메뉴 건너뛰기




Volumn 43, Issue , 2003, Pages 31-45

Protein Flexibility and Computer-Aided Drug Design

Author keywords

Dynamic pharmacophore; Free energy calculations; Molecular dynamics simulations; Relaxed complex method; Sensitivity analysis

Indexed keywords

PROTEIN;

EID: 0042853244     PISSN: 03621642     EISSN: None     Source Type: Book Series    
DOI: 10.1146/annurev.pharmtox.43.100901.140216     Document Type: Review
Times cited : (78)

References (71)
  • 3
    • 0001486087 scopus 로고
    • Dynamics and design of enzymes and inhibitors
    • Wong CF, McCammon JA. 1986. Dynamics and design of enzymes and inhibitors. J. Am. Chem. Soc. 108:3830-32
    • (1986) J. Am. Chem. Soc. , vol.108 , pp. 3830-3832
    • Wong, C.F.1    McCammon, J.A.2
  • 4
    • 85005577373 scopus 로고
    • Computer simulation and the design of new biological molecules
    • Wong CF, McCammon JA. 1986. Computer simulation and the design of new biological molecules. Isr. J. Chem. 27:211-15
    • (1986) Isr. J. Chem. , vol.27 , pp. 211-215
    • Wong, C.F.1    McCammon, J.A.2
  • 7
    • 0009590921 scopus 로고
    • Free energy calculations: A breakthrough for modeling organic chemistry in solution
    • Jorgensen WL. 1989. Free energy calculations: a breakthrough for modeling organic chemistry in solution. Acc. Chem. Res. 22:184-89
    • (1989) Acc. Chem. Res. , vol.22 , pp. 184-189
    • Jorgensen, W.L.1
  • 8
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge DL, DiCapua FM. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18:431-92
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
    • Beveridge, D.L.1    DiCapua, F.M.2
  • 9
    • 36849122972 scopus 로고
    • High-temperature equation of state by perturbation method. I. Nonpolar gases
    • Zwanzig RW. 1954. High-temperature equation of state by perturbation method. I. Nonpolar gases. J. Chem. Phys. 22: 1420-26
    • (1954) J. Chem. Phys. , vol.22 , pp. 1420-1426
    • Zwanzig, R.W.1
  • 10
    • 0004162305 scopus 로고
    • Locally enhanced sampling in free energy calculations - Application of mean field approximation to accurate calculation of free energy differences
    • Verkhivker G, Elber R, Nowak W. 1992. Locally enhanced sampling in free energy calculations - application of mean field approximation to accurate calculation of free energy differences. J. Chem. Phys. 97:7838
    • (1992) J. Chem. Phys. , vol.97 , pp. 7838
    • Verkhivker, G.1    Elber, R.2    Nowak, W.3
  • 11
    • 0025600834 scopus 로고
    • Enhanced sampling in molecular dynamics: Use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin
    • Elber R, Karplus M. 1990. Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin. J. Am. Chem. Soc. 112:9161-75
    • (1990) J. Am. Chem. Soc. , vol.112 , pp. 9161-9175
    • Elber, R.1    Karplus, M.2
  • 12
    • 0032540692 scopus 로고    scopus 로고
    • Use of locally enhanced sampling in free energy calculations: Testing and application to the alpha → beta anomerization of glucose
    • Simmerling C, Fox T, Kollman PA. 1998. Use of locally enhanced sampling in free energy calculations: testing and application to the alpha → beta anomerization of glucose. J. Am. Chem. Soc. 120:5771-82
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 5771-5782
    • Simmerling, C.1    Fox, T.2    Kollman, P.A.3
  • 13
    • 0034226506 scopus 로고    scopus 로고
    • Efficient sampling of ligand orientations and conformations in free energy calculations using the λ-dynamics method
    • Banba S, Guo ZY, Brooks CL. 2000. Efficient sampling of ligand orientations and conformations in free energy calculations using the λ-dynamics method. J. Phys. Chem. B 104:6903-10
    • (2000) J. Phys. Chem. B , vol.104 , pp. 6903-6910
    • Banba, S.1    Guo, Z.Y.2    Brooks, C.L.3
  • 14
    • 0035960174 scopus 로고    scopus 로고
    • Application of multiple topology λ-dynamics to a host-guest system: Betacyclodextrin with substituted benzenes
