메뉴 건너뛰기




Volumn 10, Issue 8, 2014, Pages 3331-3344

Binding free energy calculations for lead optimization: Assessment of their accuracy in an industrial drug design context

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84906222221     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct5000296     Document Type: Article
Times cited : (140)

References (89)
  • 1
    • 84871477664 scopus 로고    scopus 로고
    • The Truly Staggering Cost of Inventing New Drugs
    • (accessed May 24, 2014).
    • Herper, M. The Truly Staggering Cost Of Inventing New Drugs. Forbes, 2012, http://www.forbes.com/sites/matthewherper/2012/02/22/the-truly-staggering- cost-of-inventing-new-drugs-the-print-version/ (accessed May 24, 2014).
    • (2012) Forbes
    • Herper, M.1
  • 5
    • 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, 1813-1818
    • (2004) Science , vol.303 , pp. 1813-1818
    • Jorgensen, W.L.1
  • 7
    • 77955663115 scopus 로고    scopus 로고
    • Prediction of protein-ligand binding affinity by free energy simulations: Assumptions, pitfalls and expectations
    • Michel, J.; Essex, J. W. Prediction of protein-ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations J. Comput.-Aided Mol. Des. 2010, 24, 639-658
    • (2010) J. Comput.-Aided Mol. Des. , vol.24 , pp. 639-658
    • Michel, J.1    Essex, J.W.2
  • 8
    • 80052805301 scopus 로고    scopus 로고
    • Recent Theoretical and Computational Advances for Modeling Protein-Ligand Binding Affinities
    • Gallicchio, E.; Levy, R. M. Recent Theoretical and Computational Advances for Modeling Protein-Ligand Binding Affinities Adv. Protein Chem. Struct. Biol. 2011, 85, 27-80
    • (2011) Adv. Protein Chem. Struct. Biol. , vol.85 , pp. 27-80
    • Gallicchio, E.1    Levy, R.M.2
  • 9
    • 0032560959 scopus 로고    scopus 로고
    • Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices
    • Srinivasan, J.; Cheatham, T. E., III; Cieplak, P.; Kolman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120, 9401-9409
    • (1998) J. Am. Chem. Soc. , vol.120 , pp. 9401-9409
    • Srinivasan, J.1    Cheatham III, T.E.2    Cieplak, P.3    Kolman, P.A.4    Case, D.A.5
  • 10
    • 84857282935 scopus 로고    scopus 로고
    • Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method
    • Homeyer, N.; Gohlke, H. Free Energy Calculations by the Molecular Mechanics Poisson-Boltzmann Surface Area Method Mol. Inf. 2012, 31, 114-122
    • (2012) Mol. Inf. , vol.31 , pp. 114-122
    • Homeyer, N.1    Gohlke, H.2
  • 11
    • 0028155689 scopus 로고
    • A new method for predicting binding affinity in computer-aided drug design
    • Åqvist, J.; Medina, C.; Samuelsson, J. E. A new method for predicting binding affinity in computer-aided drug design Protein Eng. 1994, 7, 385-391
    • (1994) Protein Eng. , vol.7 , pp. 385-391
    • Åqvist, J.1    Medina, C.2    Samuelsson, J.E.3
  • 12
    • 84855925859 scopus 로고    scopus 로고
    • Linear Interaction Energy: Method and Applications in Drug Design
    • Baron, R. Humana Press Inc. Totowa, NJ, Vol.
    • Guitiérrez-de-Terán, H.; Åqvist, J. Linear Interaction Energy: Method and Applications in Drug Design. In Computational Drug Discovery and Design; Baron, R., Ed.; Humana Press Inc.: Totowa, NJ, 2012; Vol. 819, pp 305-323.
    • (2012) Computational Drug Discovery and Design , vol.819 , pp. 305-323
    • Guitiérrez-De-Terán, H.1    Åqvist, J.2
  • 14
    • 84555211789 scopus 로고    scopus 로고
    • Orale, direkte Thrombin- und Faktor-Xa-Hemmer: Kommt die Ablösung für Warfarin, Blutegel und Schweinedärme?
