메뉴 건너뛰기




Volumn 819, Issue , 2012, Pages 157-168

Normal mode-based approaches in receptor ensemble docking

Author keywords

Coarse grained representation; Computer aided drug discovery; Docking; Elastic network model; High throughput docking; Multiple receptor conformations; Normal mode analysis; Receptor ensemble docking

Indexed keywords

CELL SURFACE RECEPTOR;

EID: 84855925856     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-465-0_11     Document Type: Article
Times cited : (21)

References (59)
  • 1
    • 11144323163 scopus 로고    scopus 로고
    • Virtual screening of chemical libraries
    • DOI 10.1038/nature03197
    • Shoichet, B. K. (2004) Virtual screening of chemical libraries, Nature 432, 862-865. (Pubitemid 40037142)
    • (2004) Nature , vol.432 , Issue.7019 , pp. 862-865
    • Shoichet, B.K.1
  • 2
    • 34447275949 scopus 로고    scopus 로고
    • Ligand docking and structure-based virtual screening in drug discovery
    • DOI 10.2174/156802607780906753
    • Cavasotto, C. N., and Orry, A. J. (2007) Ligand Docking and Structure-based Virtual Screening in Drug Discovery, Curr. Top. Med. Chem. 7, 1006-1014. (Pubitemid 47040528)
    • (2007) Current Topics in Medicinal Chemistry , vol.7 , Issue.10 , pp. 1006-1014
    • Cavasotto, C.N.1    Orry, A.J.W.2
  • 3
    • 1642357706 scopus 로고    scopus 로고
    • The many roles of computation in drug discovery
    • DOI 10.1126/science.1096361
    • Jorgensen, W. L. (2004) The many roles of computation in drug discovery, Science 303, 1813-1818. (Pubitemid 38374866)
    • (2004) Science , vol.303 , Issue.5665 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 4
    • 54749115273 scopus 로고    scopus 로고
    • Docking and high throughput docking: Successes and the challenge of protein flexibility
    • Cavasotto, C. N., and Singh, N. (2008) Docking and High Throughput Docking: Successes and the Challenge of Protein Flexibility Curr. Comput.-Aided Drug Design 4, 221-234.
    • (2008) Curr. Comput.-Aided Drug Design , vol.4 , pp. 221-234
    • Cavasotto, C.N.1    Singh, N.2
  • 5
    • 0037666888 scopus 로고    scopus 로고
    • Implications of protein flexibility for drug discovery
    • Teague, S. J. (2003) Implications of protein flexibility for drug discovery, Nat Rev Drug Discov 2, 527-541. (Pubitemid 37361745)
    • (2003) Nature Reviews Drug Discovery , vol.2 , Issue.7 , pp. 527-541
    • Teague, S.J.1
  • 6
    • 1442351132 scopus 로고    scopus 로고
    • Protein flexibility in ligand docking and virtual screening to protein kinases
    • DOI 10.1016/j.jmb.2004.01.003
    • Cavasotto, C. N., and Abagyan, R. A. (2004) Protein flexibility in ligand docking and virtual screening to protein kinases, J. Mol. Biol. 337, 209-225. (Pubitemid 38270258)
    • (2004) Journal of Molecular Biology , vol.337 , Issue.1 , pp. 209-225
    • Cavasotto, C.N.1    Abagyan, R.A.2
  • 7
    • 21644473891 scopus 로고    scopus 로고
    • Representing receptor flexibility in ligand docking through relevant normal modes
    • DOI 10.1021/ja042260c
    • Cavasotto, C. N., Kovacs, J. A., and Abagyan, R. A. (2005) Representing Receptor Flexibility in Ligand Docking through Relevant Normal Modes, J. Am. Chem. Soc. 127, 9632-9640. (Pubitemid 40934775)
    • (2005) Journal of the American Chemical Society , vol.127 , Issue.26 , pp. 9632-9640
    • Cavasotto, C.N.1    Kovacs, J.A.2    Abagyan, R.A.3
  • 8
    • 0347361642 scopus 로고    scopus 로고
    • Lessons in molecular recognition: The effects of ligand and protein flexibility on molecular docking accuracy
    • DOI 10.1021/jm030209y
    • Erickson, J. A., Jalaie, M., Robertson, D. H., Lewis, R. A., and Vieth, M. (2004) Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy, J. Med. Chem. 47, 45-55. (Pubitemid 38040489)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.1 , pp. 45-55
    • Erickson, J.A.1    Jalaie, M.2    Robertson, D.H.3    Lewis, R.A.4    Vieth, M.5
  • 9
    • 4744365803 scopus 로고    scopus 로고
    • Soft docking and multiple receptor conformations in virtual screening
    • DOI 10.1021/jm049756p
    • Ferrari, A. M., Wei, B. Q., Costantino, L., and Shoichet, B. K. (2004) Soft docking and multiple receptor conformations in virtual screening, J. Med. Chem. 47, 5076-5084. (Pubitemid 39314905)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.21 , pp. 5076-5084
    • Ferrari, A.M.1    Wei, B.Q.2    Costantino, L.3    Shoichet, B.K.4
  • 10
    • 80051747399 scopus 로고    scopus 로고
    • Incorporating protein flexibility into docking and structure-based drug design
    • Barril, X., and Fradera, X. (2006) Incorporating protein flexibility into docking and structure-based drug design, Exp. Opin. Drug Discov. 1, 335-349.
