pp. 61-78
    • Bohm, H.J.1
  • 95
    • 33646265985 scopus 로고    scopus 로고
    • Flux (1): A virtual synthesis scheme for fragment-based de novo design
    • Fechner, U.; Schneider, G. Flux (1): a virtual synthesis scheme for fragment-based de novo design. J. Chem. Inf. Model., 2006, 46(2), 699-707.
    • (2006) J. Chem. Inf. Model. , vol.46 , Issue.2 , pp. 699-707
    • Fechner, U.1    Schneider, G.2
  • 96
    • 42149174453 scopus 로고    scopus 로고
    • Fragment-based de novo ligand design by multiobjective evolutionary optimization
    • Dey, F.; Caflisch, A. Fragment-based de novo ligand design by multiobjective evolutionary optimization. J. Chem. Inf. Model., 2008, 48(3), 679-690.
    • (2008) J. Chem. Inf. Model. , vol.48 , Issue.3 , pp. 679-690
    • Dey, F.1    Caflisch, A.2
  • 97
    • 77949345618 scopus 로고    scopus 로고
    • Computational approaches for fragment-based and de novo design
    • Loving, K.; Alberts, I.; Sherman, W. Computational approaches for fragment-based and de novo design. Curr. Top. Med. Chem., 2010, 10(1), 14-32.
    • (2010) Curr. Top. Med. Chem. , vol.10 , Issue.1 , pp. 14-32
    • Loving, K.1    Alberts, I.2    Sherman, W.3
  • 98
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • Jorgensen, W. L. The many roles of computation in drug discovery. Science 2004, 303(5665), 1813-1818.
    • (2004) Science , vol.303 , Issue.5665 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 99
    • 0028380643 scopus 로고
    • CAVEAT: A program to facilitate the design of organic molecules
    • Lauri, G.; Bartlett, P. A. CAVEAT: a program to facilitate the design of organic molecules. J.Comput-Aid Mol.Des., 1994, 8(1), 51-66.
    • (1994) J.Comput-Aid Mol.Des. , vol.8 , Issue.1 , pp. 51-66
    • Lauri, G.1    Bartlett, P.A.2
  • 101
    • 0026813925 scopus 로고
    • The computer program LUDI: A new method for the de novo design of enzyme inhibitors
    • Bohm, H.J. The computer program LUDI: a new method for the de novo design of enzyme inhibitors. J.Comput-Aid Mol.Des., 1992, 6(1), 61-78.
    • (1992) J.Comput-Aid Mol.Des. , vol.6 , Issue.1 , pp. 61-78
    • Bohm, H.J.1
  • 102
    • 1642288258 scopus 로고    scopus 로고
    • Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening
    • Boehm, H.J.; Boehringer, M.; Bur, D.; Gmuender, H.; Huber, W.; Klaus, W.; Kostrewa, D.; Kuehne, H.; Luebbers, T.; Meunier- Keller, N. Novel inhibitors of DNA gyrase: 3D structure based biased needle screening, hit validation by biophysical methods, and 3D guided optimization. A promising alternative to random screening. J. Med. Chem., 2000, 43(14), 2664-2674.
    • (2000) J. Med. Chem. , vol.43 , Issue.14 , pp. 2664-2674
    • Boehm, H.J.1    Boehringer, M.2    Bur, D.3    Gmuender, H.4    Huber, W.5    Klaus, W.6    Kostrewa, D.7    Kuehne, H.8    Luebbers, T.9    Meunier- Keller, N.10
  • 103
    • 0017776823 scopus 로고
    • Dynamics of folded proteins
    • McCamm0n, J. A. Dynamics of folded proteins. Nature 1977, 267, 585-590.
    • (1977) Nature , vol.267 , pp. 585-590
    • McCamm0n, J.A.1
  • 105
    • 33845923661 scopus 로고    scopus 로고
    • Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations
    • Tubert-Brohman, I.; Acevedo, O.; Jorgensen, W. L. Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations. J. Am. Chem. Soc.2006, 128(51), 16904-16913.