    • Straub, A.; Roehrig, S.; Hillisch, A. Orale, direkte Thrombin- und Faktor-Xa-Hemmer: Kommt die Ablösung für Warfarin, Blutegel und Schweinedärme? Angew. Chem. 2011, 123, 4670-4686
    • (2011) Angew. Chem. , vol.123 , pp. 4670-4686
    • Straub, A.1    Roehrig, S.2    Hillisch, A.3
  • 15
    • 24944536065 scopus 로고    scopus 로고
    • Discovery of the Novel Antithrombotic Agent 5-Chloro-N-({(5S)-2-oxo-3-[4- (3-oxomorpholin-4-yl)phenyl]-1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): An Oral, Direct Factor Xa Inhibitor
    • Roehrig, S.; Straub, A.; Pohlmann, J.; Lampe, T.; Pernerstorfer, J.; Schlemmer, K. H.; Reinemer, P.; Perzborn, E. Discovery of the Novel Antithrombotic Agent 5-Chloro-N-({(5S)-2-oxo-3-[4-(3-oxomorpholin-4-yl)phenyl]- 1,3-oxazolidin-5-yl}methyl)thiophene-2-carboxamide (BAY 59-7939): An Oral, Direct Factor Xa Inhibitor J. Med. Chem. 2005, 48, 5900-5908
    • (2005) J. Med. Chem. , vol.48 , pp. 5900-5908
    • Roehrig, S.1    Straub, A.2    Pohlmann, J.3    Lampe, T.4    Pernerstorfer, J.5    Schlemmer, K.H.6    Reinemer, P.7    Perzborn, E.8
  • 19
    • 84906258267 scopus 로고    scopus 로고
    • version 1.2; Tripos International: St. Louis, MO.
    • SYBYL-X, version 1.2; Tripos International: St. Louis, MO, 2010.
    • (2010) SYBYL-X
  • 20
    • 0031473847 scopus 로고    scopus 로고
    • SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling
    • Guex, N.; Peitsch, M. C. SWISS-MODEL and the Swiss-PdbViewer: An environment for comparative protein modeling Electrophoresis 1997, 18, 2714-2723
    • (1997) Electrophoresis , vol.18 , pp. 2714-2723
    • Guex, N.1    Peitsch, M.C.2
  • 21
    • 79955892524 scopus 로고    scopus 로고
    • v4.0.1; Swiss Institute of Bioinformatics & the Biozentrum, University of Basel, Switzerland.
    • Guex, N.; Peitsch, M.; Schwede, T.; Diemand, A. Swiss-PdbViewer, v4.0.1; Swiss Institute of Bioinformatics & the Biozentrum, University of Basel, Switzerland, 2008.
    • (2008) Swiss-PdbViewer
    • Guex, N.1    Peitsch, M.2    Schwede, T.3    Diemand, A.4
  • 22
    • 79955574923 scopus 로고    scopus 로고
    • version 0.99rc6; Schrödinger, LLC: Portland, OR.
    • The PyMOL Molecular Graphics System, version 0.99rc6; Schrödinger, LLC: Portland, OR, 2006.