    • (2006) Exp. Opin. Drug Discov. , vol.1 , pp. 335-349
    • Barril, X.1    Fradera, X.2
  • 12
    • 78649898335 scopus 로고    scopus 로고
    • Protein flexibility and ligand recognition: Challenges for molecular modeling
    • Spyrakis, F., Bidon-Chanal, A., Barril, X., and Luque, F. J. (2011) Protein Flexibility and Ligand Recognition: Challenges for Molecular Modeling, Curr Top Med Chem 11, 192-210.
    • (2011) Curr Top Med Chem , vol.11 , pp. 192-210
    • Spyrakis, F.1    Bidon-Chanal, A.2    Barril, X.3    Luque, F.J.4
  • 13
    • 0026310932 scopus 로고
    • 'Soft docking': Matching of molecular surface cubes
    • Jiang, F., and Kim, S. H. (1991) "Soft docking": matching of molecular surface cubes, J. Mol. Biol. 219, 79-102. (Pubitemid 121003975)
    • (1991) Journal of Molecular Biology , vol.219 , Issue.1 , pp. 79-102
    • Jiang, F.1    Kim, S.-H.2
  • 14
    • 0028854034 scopus 로고
    • Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation
    • Jones, G., Willett, P., and Glen, R. C. (1995) Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation, J. Mol. Biol. 245, 43-53.
    • (1995) J. Mol. Biol. , vol.245 , pp. 43-53
    • Jones, G.1    Willett, P.2    Glen, R.C.3
  • 15
    • 0028158936 scopus 로고
    • Ligand docking to proteins with discrete side-chain flexibility
    • Leach, A. R. (1994) Ligand docking to proteins with discrete side-chain flexibility, J. Mol. Biol. 235, 345-356. (Pubitemid 24049519)
    • (1994) Journal of Molecular Biology , vol.235 , Issue.1 , pp. 345-356
    • Leach, A.R.1
  • 16
    • 77949351042 scopus 로고    scopus 로고
    • Emerging methods for ensemble-based virtual screening
    • Amaro, R. E., and Li, W. W. (2010) Emerging methods for ensemble-based virtual screening, Curr Top Med Chem 10, 3-13.
    • (2010) Curr Top Med Chem , vol.10 , pp. 3-13
    • Amaro, R.E.1    Li, W.W.2
  • 17
    • 77949634796 scopus 로고    scopus 로고
    • Normal mode analysis of biomolecular structures: Functional mechanisms of membrane proteins
    • Bahar, I., Lezon, T. R., Bakan, A., and Shrivastava, I. H. (2010) Normal mode analysis of biomolecular structures: functional mechanisms of membrane proteins, Chem Rev 110, 1463-1497.