    • Damodaran KV, Banba S, Brooks CL. 2001. Application of multiple topology λ-dynamics to a host-guest system: betacyclodextrin with substituted benzenes. J. Phys. Chem. B 105:9316-22
    • (2001) J. Phys. Chem. B , vol.105 , pp. 9316-9322
    • Damodaran, K.V.1    Banba, S.2    Brooks, C.L.3
  • 15
    • 0032481614 scopus 로고    scopus 로고
    • Rapid screening of binding affinities: Application of the λ-dynamics method to a trypsin-inhibitor system
    • Guo ZY, Brooks CL. 1998. Rapid screening of binding affinities: application of the λ-dynamics method to a trypsin-inhibitor system. J. Am. Chem. Soc. 120:1920-21
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 1920-1921
    • Guo, Z.Y.1    Brooks, C.L.2
  • 18
    • 0242425364 scopus 로고
    • Application of sensitivity analysis to the establishment of intermolecular potential function
    • Thacher TS, Hagler AT, Rabitz H. 1991. Application of sensitivity analysis to the establishment of intermolecular potential function. J. Am. Chem. Soc. 113:2020
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 2020
    • Thacher, T.S.1    Hagler, A.T.2    Rabitz, H.3
  • 19
    • 0141596988 scopus 로고
    • Sensitivity of molecular structure to intramolecular potentials
    • Susnow R, Nachbar RB Jr, Schutt C, Rabitz H. 1991. Sensitivity of molecular structure to intramolecular potentials. J. Phys. Chem. 95:8585-97
    • (1991) J. Phys. Chem. , vol.95 , pp. 8585-8597
    • Susnow, R.1    Nachbar R.B., Jr.2    Schutt, C.3    Rabitz, H.4
  • 20
    • 0242677236 scopus 로고
    • Systematic sensitivity analyses in free energy perturbation calculations
    • Wong CF. 1991. Systematic sensitivity analyses in free energy perturbation calculations. J. Am. Chem. Soc. 113:3208-9
    • (1991) J. Am. Chem. Soc. , vol.113 , pp. 3208-3209
    • Wong, C.F.1
  • 21
    • 0038369507 scopus 로고
    • Sensitivity analysis and principal component analysis in free energy calculations
    • Wong CF, Rabitz H. 1991. Sensitivity analysis and principal component analysis in free energy calculations. J. Phys. Chem. 95:9628-30
    • (1991) J. Phys. Chem. , vol.95 , pp. 9628-9630
    • Wong, C.F.1    Rabitz, H.2
  • 22
    • 0000315458 scopus 로고
    • Sensitivity analysis of distribution functions of liquid water
    • Zhu S-B, Wong CF. 1993. Sensitivity analysis of distribution functions of liquid water. J. Chem. Phys. 99:9047-53
    • (1993) J. Chem. Phys. , vol.99 , pp. 9047-9053
    • Zhu, S.-B.1    Wong, C.F.2
  • 23
    • 36449008867 scopus 로고
    • Sensitivity analysis of water thermodynamics
    • Zhu S-B, Wong CF. 1993. Sensitivity analysis of water thermodynamics. J. Chem. Phys. 98:8892-99
    • (1993) J. Chem. Phys. , vol.98 , pp. 8892-8899
    • Zhu, S.-B.1    Wong, C.F.2
  • 24
    • 84986432913 scopus 로고
    • Conformational study of dipeptides: A sensitivity analysis approach
    • Susnow R, Schutt C, Rabitz H, Subramaniam S. 1994. Conformational study of dipeptides: a sensitivity analysis approach. J. Comp. Chem. 15:947-62
    • (1994) J. Comp. Chem. , vol.15 , pp. 947-962
    • Susnow, R.1    Schutt, C.2    Rabitz, H.3    Subramaniam, S.4
  • 25
    • 0000471729 scopus 로고
    • Sensitivity analysis of a polarizable water model
    • Zhu S-B, Wong CF. 1994. Sensitivity analysis of a polarizable water model. J. Phys. Chem. 98:4695-701
    • (1994) J. Phys. Chem. , vol.98 , pp. 4695-4701
    • Zhu, S.-B.1    Wong, C.F.2
  • 26
    • 0242677229 scopus 로고
    • Sensitivity analysis of a 2-dimensional lattice model of protein folding
    • Bleil RE, Wong CF, Rabitz H. 1995. Sensitivity analysis of a 2-dimensional lattice model of protein folding. J. Phys. Chem. 99:3379-86
    • (1995) J. Phys. Chem. , vol.99 , pp. 3379-3386
    • Bleil, R.E.1    Wong, C.F.2    Rabitz, H.3
  • 28
    • 0003790282 scopus 로고    scopus 로고
    • Sensitivity analysis in biomolecular simulation
    • ed. KB Lipkowitz, DB Boyd. New York: Wiley-VCH