    • (2006) The PyMOL Molecular Graphics System
  • 25
    • 35248833733 scopus 로고    scopus 로고
    • Significance of Water Molecules in the Inhibition of Cylin-dependent Kinase 2 and 5 Complexes
    • Zhang, B.; Tan, V. B. C.; Lim, K. M.; Tay, T. E. Significance of Water Molecules in the Inhibition of Cylin-dependent Kinase 2 and 5 Complexes J. Chem. Inf. Model. 2007, 47, 1877-1885
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1877-1885
    • Zhang, B.1    Tan, V.B.C.2    Lim, K.M.3    Tay, T.E.4
  • 27
    • 0001041959 scopus 로고    scopus 로고
    • Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method
    • Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC Model: I. Method J. Comput. Chem. 2000, 21, 132-146
    • (2000) J. Comput. Chem. , vol.21 , pp. 132-146
    • Jakalian, A.1    Bush, B.L.2    Jack, D.B.3    Bayly, C.I.4
  • 28
    • 0036890178 scopus 로고    scopus 로고
    • Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC model: II. Parameterization and Validation
    • Jakalian, A.; Jack, D. B.; Bayly, C. I. Fast, Efficient Generation of High-Quality Atomic Charges. AM1-BCC model: II. Parameterization and Validation J. Comput. Chem. 2002, 23, 1623-1641
    • (2002) J. Comput. Chem. , vol.23 , pp. 1623-1641
    • Jakalian, A.1    Jack, D.B.2    Bayly, C.I.3
  • 29
    • 3042524904 scopus 로고
    • A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model
    • Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. A Well-Behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: The RESP Model J. Phys. Chem. 1993, 97, 10269-10280
    • (1993) J. Phys. Chem. , vol.97 , pp. 10269-10280
    • Bayly, C.I.1    Cieplak, P.2    Cornell, W.D.3    Kollman, P.A.4
  • 34
    • 0347602124 scopus 로고    scopus 로고
    • Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf
    • Gohlke, H.; Case, D. A. Converging Free Energy Estimates: MM-PB(GB)SA Studies on the Protein-Protein Complex Ras-Raf J. Comput. Chem. 2004, 25, 238-250
    • (2004) J. Comput. Chem. , vol.25 , pp. 238-250
    • Gohlke, H.1    Case, D.A.2
  • 35
    • 76249085850 scopus 로고    scopus 로고
    • How to Obtain Statistically Converged MM/GBSA Results
    • Genheden, S.; Ryde, U. How to Obtain Statistically Converged MM/GBSA Results J. Comput. Chem. 2010, 31, 837-846
    • (2010) J. Comput. Chem. , vol.31 , pp. 837-846
    • Genheden, S.1    Ryde, U.2
  • 36
    • 1842479952 scopus 로고    scopus 로고
    • Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model
    • Onufriev, A.; Bashford, D.; Case, D. A. Exploring Protein Native States and Large-Scale Conformational Changes with a Modified Generalized Born Model Proteins: Struct., Funct., Bioinf. 2004, 55, 383-394
    • (2004) Proteins: Struct., Funct., Bioinf. , vol.55 , pp. 383-394
    • Onufriev, A.1    Bashford, D.2    Case, D.A.3
  • 37
    • 14244273182 scopus 로고    scopus 로고
    • Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations
    • Tsui, V.; Case, D. A. Theory and Applications of the Generalized Born Solvation Model in Macromolecular Simulations Biopolymers 2001, 56, 275-291
    • (2001) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 38
    • 32844457567 scopus 로고
    • Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models
    • Sitkoff, D.; Sharp, K. A.; Honig, B. Accurate Calculation of Hydration Free Energies Using Macroscopic Solvent Models J. Phys. Chem. 1994, 98, 1978-1988
    • (1994) J. Phys. Chem. , vol.98 , pp. 1978-1988
    • Sitkoff, D.1    Sharp, K.A.2    Honig, B.3
  • 39
    • 33750467966 scopus 로고    scopus 로고
    • Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field
    • Weis, A.; Katebzadeh, K.; Söderhjelm, P.; Nilsson, I.; Ryde, U. Ligand Affinities Predicted with the MM/PBSA Method: Dependence on the Simulation Method and the Force Field J. Med. Chem. 2006, 49, 6596-6606