    • (2006) J. Am. Chem. Soc , vol.128 , Issue.51 , pp. 16904-16913
    • Tubert-Brohman, I.1    Acevedo, O.2    Jorgensen, W.L.3
  • 106
    • 84863775602 scopus 로고    scopus 로고
    • Refinement of protein structure homology models via long, all-atom molecular dynamics simulations
    • Raval, A.; Piana, S.; Eastwood, M. P.; Dror, R. O.; Shaw, D. E. Refinement of protein structure homology models via long, all-atom molecular dynamics simulations. Proteins, 2012, 80(8), 2071-2079.
    • (2012) Proteins , vol.80 , Issue.8 , pp. 2071-2079
    • Raval, A.1    Piana, S.2    Eastwood, M.P.3    Dror, R.O.4    Shaw, D.E.5
  • 107
    • 76749152401 scopus 로고    scopus 로고
    • Structure and dynamics of double helical DNA in torsion angle hyperspace: A molecular mechanics approach
    • Borkar, A.; Ghosh, I.; Bhattacharyya, D. Structure and dynamics of double helical DNA in torsion angle hyperspace: A molecular mechanics approach. J. Biomol. Struct. Dyn., 2010, 27(5), 695-712.
    • (2010) J. Biomol. Struct. Dyn. , vol.27 , Issue.5 , pp. 695-712
    • Borkar, A.1    Ghosh, I.2    Bhattacharyya, D.3
  • 108
    • 0037436001 scopus 로고    scopus 로고
    • Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydr
    • Eklund, R.; Widmalm, G. Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates. Carbohydr. Res., 2003, 338(5), 393-398.
    • (2003) Res. , vol.338 , Issue.5 , pp. 393-398
    • Eklund, R.1    Widmalm, G.2
  • 110
    • 84934924023 scopus 로고    scopus 로고
    • Sansom, M. Molecular simulation studies of hydrophobic gating in nanopores and ion channels
    • Trick, J. L.; Aryal, P.; Tucker, S. J.; Sansom, M. Molecular simulation studies of hydrophobic gating in nanopores and ion channels. Biochem. Soc.Trans., 2015, 43(2), 146-150.
    • (2015) Biochem. Soc.Trans. , vol.43 , Issue.2 , pp. 146-150
    • Trick, J.L.1    Aryal, P.2    Tucker, S.J.3
  • 111
    • 51349134973 scopus 로고    scopus 로고
    • Refining homology models by combining replica-exchange molecular dynamics and statistical potentials
    • Zhu, J.; Fan, H.; Periole, X.; Honig, B.; Mark, A. E. Refining homology models by combining replica-exchange molecular dynamics and statistical potentials. Proteins, 2008, 72(4), 1171-1188.
    • (2008) Proteins , vol.72 , Issue.4 , pp. 1171-1188
    • Zhu, J.1    Fan, H.2    Periole, X.3    Honig, B.4    Mark, A.E.5
  • 112
    • 34248549547 scopus 로고    scopus 로고
    • Can molecular dynamics simulations provide high-resolution refinement of protein structure?
    • Chen, J.; Brooks, C. L. Can molecular dynamics simulations provide high-resolution refinement of protein structure? Proteins, 2007, 67(4), 922-930.
    • (2007) Proteins , vol.67 , Issue.4 , pp. 922-930
    • Chen, J.1    Brooks, C.L.2
  • 113
    • 79955880283 scopus 로고    scopus 로고
    • Using Theory to Reconcile Experiment: The Structural and Thermodynamic Basis of Ligand Recognition by Phenylethanolamine N-Methyltransferase (PNMT)
    • Nair, P. C.; Malde, A. K.; Mark, A. E. Using Theory to Reconcile Experiment: The Structural and Thermodynamic Basis of Ligand Recognition by Phenylethanolamine N-Methyltransferase (PNMT).J. Chem. Theory Comput., 2011, 7(5), 1458-1468.
    • (2011) J. Chem. Theory Comput. , vol.7 , Issue.5 , pp. 1458-1468
    • Nair, P.C.1    Malde, A.K.2    Mark, A.E.3
  • 114
    • 84859782888 scopus 로고    scopus 로고
    • Missing fragments: Detecting cooperative binding in fragment-based drug design
    • Nair, P. C.; Malde, A. K.; Drinkwater, N.; Mark, A. E. Missing fragments: Detecting cooperative binding in fragment-based drug design. ACS Med. Chem. Lett., 2012, 3(4), 322-326.