    • (2010) Chem Rev , vol.110 , pp. 1463-1497
    • Bahar, I.1    Lezon, T.R.2    Bakan, A.3    Shrivastava, I.H.4
  • 18
    • 0036721233 scopus 로고    scopus 로고
    • Normal mode analysis of macromolecular motions in a database framework: Developing mode concentration as a useful classifying statistic
    • DOI 10.1002/prot.10168
    • Krebs, W. G., Alexandrov, V., Wilson, C. A., Echols, N., Yu, H., and Gerstein, M. (2002) Normal mode analysis of macromolecular motions in a database framework: developing mode concentration as a useful classifying statistic, Proteins 48, 682-695. (Pubitemid 34925457)
    • (2002) Proteins: Structure, Function and Genetics , vol.48 , Issue.4 , pp. 682-695
    • Krebs, W.G.1    Alexandrov, V.2    Wilson, C.A.3    Echols, N.4    Yu, H.5    Gerstein, M.6
  • 19
    • 0000197372 scopus 로고    scopus 로고
    • Large amplitude elastic motions in proteins from a single-parameter, atomic analysis
    • Tirion, M. M. (1996) Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis, Phys. Rev. Lett. 77, 1905-1908. (Pubitemid 126625816)
    • (1996) Physical Review Letters , vol.77 , Issue.9 , pp. 1905-1908
    • Tirion, M.M.1
  • 20
    • 0030623823 scopus 로고    scopus 로고
    • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    • Bahar, I., Atilgan, A. R., and Erman, B. (1997) Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential, Fold Des 2, 173-181. (Pubitemid 127740467)
    • (1997) Folding and Design , vol.2 , Issue.3 , pp. 173-181
    • Bahar, I.1    Atilgan, A.R.2    Erman, B.3
  • 21
    • 84872980168 scopus 로고    scopus 로고
    • Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments
    • Bakan, A., and Bahar, I. (2010) Computational generation inhibitor-bound conformers of p38 map kinase and comparison with experiments, Pac Symp Biocomput, 181-192.
    • (2010) Pac Symp Biocomput , pp. 181-192
    • Bakan, A.1    Bahar, I.2
  • 22
    • 33748759844 scopus 로고    scopus 로고
    • Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors
    • DOI 10.1016/j.febslet.2006.08.037, PII S0014579306010131
    • Floquet, N., Marechal, J. D., Badet-Denisot, M. A., Robert, C. H., Dauchez, M., and Perahia, D. (2006) Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors, FEBS Lett 580, 5130-5136. (Pubitemid 44415782)
    • (2006) FEBS Letters , vol.580 , Issue.22 , pp. 5130-5136
    • Floquet, N.1    Marechal, J.-D.2    Badet-Denisot, M.-A.3    Robert, C.H.4    Dauchez, M.5    Perahia, D.6
  • 23
    • 73649109875 scopus 로고    scopus 로고
    • Activation of the ghrelin receptor is described by a privileged collective motion: A model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR)
    • Floquet, N., M'Kadmi, C., Perahia, D., Gagne, D., Berge, G., Marie, J., Baneres, J. L., Galleyrand, J. C., Fehrentz, J. A., and Martinez, J. (2010) Activation of the ghrelin receptor is described by a privileged collective motion: a model for constitutive and agonist-induced activation of a sub-class A G-protein coupled receptor (GPCR), J Mol Biol 395, 769-784.