    • Wong CF, Thacher T, Rabitz H. 1998. Sensitivity analysis in biomolecular simulation. In Reviews in Computational Chemistry, ed. KB Lipkowitz, DB Boyd, pp. 281-326. New York: Wiley-VCH
    • (1998) Reviews in Computational Chemistry , pp. 281-326
    • Wong, C.F.1    Thacher, T.2    Rabitz, H.3
  • 30
    • 5544264558 scopus 로고
    • Gaussian fluctuation formula for electrostatic free-energy changes in solution
    • Levy RM, Belhadj M, Kitchen DB. 1991. Gaussian fluctuation formula for electrostatic free-energy changes in solution. J. Chem. Phys. 95:3627-33
    • (1991) J. Chem. Phys. , vol.95 , pp. 3627-3633
    • Levy, R.M.1    Belhadj, M.2    Kitchen, D.B.3
  • 31
    • 0001085206 scopus 로고    scopus 로고
    • Classical and quantum simulations of tryptophan in solution
    • Simonson T, Wong CF, Brünger AT. 1997. Classical and quantum simulations of tryptophan in solution. J. Phys. Chem. A 101:1935-45
    • (1997) J. Phys. Chem. A , vol.101 , pp. 1935-1945
    • Simonson, T.1    Wong, C.F.2    Brünger, A.T.3
  • 33
    • 0035990910 scopus 로고    scopus 로고
    • Designing specific protein kinase inhibitors: Insights from computer simulations and comparative sequence/structure analysis
    • In press
    • Gould C, Wong CF. 2002. Designing specific protein kinase inhibitors: insights from computer simulations and comparative sequence/structure analysis. Pharmacol. Ther. In press
    • (2002) Pharmacol. Ther.
    • Gould, C.1    Wong, C.F.2
  • 34
    • 0030134642 scopus 로고    scopus 로고
    • Estimating the relative free energy of different molecular states with respect to a single reference state
    • Liu HY, Mark AE, van Gunsteren WF. 1996. Estimating the relative free energy of different molecular states with respect to a single reference state. J. Phys. Chem. 100:9485-94
    • (1996) J. Phys. Chem. , vol.100 , pp. 9485-9494
    • Liu, H.Y.1    Mark, A.E.2    Van Gunsteren, W.F.3
  • 35
    • 0034688433 scopus 로고    scopus 로고
    • Calculations of relative hydration free energies: A comparative study using thermo-dynamic integration and an extrapolation method based on a single reference state
    • Mordasini TZ, McCammon JA. 2000. Calculations of relative hydration free energies: a comparative study using thermo-dynamic integration and an extrapolation method based on a single reference state. J. Phys. Chem. B 104:360-67
    • (2000) J. Phys. Chem. B , vol.104 , pp. 360-367
    • Mordasini, T.Z.1    McCammon, J.A.2
  • 36
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model
    • Vorobjev YN, Almagro JC, Hermans J. 1998. Discrimination between native and intentionally misfolded conformations of proteins: ES/IS, a new method for calculating conformational free energy that uses both dynamics simulations with an explicit solvent and an implicit solvent continuum model. Proteins Struct. Funct. Genet. 32:399-413
    • (1998) Proteins Struct. Funct. Genet. , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 37
    • 0033003955 scopus 로고    scopus 로고
    • ES/IS: Estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model
    • Vorobjev YN, Hermans J. 1999. ES/IS: estimation of conformational free energy by combining dynamics simulations with explicit solvent with an implicit solvent continuum model. Biophys. Chem. 78:195-205
    • (1999) Biophys. Chem. , vol.78 , pp. 195-205
    • Vorobjev, Y.N.1    Hermans, J.2
  • 38
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a diverse set of ligands to avidin and streptavidin: An accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models
    • Kuhn B, Kollman PA. 2000. Binding of a diverse set of ligands to avidin and streptavidin: an accurate quantitative prediction of their relative affinities by a combination of molecular mechanics and continuum solvent models. J. Med. Chem. 43:3786-91
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 39
    • 0034212858 scopus 로고    scopus 로고