    • (2012) ACS Med. Chem. Lett. , vol.3 , Issue.4 , pp. 322-326
    • Nair, P.C.1    Malde, A.K.2    Drinkwater, N.3    Mark, A.E.4
  • 116
  • 117
    • 77955249382 scopus 로고    scopus 로고
    • Mapping the druggable allosteric space of G-protein coupled receptors: A fragment-based molecular dynamics approach
    • Ivetac, A.; Andrew McCammon, J. Mapping the druggable allosteric space of G-protein coupled receptors: a fragment-based molecular dynamics approach. Chem.Biol.Drug Des., 2010, 76(3), 201-217.
    • (2010) Chem.Biol.Drug Des. , vol.76 , Issue.3 , pp. 201-217
    • Ivetac, A.1    Andrew McCammon, J.2
  • 122
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma, B.; Shatsky, M.; Wolfson, H. J.; Nussinov, R. Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations. Protein Sci., 2002, 11(2), 184-197.
    • (2002) Protein Sci. , vol.11 , Issue.2 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 123
    • 79960007037 scopus 로고    scopus 로고
    • Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations
    • Buch, I.; Giorgino, T.; De Fabritiis, G. Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Proc. Natl. Acad. Sci. USA., 2011, 108(25), 10184-10189.
    • (2011) Proc. Natl. Acad. Sci. USA. , vol.108 , Issue.25 , pp. 10184-10189
    • Buch, I.1    Giorgino, T.2    De Fabritiis, G.3
  • 124
    • 80051595050 scopus 로고    scopus 로고
    • Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2
    • Wang, J.; Ma, C.; Fiorin, G.; Carnevale, V.; Wang, T.; Hu, F.; Lamb, R. A.; Pinto, L. H.; Hong, M.; Klein, M. L. Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2. J. Am. Chem. Soc., 2011, 133(32), 12834-12841.
    • (2011) J. Am. Chem. Soc. , vol.133 , Issue.32 , pp. 12834-12841
    • Wang, J.1    Ma, C.2    Fiorin, G.3    Carnevale, V.4    Wang, T.5    Hu, F.6    Lamb, R.A.7    Pinto, L.H.8    Hong, M.9    Klein, M.L.10
  • 126
    • 0023751431 scopus 로고
    • Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins
    • Cramer, R. D.; Patterson, D. E.; Bunce, J. D. Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J. Am. Chem. Soc., 1988, 110(18), 5959-5967.
    • (1988) J. Am. Chem. Soc. , vol.110 , Issue.18 , pp. 5959-5967
    • Cramer, R.D.1    Patterson, D.E.2    Bunce, J.D.3
  • 127
    • 0027944195 scopus 로고
    • Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity
    • Klebe, G.; Abraham, U.; Mietzner, T. Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J. Med. Chem., 1994, 37(24), 4130-4146.
    • (1994) J. Med. Chem. , vol.37 , Issue.24 , pp. 4130-4146
    • Klebe, G.1    Abraham, U.2    Mietzner, T.3
  • 128
    • 13844320566 scopus 로고    scopus 로고
    • LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters
    • Wolber, G.; Langer, T. LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters. J.Chem.Inf. model., 2005, 45(1), 160-169.
    • (2005) J.Chem.Inf. Model. , vol.45 , Issue.1 , pp. 160-169
    • Wolber, G.1    Langer, T.2
  • 129
    • 33845727607 scopus 로고    scopus 로고
    • Pocket v. 2: Further developments on receptorbased pharmacophore modeling
    • Chen, J.; Lai, L. Pocket v. 2: further developments on receptorbased pharmacophore modeling. J.Chem.Inf. model., 2006, 46(6), 2684-2691.