    • (2010) J Mol Biol , vol.395 , pp. 769-784
    • Floquet, N.1    M'kadmi, C.2    Perahia, D.3    Gagne, D.4    Berge, G.5    Marie, J.6    Baneres, J.L.7    Galleyrand, J.C.8    Fehrentz, J.A.9    Martinez, J.10
  • 24
    • 27644450220 scopus 로고    scopus 로고
    • Conformational sampling of protein flexibility in generalized coordinates: Application to ligand docking
    • DOI 10.1166/jctn.2005.204
    • Kovacs, J. A., Cavasotto, C. N., and Abagyan, R. A. (2005) Conformational Sampling of Protein Flexibility in Generalized Coordinates: Application to ligand docking, J. Comp. Theor. Nanosci. 2, 354-361. (Pubitemid 41556042)
    • (2005) Journal of Computational and Theoretical Nanoscience , vol.2 , Issue.3 , pp. 354-361
    • Kovacs, J.A.1    Cavasotto, C.N.2    Abagyan, R.3
  • 25
    • 23344454719 scopus 로고    scopus 로고
    • Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization
    • DOI 10.1093/nar/gki730
    • Lindahl, E., and Delarue, M. (2005) Refinement of docked protein-ligand and protein-DNA structures using low frequency normal mode amplitude optimization, Nucleic Acids Res 33, 4496-4506. (Pubitemid 41222564)
    • (2005) Nucleic Acids Research , vol.33 , Issue.14 , pp. 4496-4506
    • Lindahl, E.1    Delarue, M.2
  • 26
    • 29144485503 scopus 로고    scopus 로고
    • Accounting for global protein deformability during protein-protein and protein-ligand docking
    • DOI 10.1016/j.bbapap.2005.07.045, PII S1570963905003092
    • May, A., and Zacharias, M. (2005) Accounting for global protein deformability during protein-protein and protein-ligand docking, Biochim Biophys Acta 1754, 225-231. (Pubitemid 41797702)
    • (2005) Biochimica et Biophysica Acta - Proteins and Proteomics , vol.1754 , Issue.1-2 , pp. 225-231
    • May, A.1    Zacharias, M.2
  • 27
    • 45749139232 scopus 로고    scopus 로고
    • Protein-ligand docking accounting for receptor side chain and global flexibility in normal modes: Evaluation on kinase inhibitor cross docking
    • DOI 10.1021/jm800071v
    • May, A., and Zacharias, M. (2008) Proteinligand docking accounting for receptor side chain and global flexibility in normal modes: evaluation on kinase inhibitor cross docking, J Med Chem 51, 3499-3506. (Pubitemid 351875006)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.12 , pp. 3499-3506
    • May, A.1    Zacharias, M.2
  • 28
    • 77449138099 scopus 로고    scopus 로고
    • Modeling G proteincoupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: Application to H3 antagonists
    • Rai, B. K., Tawa, G. J., Katz, A. H., and Humblet, C. (2010) Modeling G proteincoupled receptors for structure-based drug discovery using low-frequency normal modes for refinement of homology models: application to H3 antagonists, Proteins 78, 457-473.
    • (2010) Proteins , vol.78 , pp. 457-473
    • Rai, B.K.1    Tawa, G.J.2    Katz, A.H.3    Humblet, C.4
  • 29
    • 65249120827 scopus 로고    scopus 로고
    • Consistent improvement of crossdocking results using binding site ensembles generated with elastic network normal modes
    • Rueda, M., Bottegoni, G., and Abagyan, R. (2009) Consistent improvement of crossdocking results using binding site ensembles generated with elastic network normal modes, J Chem Inf Model 49, 716-725.
    • (2009) J Chem Inf Model , vol.49 , pp. 716-725
    • Rueda, M.1    Bottegoni, G.2    Abagyan, R.3
  • 30
    • 77955627131 scopus 로고    scopus 로고
    • How to choose relevant multiple receptor conformations for virtual screening: A test case of Cdk2 and normal mode analysis
    • Sperandio, O., Mouawad, L., Pinto, E., Villoutreix, B. O., Perahia, D., and Miteva, M. A. (2010) How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis, Eur Biophys J 39, 1365-1372.
    • (2010) Eur Biophys J , vol.39 , pp. 1365-1372
    • Sperandio, O.1    Mouawad, L.2    Pinto, E.3    Villoutreix, B.O.4    Perahia, D.5    Miteva, M.A.6
  • 31
    • 77951588413 scopus 로고    scopus 로고
    • A flexible docking scheme to explore the binding selectivity of PDZ domains
    • Gerek, Z. N., and Ozkan, S. B. (2010) A flexible docking scheme to explore the binding selectivity of PDZ domains, Protein Sci 19, 914-928.
    • (2010) Protein Sci , vol.19 , pp. 914-928
    • Gerek, Z.N.1    Ozkan, S.B.2
  • 32
    • 67649518035 scopus 로고    scopus 로고
    • Homology modeling in drug discovery: Current trends and applications
    • Cavasotto, C. N., and Phatak, S. S. (2009) Homology modeling in drug discovery: current trends and applications, Drug Discovery Today 14, 676-683.