    • Use of MM-PB/SA in estimating the free energies of proteins: Application to native, intermediates, and unfolded villin headpiece
    • Lee MR, Duan Y, Kollman PA. 2000. Use of MM-PB/SA in estimating the free energies of proteins: application to native, intermediates, and unfolded villin headpiece. Proteins Struct. Funct. Genet. 39:309-16
    • (2000) Proteins Struct. Funct. Genet. , vol.39 , pp. 309-316
    • Lee, M.R.1    Duan, Y.2    Kollman, P.A.3
  • 40
    • 0034084991 scopus 로고    scopus 로고
    • Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding
    • Massova I, Kollman PA. 2000. Combined molecular mechanical and continuum solvent approach (MM-PBSA/GBSA) to predict ligand binding. Perspect. Drug Discov. Des. 18:113-135
    • (2000) Perspect. Drug Discov. Des. , vol.18 , pp. 113-135
    • Massova, I.1    Kollman, P.A.2
  • 41
    • 0001585447 scopus 로고
    • Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation
    • Gilson MK, Davis ME, Luty BA, McCammon JA. 1993. Computation of electrostatic forces on solvated molecules using the Poisson-Boltzmann equation. J. Phys. Chem. 97:3591-600
    • (1993) J. Phys. Chem. , vol.97 , pp. 3591-3600
    • Gilson, M.K.1    Davis, M.E.2    Luty, B.A.3    McCammon, J.A.4
  • 42
    • 0032096837 scopus 로고    scopus 로고
    • Continuum solvation model: Computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation
    • Im W, Beglov D, Roux B. 1998. Continuum solvation model: computation of electrostatic forces from numerical solutions to the Poisson-Boltzmann equation. Comput. Phys. Commun. 111:59-75
    • (1998) Comput. Phys. Commun. , vol.111 , pp. 59-75
    • Im, W.1    Beglov, D.2    Roux, B.3
  • 43
    • 84986534141 scopus 로고
    • A rapid method for calculating derivatives of solvent accessible surface areas of molecules
    • Sridharan S, Nicholls A, Sharp KA. 1995. A rapid method for calculating derivatives of solvent accessible surface areas of molecules. J. Comput. Chem. 16:1038-44
    • (1995) J. Comput. Chem. , vol.16 , pp. 1038-1044
    • Sridharan, S.1    Nicholls, A.2    Sharp, K.A.3
  • 44
    • 84961985307 scopus 로고    scopus 로고
    • Development of a generalized Born model parametrization for proteins and nucleic acids
    • Dominy BN, Brooks CL. 1999. Development of a generalized Born model parametrization for proteins and nucleic acids. J. Phys. Chem. B 103:3765-73
    • (1999) J. Phys. Chem. B , vol.103 , pp. 3765-3773
    • Dominy, B.N.1    Brooks, C.L.2
  • 45
    • 4043171970 scopus 로고    scopus 로고
    • The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Bom radii
    • Qiu D, Shenkin PS, Hollinger FP, Still WC. 1997. The GB/SA continuum model for solvation. A fast analytical method for the calculation of approximate Bom radii. J. Phys. Chem. A 101:3005-14
    • (1997) J. Phys. Chem. A , vol.101 , pp. 3005-3014
    • Qiu, D.1    Shenkin, P.S.2    Hollinger, F.P.3    Still, W.C.4
  • 47
    • 0029633152 scopus 로고
    • Electrostatics and diffusion of molecules in solution - Simulations with the University of Houston Brownian Dynamics Program
    • Madura JD, Briggs JM, Wade RC, Davis ME, Luty BA, et al. 1995. Electrostatics and diffusion of molecules in solution - simulations with the University of Houston Brownian Dynamics Program. Comput. Phys. Commun. 91:57-95
    • (1995) Comput. Phys. Commun. , vol.91 , pp. 57-95
    • Madura, J.D.1    Briggs, J.M.2    Wade, R.C.3    Davis, M.E.4    Luty, B.A.5
  • 48
    • 0026124585 scopus 로고
    • Electrostatics and diffusion of molecules in solution - Simulations with the University-of-Houston-Brownian Dynamics Program
    • Davis ME, Madura JD, Luty BA, McCammon JA. 1991. Electrostatics and diffusion of molecules in solution - simulations with the University-of-Houston-Brownian Dynamics Program. Comput. Phys. Commun. 62:187-97
    • (1991) Comput. Phys. Commun. , vol.62 , pp. 187-197
    • Davis, M.E.1    Madura, J.D.2    Luty, B.A.3    McCammon, J.A.4
  • 49
    • 0035913754 scopus 로고    scopus 로고