    • (2006) J.Chem.Inf. Model. , vol.46 , Issue.6 , pp. 2684-2691
    • Chen, J.1    Lai, L.2
  • 130
    • 33745584385 scopus 로고    scopus 로고
    • GRID-based pharmacophore model: Concept and application studies to protein–protein recognition
    • Ortuso, F.; Langer, T.; Alcaro, S. GBPM: GRID-based pharmacophore model: concept and application studies to protein–protein recognition. Bioinformatics, 2006, 22(12), 1449-1455.
    • (2006) Bioinformatics , vol.22 , Issue.12 , pp. 1449-1455
    • Ortuso, F.1    Langer, T.2    Alcaro, S.3
  • 131
    • 79952171625 scopus 로고    scopus 로고
    • Probing the links between in vitro potency, ADMET and physicochemical parameters
    • Gleeson, M. P.; Hersey, A.; Montanari, D.; Overington, J. Probing the links between in vitro potency, ADMET and physicochemical parameters. Nat. Rev. Drug Discov., 2011, 10(3), 197-208.
    • (2011) Nat. Rev. Drug Discov. , vol.10 , Issue.3 , pp. 197-208
    • Gleeson, M.P.1    Hersey, A.2    Montanari, D.3    Overington, J.4
  • 132
    • 0036606241 scopus 로고    scopus 로고
    • Predicting ADME properties in silico: Methods and models
    • Butina, D.; Segall, M. D.; Frankcombe, K. Predicting ADME properties in silico: methods and models. Drug Discov. Today, 2002, 7(11), 83-88.
    • (2002) Drug Discov. Today , vol.7 , Issue.11 , pp. 83-88
    • Butina, D.1    Segall, M.D.2    Frankcombe, K.3
  • 133
    • 78650194463 scopus 로고    scopus 로고
    • Rigorous Free Energy Calculations in Structure-Based Drug Design
    • Michel, J.; Foloppe, N.; Essex, J. W. Rigorous Free Energy Calculations in Structure-Based Drug Design. Mol. Inf., 2010, 29(9), 570-578.
    • (2010) Mol. Inf. , vol.29 , Issue.9 , pp. 570-578
    • Michel, J.1    Foloppe, N.2    Essex, J.W.3
  • 134
    • 0031804609 scopus 로고    scopus 로고
    • INHIBITORS OF HIV-1 PROTEASE: Amajor success of structure-assisted drug design 1
    • Wlodawer, A.; Vondrasek, J. INHIBITORS OF HIV-1 PROTEASE: amajor success of structure-assisted drug design 1. Annu. Rev. Biophys. Biomol. Struct., 1998, 27(1), 249-284.
    • (1998) Annu. Rev. Biophys. Biomol. Struct. , vol.27 , Issue.1 , pp. 249-284
    • Wlodawer, A.1    Vondrasek, J.2
  • 136
    • 50249083873 scopus 로고    scopus 로고
    • Identification of N-(4-Piperidinyl)-4-(2, 6- dichlorobenzoylamino)-1 H-pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design†
    • Wyatt, P. G.; Woodhead, A. J.; Berdini, V.; Boulstridge, J. A.; Carr, M. G.; Cross, D. M.; Davis, D. J.; Devine, L. A.; Early, T. R.; Feltell, R. E. Identification of N-(4-Piperidinyl)-4-(2, 6- dichlorobenzoylamino)-1 H-pyrazole-3-carboxamide (AT7519), a Novel Cyclin Dependent Kinase Inhibitor Using Fragment-Based X-Ray Crystallography and Structure Based Drug Design†. J. Med. Chem., 2008, 51(16), 4986-4999.
    • (2008) J. Med. Chem. , vol.51 , Issue.16 , pp. 4986-4999
    • Wyatt, P.G.1    Woodhead, A.J.2    Berdini, V.3    Boulstridge, J.A.4    Carr, M.G.5    Cross, D.M.6    Davis, D.J.7    Devine, L.A.8    Early, T.R.9    Feltell, R.E.10
  • 137
    • 80052806086 scopus 로고    scopus 로고
    • Structure based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal–epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK)
    • Cui, J. J.; Tran-Dube, M.; Shen, H.; Nambu, M.; Kung, P.-P.; Pairish, M.; Jia, L.; Meng, J.; Funk, L.; Botrous, I. Structure based drug design of crizotinib (PF-02341066), a potent and selective dual inhibitor of mesenchymal–epithelial transition factor (c-MET) kinase and anaplastic lymphoma kinase (ALK). J. Med. Chem., 2011, 54(18), 6342-6363.