    • (2009) Drug Discovery Today , vol.14 , pp. 676-683
    • Cavasotto, C.N.1    Phatak, S.S.2
  • 35
    • 0022419152 scopus 로고
    • Protein normal-mode dynamics: Trypsin inhibitor, crambin, ribonuclease and lysozyme
    • Levitt, M., Sander, C., and Stern, P. S. (1985) Protein normal-mode dynamics: trypsin inhibitor, crambin, ribonuclease and lysozyme, J. Mol. Biol. 181, 423-447.
    • (1985) J. Mol. Biol. , vol.181 , pp. 423-447
    • Levitt, M.1    Sander, C.2    Stern, P.S.3
  • 36
    • 0035132230 scopus 로고    scopus 로고
    • Anisotropy of fluctuation dynamics of proteins with an elastic network model
    • Atilgan, A. R., Durell, S. R., Jernigan, R. L., Demirel, M. C., Keskin, O., and Bahar, I. (2001) Anisotropy of fluctuation dynamics of proteins with an elastic network model, Biophys J 80, 505-515.
    • (2001) Biophys J , vol.80 , pp. 505-515
    • Atilgan, A.R.1    Durell, S.R.2    Jernigan, R.L.3    Demirel, M.C.4    Keskin, O.5    Bahar, I.6
  • 37
    • 33750407288 scopus 로고    scopus 로고
    • Anisotropic network model: Systematic evaluation and a new web interface
    • DOI 10.1093/bioinformatics/btl448
    • Eyal, E., Yang, L. W., and Bahar, I. (2006) Anisotropic network model: systematic evaluation and a new web interface, Bioinformatics 22, 2619-2627. (Pubitemid 44642600)
    • (2006) Bioinformatics , vol.22 , Issue.21 , pp. 2619-2627
    • Eyal, E.1    Yang, L.-W.2    Bahar, I.3
  • 38
    • 0032533790 scopus 로고    scopus 로고
    • Analysis of domain motions by approximate normal mode calculations
    • DOI 10.1002/(SICI)1097-0134(19981115)33:3<417::AID-PROT10>3.0.CO;2- 8
    • Hinsen, K. (1998) Analysis of domain motions by approximate normal mode calculations, Proteins 33, 417-429. (Pubitemid 28516346)
    • (1998) Proteins: Structure, Function and Genetics , vol.33 , Issue.3 , pp. 417-429
    • Hinsen, K.1
  • 39
    • 77951232176 scopus 로고    scopus 로고
    • FiberDock: Flexible induced-fit backbone refinement in molecular docking
    • Mashiach, E., Nussinov, R., andWolfson, H. J. (2010) FiberDock: Flexible induced-fit backbone refinement in molecular docking, Proteins 78, 1503-1519.
    • (2010) Proteins , vol.78 , pp. 1503-1519
    • Mashiach, E.1    Nussinov, R.2    Wolfson, H.J.3
  • 40
    • 33749521415 scopus 로고    scopus 로고
    • Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data
    • DOI 10.1529/biophysj.106.085894
    • Kondrashov, D. A., Cui, Q., and Phillips, G. N., Jr. (2006) Optimization and evaluation of a coarse-grained model of protein motion using x-ray crystal data, Biophys J 91, 2760-2767. (Pubitemid 44526467)
    • (2006) Biophysical Journal , vol.91 , Issue.8 , pp. 2760-2767
    • Kondrashov, D.A.1    Cui, Q.2    Phillips Jr., G.N.3
  • 41
    • 0029633186 scopus 로고
    • AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules
    • Pearlman, D. A., Case, D. A., Caldwell, J. W., Ross, W. R., Cheatham, T. E., 3rd, DeBolt, S., Ferguson, D., Seibel, G., and Kollman, P. A. (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate the structural and energetic properties of molecules, Comput. Phys. Commun. 91, 1-41.
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 1-41
    • Pearlman, D.A.1    Case, D.A.2    Caldwell, J.W.3    Ross, W.R.4    Cheatham III, T.E.5    Debolt, S.6    Ferguson, D.7    Seibel, G.8    Kollman, P.A.9
  • 43
    • 0037406075 scopus 로고    scopus 로고
    • Cyclic coordinate descent: A robotics algorithm for protein loop closure
    • DOI 10.1110/ps.0242703
    • Canutescu, A. A., and Dunbrack, R. L., Jr. (2003) Cyclic coordinate descent: A robotics algorithm for protein loop closure, Protein Sci 12, 963-972. (Pubitemid 36505431)
    • (2003) Protein Science , vol.12 , Issue.5 , pp. 963-972
    • Canutescu, A.A.1    Dunbrack Jr., R.L.2
  • 44
    • 33646145523 scopus 로고    scopus 로고
    • Can conformational change be described by only a few normal modes?