    • Atomistic Brownian dynamics simulation of peptide phosphorylation
    • Shen TY, Wong CF, McCammon JA. 2001. Atomistic Brownian dynamics simulation of peptide phosphorylation. J. Am. Chem. Soc. 123:9107-11
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 9107-9111
    • Shen, T.Y.1    Wong, C.F.2    McCammon, J.A.3
  • 50
    • 0034716751 scopus 로고    scopus 로고
    • A ligand that is predicted to bind better to avidin than biotin: Insights from computational fluorine scanning
    • Kuhn B, Kolhnan PA. 2000. A ligand that is predicted to bind better to avidin than biotin: insights from computational fluorine scanning. J. Am. Chem. Soc. 122:3909-16
    • (2000) J. Am. Chem. Soc. , vol.122 , pp. 3909-3916
    • Kuhn, B.1    Kolhnan, P.A.2
  • 51
    • 0033568644 scopus 로고    scopus 로고
    • Computational alanine scanning to probe protein-protein interactions: A novel approach to evaluate binding free energies
    • Massova I, Kollman PA. 1999. Computational alanine scanning to probe protein-protein interactions: a novel approach to evaluate binding free energies. J. Am. Chem. Soc. 121:8133-43
    • (1999) J. Am. Chem. Soc. , vol.121 , pp. 8133-8143
    • Massova, I.1    Kollman, P.A.2
  • 52
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Aqvist J, Medina C, Samuelsson J-E. 1994. A new method for predicting binding affinity in computer-aided drug design. Protein Eng. 7:385-91
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Aqvist, J.1    Medina, C.2    Samuelsson, J.-E.3
  • 53
    • 0001389474 scopus 로고
    • An extended linear response method for determining free energies of hydration
    • Carlson HA, Jorgensen WL. 1995. An extended linear response method for determining free energies of hydration. J. Phys. Chem. 99:10667-673
    • (1995) J. Phys. Chem. , vol.99 , pp. 10667-10673
    • Carlson, H.A.1    Jorgensen, W.L.2
  • 54
    • 0029975720 scopus 로고    scopus 로고
    • Binding free energy calculations for P450camsubstrate complexes
    • Paulsen MD, Ornstein RL. 1996. Binding free energy calculations for P450camsubstrate complexes. Protein Eng. 9:567-71
    • (1996) Protein Eng. , vol.9 , pp. 567-571
    • Paulsen, M.D.1    Ornstein, R.L.2
  • 55
    • 0001127721 scopus 로고    scopus 로고
    • Free energies of solvation in chloroform and water from a linear response approach
    • McDonald NA, Carlson HA, Jorgensen WL. 1997. Free energies of solvation in chloroform and water from a linear response approach. J. Phys. Org. Chem. 10: 563-76
    • (1997) J. Phys. Org. Chem. , vol.10 , pp. 563-576
    • McDonald, N.A.1    Carlson, H.A.2    Jorgensen, W.L.3
  • 56
    • 20644437755 scopus 로고    scopus 로고
    • Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method
    • Smith RH Jr, Jorgensen WL, Tirado-Rives J, Lamb ML, Janssen PA, et al. 1998. Prediction of binding affinities for TIBO inhibitors of HIV-1 reverse transcriptase using Monte Carlo simulations in a linear response method. J. Med. Chem. 41:5272-86
    • (1998) J. Med. Chem. , vol.41 , pp. 5272-5286
    • Smith R.H., Jr.1    Jorgensen, W.L.2    Tirado-Rives, J.3    Lamb, M.L.4    Janssen, P.A.5
  • 57
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson T, Marelius J, Aqvist J. 1998. Ligand binding affinity prediction by linear interaction energy methods. J. Comput.-Aided Molec. Des. 12:27-35
    • (1998) J. Comput.-Aided Molec. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Aqvist, J.3
  • 58
    • 0032014129 scopus 로고    scopus 로고
    • Computation of affinity and selectivity: Binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases
    • Marelius J, GraffnerNordberg M, Hansson T, Hallberg A, Aqvist J. 1998. Computation of affinity and selectivity: binding of 2,4-diaminopteridine and 2,4-diaminoquinazoline inhibitors to dihydrofolate reductases. J. Comput.-Aided Molec. Des. 12:119-31
    • (1998) J. Comput.-Aided Molec. Des. , vol.12 , pp. 119-131