    • (2011) J. Med. Chem. , vol.54 , Issue.18 , pp. 6342-6363
    • Cui, J.J.1    Tran-Dube, M.2    Shen, H.3    Nambu, M.4    Kung, P.-P.5    Pairish, M.6    Jia, L.7    Meng, J.8    Funk, L.9    Botrous, I.10
  • 138
    • 73949094934 scopus 로고    scopus 로고
    • Structure- based drug design identifies novel LPA 3 antagonists. Biorg. Med
    • Fells, J. I.; Tsukahara, R.; Liu, J.; Tigyi, G.; Parrill, A. L., Structure- based drug design identifies novel LPA 3 antagonists. Biorg. Med. Chem., 2009, 17(21), 7457-7464.
    • (2009) Chem. , vol.17 , Issue.21 , pp. 7457-7464
    • Fells, J.I.1    Tsukahara, R.2    Liu, J.3    Tigyi, G.4    Parrill, A.L.5
  • 139
    • 66249144426 scopus 로고    scopus 로고
    • The structure and function of G-protein-coupled receptors
    • Rosenbaum, D. M.; Rasmussen, S. G.; Kobilka, B. K. The structure and function of G-protein-coupled receptors. Nature, 2009, 459(7245), 356-363.
    • (2009) Nature , vol.459 , Issue.7245 , pp. 356-363
    • Rosenbaum, D.M.1    Rasmussen, S.G.2    Kobilka, B.K.3
  • 140
    • 84877716938 scopus 로고    scopus 로고
    • Biophysical fragment screening of the β1-adrenergic receptor: Identification of high affinity arylpiperazine leads using structurebased drug design
    • Christopher, J. A.; Brown, J.; Dore, A. S.; Errey, J. C.; Koglin, M.; Marshall, F. H.; Myszka, D. G.; Rich, R. L.; Tate, C. G.; Tehan, B. Biophysical fragment screening of the β1-adrenergic receptor: identification of high affinity arylpiperazine leads using structurebased drug design. J. Med. Chem., 2013, 56(9), 3446-3455.
    • (2013) J. Med. Chem. , vol.56 , Issue.9 , pp. 3446-3455
    • Christopher, J.A.1    Brown, J.2    Dore, A.S.3    Errey, J.C.4    Koglin, M.5    Marshall, F.H.6    Myszka, D.G.7    Rich, R.L.8    Tate, C.G.9    Tehan, B.10
  • 143
    • 84877279350 scopus 로고    scopus 로고
    • Platforms for antibiotic discovery
    • Lewis, K., Platforms for antibiotic discovery. Nat. Rev. Drug Discov., 2013, 12(5), 371-387.
    • (2013) Nat. Rev. Drug Discov. , vol.12 , Issue.5 , pp. 371-387
    • Lewis, K.1
  • 147
    • 2342591455 scopus 로고    scopus 로고
    • The discovery of receptor tyrosine kinases: Targets for cancer therapy
    • Gschwind, A.; Fischer, O. M.; Ullrich, A. The discovery of receptor tyrosine kinases: targets for cancer therapy. Nat. Rev. Cancer, 2004, 4(5), 361-370.
    • (2004) Nat. Rev. Cancer , vol.4 , Issue.5 , pp. 361-370
    • Gschwind, A.1    Fischer, O.M.2    Ullrich, A.3
  • 148
    • 22044442973 scopus 로고    scopus 로고
    • Tyrosine kinases as targets for cancer therapy
    • Krause, D. S.; Van Etten, R. A. Tyrosine kinases as targets for cancer therapy.N. Engl. J. Med., 2005, 353(2), 172-187.
    • (2005) N. Engl. J. Med. , vol.353 , Issue.2 , pp. 172-187
    • Krause, D.S.1    Van Etten, R.A.2
  • 149
    • 84876215753 scopus 로고    scopus 로고
    • Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells
    • Micco, M.; Collie, G. W.; Dale, A. G.; Ohnmacht, S. A.; Pazitna, I.; Gunaratnam, M.; Reszka, A. P.; Neidle, S. Structure-based design and evaluation of naphthalene diimide G-quadruplex ligands as telomere targeting agents in pancreatic cancer cells. J. Med. Chem., 2013, 56(7), 2959-2974.