    • Petrone, P., and Pande, V. S. (2006) Can conformational change be described by only a few normal modes?, Biophys. J. 90, 1583-1593.
    • (2006) Biophys. J. , vol.90 , pp. 1583-1593
    • Petrone, P.1    Pande, V.S.2
  • 45
    • 0023430366 scopus 로고
    • Monte Carlo-minimization approach to the multiple-minima problem in protein folding
    • Li, Z., and Scheraga, H. A. (1987) Monte Carlo-minimization approach to the multiple-minima problem in protein folding, Proc. Natl. Acad. Sci. U S A 84, 6611-6615.
    • (1987) Proc. Natl. Acad. Sci. U S A , vol.84 , pp. 6611-6615
    • Li, Z.1    Scheraga, H.A.2
  • 46
    • 34548762412 scopus 로고    scopus 로고
    • 2 inactivation
    • DOI 10.1002/cbic.200700217
    • Monti, M. C., Casapullo, A., Cavasotto, C. N., Napolitano, A., and Riccio, R. (2007) Scalaradial, a Dialdehyde-Containing Marine Metabolite That Causes an Unexpected Noncovalent PLA(2) Inactivation, ChemBioChem 8, 1585-1591. (Pubitemid 47436916)
    • (2007) ChemBioChem , vol.8 , Issue.13 , pp. 1585-1591
    • Monti, M.C.1    Casapullo, A.2    Cavasotto, C.N.3    Napolitano, A.4    Riccio, R.5
  • 47
    • 58449114054 scopus 로고    scopus 로고
    • The binding mode of petrosaspongiolide M to the human group IIA phospholipase A(2): Exploring the role of covalent and noncovalent interactions in the inhibition process
    • Monti, M. C., Casapullo, A., Cavasotto, C. N., Tosco, A., Dal Piaz, F., Ziemys, A., Margarucci, L., and Riccio, R. (2009) The binding mode of petrosaspongiolide M to the human group IIA phospholipase A(2): exploring the role of covalent and noncovalent interactions in the inhibition process, Chem.-Eur. J. 15, 1155-1163.
    • (2009) Chem.-Eur. J. , vol.15 , pp. 1155-1163
    • Monti, M.C.1    Casapullo, A.2    Cavasotto, C.N.3    Tosco, A.4    Dal Piaz, F.5    Ziemys, A.6    Margarucci, L.7    Riccio, R.8
  • 49
    • 78650701635 scopus 로고    scopus 로고
    • Ligand-steered modeling and docking: A benchmarking study in class A G-protein-coupled receptors
    • Phatak, S. S., Gatica, E. A., and Cavasotto, C. N. (2010) Ligand-steered modeling and docking: A benchmarking study in Class A G-Protein-Coupled Receptors, J. Chem. Inf. Model. 50, 2119-2128.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2119-2128
    • Phatak, S.S.1    Gatica, E.A.2    Cavasotto, C.N.3
  • 50
    • 46849105028 scopus 로고    scopus 로고
    • Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase
    • DOI 10.1021/jm8001197
    • Cheng, L. S., Amaro, R. E., Xu, D., Li, W. W., Arzberger, P. W., and McCammon, J. A. (2008) Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase, J. Med. Chem. 51, 3878-3894. (Pubitemid 351956517)
    • (2008) Journal of Medicinal Chemistry , vol.51 , Issue.13 , pp. 3878-3894
    • Cheng, L.S.1    Amaro, R.E.2    Xu, D.3    Li, W.W.4    Arzberger, P.W.5    McCammon, J.A.6
  • 51
    • 0342424187 scopus 로고    scopus 로고
    • Fast prediction and visualization of protein binding pockets with PASS
    • DOI 10.1023/A:1008124202956
    • Brady, G. P., Jr., and Stouten, P. F. (2000) Fast prediction and visualization of protein binding pockets with PASS, J Comput Aided Mol Des 14, 383-401. (Pubitemid 30219399)
    • (2000) Journal of Computer-Aided Molecular Design , vol.14 , Issue.4 , pp. 383-401
    • Brady Jr., G.P.1    Stouten, P.F.W.2
  • 52
    • 78349254189 scopus 로고    scopus 로고
    • Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses
    • Ahmed, A., Villinger, S., and Gohlke, H. (2010) Large-scale comparison of protein essential dynamics from molecular dynamics simulations and coarse-grained normal mode analyses, Proteins 78, 3341-3352.