    • Marelius, J.1    GraffnerNordberg, M.2    Hansson, T.3    Hallberg, A.4    Aqvist, J.5
  • 59
    • 0001105311 scopus 로고    scopus 로고
    • Method for including the dynamic fluctuations of a protein in computer-aided drug design
    • Carlson HA, Masukawa KM, McCammon JA. 1999. Method for including the dynamic fluctuations of a protein in computer-aided drug design. J. Phys. Chem. A 103:10213-19
    • (1999) J. Phys. Chem. A , vol.103 , pp. 10213-10219
    • Carlson, H.A.1    Masukawa, K.M.2    McCammon, J.A.3
  • 60
    • 0033974667 scopus 로고    scopus 로고
    • Accommodating protein flexibility in computational drug design
    • Carlson HA, McCammon JA. 2000. Accommodating protein flexibility in computational drug design. Mol. Pharmacol. 57:213-18
    • (2000) Mol. Pharmacol. , vol.57 , pp. 213-218
    • Carlson, H.A.1    McCammon, J.A.2
  • 62
    • 0343012941 scopus 로고    scopus 로고
    • New Haven: Yale Univ. Press
    • Jorgensen WL. 1997. BOSS. New Haven: Yale Univ. Press
    • (1997) BOSS
    • Jorgensen, W.L.1
  • 63
    • 0037157153 scopus 로고    scopus 로고
    • Computational drug design accommodating receptor flexibility: The relaxed complex scheme
    • Lin JH, Perryman A, Schames J, McCammon JA. 2002. Computational drug design accommodating receptor flexibility: the relaxed complex scheme. J. Am. Chem. Soc. 124:5632-33
    • (2002) J. Am. Chem. Soc. , vol.124 , pp. 5632-5633
    • Lin, J.H.1    Perryman, A.2    Schames, J.3    McCammon, J.A.4
  • 64
    • 0242694789 scopus 로고    scopus 로고
    • The Relaxed Complex Method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    • In press
    • Lin JH, Perryman A, Schames J, McCammon JA. 2002. The Relaxed Complex Method: accommodating receptor flexibility for drug design with an improved scoring scheme. Biopolymers. In press
    • (2002) Biopolymers
    • Lin, J.H.1    Perryman, A.2    Schames, J.3    McCammon, J.A.4
  • 65
    • 0029836953 scopus 로고    scopus 로고
    • Discovering high-affinity ligands for proteins - SAR by NMR
    • Shuker SB, Hajduk PJ, Meadows RP, Fesik SW. 1996. Discovering high-affinity ligands for proteins - SAR by NMR. Science 274:1531-34
    • (1996) Science , vol.274 , pp. 1531-1534
    • Shuker, S.B.1    Hajduk, P.J.2    Meadows, R.P.3    Fesik, S.W.4
  • 67
    • 0030203710 scopus 로고    scopus 로고
    • Distributed automated docking of flexible ligands to proteins - Parallel applications of Autodock 2.4
    • Morris GM, Goodsell DS, Huey R, Olson AJ. 1996. Distributed automated docking of flexible ligands to proteins - parallel applications of Autodock 2.4. J. Comput.-Aided Molec. Des. 10:293-304
    • (1996) J. Comput.-Aided Molec. Des. , vol.10 , pp. 293-304
    • Morris, G.M.1    Goodsell, D.S.2    Huey, R.3    Olson, A.J.4
  • 68
    • 0029705324 scopus 로고    scopus 로고
    • Automated docking of flexible ligands: Applications of AutoDock
    • Goodsell DS, Morris GM, Olson AJ. 1996. Automated docking of flexible ligands: applications of AutoDock. J. Mol. Recognit. 9:1-5
    • (1996) J. Mol. Recognit. , vol.9 , pp. 1-5
    • Goodsell, D.S.1    Morris, G.M.2    Olson, A.J.3
  • 69
    • 11644261806 scopus 로고    scopus 로고
    • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    • Morris GM, Goodsell DS, Halliday RS, Huey R, Hart WE, et al. 1998. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 19:1639-62
    • (1998) J. Comput. Chem. , vol.19 , pp. 1639-1662
    • Morris, G.M.1    Goodsell, D.S.2    Halliday, R.S.3    Huey, R.4    Hart, W.E.5
  • 70
    • 0034979318 scopus 로고    scopus 로고
    • Biomolecular simulations: Recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions
    • Wang W, Donini O, Reyes CM, Kollman PA. 2001. Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions. Annu. Rev. Biophys. Biomolec. Struct. 30:211-43
    • (2001) Annu. Rev. Biophys. Biomolec. Struct. , vol.30 , pp. 211-243
    • Wang, W.1    Donini, O.2    Reyes, C.M.3    Kollman, P.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.