    • (2013) J. Med. Chem. , vol.56 , Issue.7 , pp. 2959-2974
    • Micco, M.1    Collie, G.W.2    Dale, A.G.3    Ohnmacht, S.A.4    Pazitna, I.5    Gunaratnam, M.6    Reszka, A.P.7    Neidle, S.8
  • 150
    • 74049084628 scopus 로고    scopus 로고
    • Structure-based drug design of tricyclic 8H-indeno[1, 2-d][1, 3]thiazoles as potent FBPase inhibitors
    • Tsukada, T.; Takahashi, M.; Takemoto, T.; Kanno, O.; Yamane, T.; Kawamura, S.; Nishi, T. Structure-based drug design of tricyclic 8H-indeno[1, 2-d][1, 3]thiazoles as potent FBPase inhibitors. Bioorg. Med. Chem. Lett., 2010, 20(3), 1004-1007.
    • (2010) Bioorg. Med. Chem. Lett. , vol.20 , Issue.3 , pp. 1004-1007
    • Tsukada, T.1    Takahashi, M.2    Takemoto, T.3    Kanno, O.4    Yamane, T.5    Kawamura, S.6    Nishi, T.7
  • 152
    • 84868515345 scopus 로고    scopus 로고
    • Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors
    • Claffey, M. M.; Helal, C. J.; Verhoest, P. R.; Kang, Z.; Fors, K. S.; Jung, S.; Zhong, J.; Bundesmann, M. W.; Hou, X.; Lui, S. Application of structure-based drug design and parallel chemistry to identify selective, brain penetrant, in vivo active phosphodiesterase 9A inhibitors. J. Med. Chem., 2012, 55(21), 9055-9068.
    • (2012) J. Med. Chem. , vol.55 , Issue.21 , pp. 9055-9068
    • Claffey, M.M.1    Helal, C.J.2    Verhoest, P.R.3    Kang, Z.4    Fors, K.S.5    Jung, S.6    Zhong, J.7    Bundesmann, M.W.8    Hou, X.9    Lui, S.10
  • 153
    • 84868550667 scopus 로고    scopus 로고
    • Spirocyclic sulfamides as β-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer’s disease: Utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors
    • Brodney, M. A.; Barreiro, G.; Ogilvie, K.; Hajos-Korcsok, E.; Murray, J.; Vajdos, F.; Ambroise, C.; Christoffersen, C.; Fisher, K.; Lanyon, L. Spirocyclic sulfamides as β-secretase 1 (BACE-1) inhibitors for the treatment of Alzheimer’s disease: utilization of structure based drug design, WaterMap, and CNS penetration studies to identify centrally efficacious inhibitors. J. Med. Chem., 2012, 55(21), 9224-9239.
    • (2012) J. Med. Chem. , vol.55 , Issue.21 , pp. 9224-9239
    • Brodney, M.A.1    Barreiro, G.2    Ogilvie, K.3    Hajos-Korcsok, E.4    Murray, J.5    Vajdos, F.6    Ambroise, C.7    Christoffersen, C.8    Fisher, K.9    Lanyon, L.10
  • 156
    • 84855832075 scopus 로고    scopus 로고
    • Ethionamide boosters. 2. Combining bioisosteric replacement and structure-based drug design to solve pharmacokinetic issues in a series of potent 1, 2, 4-oxadiazole EthR inhibitors
    • Flipo, M.; Desroses, M.; Lecat-Guillet, N.; Villemagne, B.; Blondiaux, N.; Leroux, F.; Piveteau, C.; Mathys, V.; Flament, M.- P.; Siepmann, J. Ethionamide boosters. 2. Combining bioisosteric replacement and structure-based drug design to solve pharmacokinetic issues in a series of potent 1, 2, 4-oxadiazole EthR inhibitors. J. Med. Chem., 2011, 55(1), 68-83.