    • (2010) Proteins , vol.78 , pp. 3341-3352
    • Ahmed, A.1    Villinger, S.2    Gohlke, H.3
  • 53
    • 21244479779 scopus 로고    scopus 로고
    • Unveiling the full potential of flexible receptor docking using multiple crystallographic structures
    • DOI 10.1021/jm048972v
    • Barril, X., and Morley, S. D. (2005) Unveiling the full potential of flexible receptor docking using multiple crystallographic structures, J Med Chem 48, 4432-4443. (Pubitemid 40884945)
    • (2005) Journal of Medicinal Chemistry , vol.48 , Issue.13 , pp. 4432-4443
    • Barril, X.1    Morley, S.D.2
  • 54
    • 57349156167 scopus 로고    scopus 로고
    • In pursuit of virtual lead optimization: The role of the receptor structure and ensembles in accurate docking
    • DOI 10.1002/prot.22081
    • Bolstad, E. S., and Anderson, A. C. (2008) In pursuit of virtual lead optimization: the role of the receptor structure and ensembles in accurate docking, Proteins 73, 566-580. (Pubitemid 352788641)
    • (2008) Proteins: Structure, Function and Genetics , vol.73 , Issue.3 , pp. 566-580
    • Bolstad, E.S.D.1    Anderson, A.C.2
  • 56
    • 35348821202 scopus 로고    scopus 로고
    • Virtual screening strategies in drug discovery
    • DOI 10.1016/j.cbpa.2007.08.033, PII S1367593107001172
    • McInnes, C. (2007) Virtual screening strategies in drug discovery, Curr Opin Chem Biol 11, 494-502. (Pubitemid 47589008)
    • (2007) Current Opinion in Chemical Biology , vol.11 , Issue.5 , pp. 494-502
    • McInnes, C.1
  • 57
    • 0141676629 scopus 로고    scopus 로고
    • The process of structure-based drug design
    • DOI 10.1016/j.chembiol.2003.09.002
    • Anderson, A. C. (2003) The process of structure-based drug design, Chem. Biol. 10, 787-797. (Pubitemid 37171897)
    • (2003) Chemistry and Biology , vol.10 , Issue.9 , pp. 787-797
    • Anderson, A.C.1
  • 58
    • 25844431698 scopus 로고    scopus 로고
    • Coarse-grained normal mode analysis in structural biology
    • DOI 10.1016/j.sbi.2005.08.007, PII S0959440X05001557, Carbohydrates and Glycoconjugates/Biophysical Methods
    • Bahar, I., and Rader, A. J. (2005) Coarsegrained normal mode analysis in structural biology, Curr Opin Struct Biol 15, 586-592. (Pubitemid 41393491)
    • (2005) Current Opinion in Structural Biology , vol.15 , Issue.5 , pp. 586-592
    • Bahar, I.1    Rader, A.J.2
  • 59
    • 25844440811 scopus 로고    scopus 로고
    • Elastic network models for understanding biomolecular machinery: From enzymes to supramolecular assemblies
    • DOI 10.1088/1478-3975/2/4/S12, PII S1478397505050612
    • Chennubhotla, C., Rader, A. J., Yang, L. W., and Bahar, I. (2005) Elastic network models for understanding biomolecular machinery: from enzymes to supramolecular assemblies, Phys Biol 2, S173-180. (Pubitemid 41609444)
    • (2005) Physical Biology , vol.2 , Issue.4
    • Chennubhotla, C.1    Rader, A.J.2    Yang, L.-W.3    Bahar, I.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.