    • (2011) J. Med. Chem. , vol.55 , Issue.1 , pp. 68-83
    • Flipo, M.1    Desroses, M.2    Lecat-Guillet, N.3    Villemagne, B.4    Blondiaux, N.5    Leroux, F.6    Piveteau, C.7    Mathys, V.8    Flament, M.-P.9    Siepmann, J.10
  • 157
    • 84899578167 scopus 로고    scopus 로고
    • Identification of novel HSP90α/β isoform selective inhibitors using structure-based drug design. Demonstration of potential utility in treating CNS disorders such as huntington’s disease
    • Ernst, J. T.; Neubert, T.; Liu, M.; Sperry, S.; Zuccola, H.; Turnbull, A.; Fleck, B.; Kargo, W.; Woody, L.; Chiang, P. Identification of novel HSP90α/β isoform selective inhibitors using structure-based drug design. demonstration of potential utility in treating CNS disorders such as huntington’s disease. J. Med. Chem., 2014, 57(8), 3382-3400.
    • (2014) J. Med. Chem. , vol.57 , Issue.8 , pp. 3382-3400
    • Ernst, J.T.1    Neubert, T.2    Liu, M.3    Sperry, S.4    Zuccola, H.5    Turnbull, A.6    Fleck, B.7    Kargo, W.8    Woody, L.9    Chiang, P.10
  • 158
    • 84875229571 scopus 로고    scopus 로고
    • PF-04859989 as a template for structure-based drug design: Identification of new pyrazole series of irreversible KAT II inhibitors with improved lipophilic efficiency
    • Dounay, A. B.; Anderson, M.; Bechle, B. M.; Evrard, E.; Gan, X.; Kim, J.-Y.; McAllister, L. A.; Pandit, J.; Rong, S.; Salafia, M. A. PF-04859989 as a template for structure-based drug design: identification of new pyrazole series of irreversible KAT II inhibitors with improved lipophilic efficiency. Bioorg. Med. Chem. Lett., 2013, 23(7), 1961-1966.
    • (2013) Bioorg. Med. Chem. Lett. , vol.23 , Issue.7 , pp. 1961-1966
    • Dounay, A.B.1    Anderson, M.2    Bechle, B.M.3    Evrard, E.4    Gan, X.5    Kim, J.-Y.6    McAllister, L.A.7    Pandit, J.8    Rong, S.9    Salafia, M.A.10
  • 159
    • 53549099432 scopus 로고    scopus 로고
    • Novel aldosterone synthase inhibitors with extended carbocyclic skeleton by a combined ligand-based and structure-based drug design approach
    • Lucas, S.; Heim, R.; Negri, M.; Antes, I.; Ries, C.; Schewe, K. E.; Bisi, A.; Gobbi, S.; Hartmann, R. W. Novel aldosterone synthase inhibitors with extended carbocyclic skeleton by a combined ligand-based and structure-based drug design approach. J. Med. Chem., 2008, 51(19), 6138-6149.
    • (2008) J. Med. Chem. , vol.51 , Issue.19 , pp. 6138-6149
    • Lucas, S.1    Heim, R.2    Negri, M.3    Antes, I.4    Ries, C.5    Schewe, K.E.6    Bisi, A.7    Gobbi, S.8    Hartmann, R.W.9
  • 161
    • 78650383453 scopus 로고    scopus 로고
    • W.Structure-based design of antiinfectives
    • Agarwal, A. K.; Fishwick, C. W.Structure-based design of antiinfectives. Ann. NY Acad. Sci., 2010, 1213, 20-45.
    • (2010) Ann. NY Acad. Sci. , vol.1213 , pp. 20-45
    • Agarwal, A.K.1    Fishwick, C.2
  • 163
    • 44949211332 scopus 로고    scopus 로고
    • Fragment-based activity space: Smaller is better
    • Hesterkamp, T.; Whittaker, M., Fragment-based activity space: smaller is better. Curr.Opin.Chem. Biol., 2008, 12(3), 260-268.
    • (2008) Curr.Opin.Chem. Biol. , vol.12 , Issue.3 , pp. 260-268
    • Hesterkamp, T.1    Whittaker, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.