    • (2006) J. Med. Chem. , vol.49 , pp. 6596-6606
    • Weis, A.1    Katebzadeh, K.2    Söderhjelm, P.3    Nilsson, I.4    Ryde, U.5
  • 40
    • 79952588669 scopus 로고    scopus 로고
    • Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
    • Hou, T.; Wang, J.; Li, Y.; Wang, W. Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations J. Chem. Inf. Model. 2011, 51, 69-82
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 69-82
    • Hou, T.1    Wang, J.2    Li, Y.3    Wang, W.4
  • 41
    • 84961980685 scopus 로고    scopus 로고
    • Binding of a Diverse Set of Ligands to Avidin and Atreptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models
    • Kuhn, B.; Kollman, P. A. Binding of a Diverse Set of Ligands to Avidin and Atreptavidin: An Accurate Quantitative Prediction of Their Relative Affinities by a Combination of Molecular Mechanics and Continuum Solvent Models J. Med. Chem. 2000, 43, 3786-3791
    • (2000) J. Med. Chem. , vol.43 , pp. 3786-3791
    • Kuhn, B.1    Kollman, P.A.2
  • 42
    • 84865511407 scopus 로고    scopus 로고
    • The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant
    • Genheden, S.; Kuhn, O.; Mikulskis, P.; Hoffmann, D.; Ryde, U. The Normal-Mode Entropy in the MM/GBSA Method: Effect of System Truncation, Buffer Region, and Dielectric Constant J. Chem. Inf. Model. 2012, 52, 2079-2088
    • (2012) J. Chem. Inf. Model. , vol.52 , pp. 2079-2088
    • Genheden, S.1    Kuhn, O.2    Mikulskis, P.3    Hoffmann, D.4    Ryde, U.5
  • 43
    • 33947644064 scopus 로고    scopus 로고
    • Molecular dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-related Inhibitors: Mechanism for Binding and Drug Resistance
    • Hou, T.; Yu, R. Molecular dynamics and Free Energy Studies on the Wild-type and Double Mutant HIV-1 Protease Complexed with Amprenavir and Two Amprenavir-related Inhibitors: Mechanism for Binding and Drug Resistance J. Med. Chem. 2007, 50, 1177-1188
    • (2007) J. Med. Chem. , vol.50 , pp. 1177-1188
    • Hou, T.1    Yu, R.2
  • 44
    • 35348864558 scopus 로고    scopus 로고
    • Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors
    • Ferrari, A. M.; Degliesposti, G.; Sgobba, M.; Rastelli, G. Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors Bioorg. Med. Chem. 2007, 15, 7865-7877
    • (2007) Bioorg. Med. Chem. , vol.15 , pp. 7865-7877
    • Ferrari, A.M.1    Degliesposti, G.2    Sgobba, M.3    Rastelli, G.4
  • 45
    • 70350560811 scopus 로고    scopus 로고
    • Activity Prediction and Structural Insights of Extracellular Signal-Regulated Kinase 2 Inhibitors with Molecular Dynamics Simulations
    • Del Rio, A.; Baldi, B. F.; Rastelli, G. Activity Prediction and Structural Insights of Extracellular Signal-Regulated Kinase 2 Inhibitors with Molecular Dynamics Simulations Chem. Biol. Drug Des. 2009, 74, 630-635
    • (2009) Chem. Biol. Drug Des. , vol.74 , pp. 630-635
    • Del Rio, A.1    Baldi, B.F.2    Rastelli, G.3
  • 46
    • 34547666868 scopus 로고    scopus 로고
    • Rapid Estimation of Relative Protein-Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA
    • Brown, S. P.; Muchmore, S. W. Rapid Estimation of Relative Protein-Ligand Binding Affinities Using a High-Throughput Version of MM-PBSA J. Chem. Inf. Model. 2007, 47, 1493-1503
    • (2007) J. Chem. Inf. Model. , vol.47 , pp. 1493-1503
    • Brown, S.P.1    Muchmore, S.W.2
  • 47
    • 84875365821 scopus 로고    scopus 로고
    • FEW: A Workflow Tool for Free Energy Calculations of Ligand Binding
    • Homeyer, N.; Gohlke, H. FEW: A Workflow Tool for Free Energy Calculations of Ligand Binding J. Comput. Chem. 2012, 34, 965-973
    • (2012) J. Comput. Chem. , vol.34 , pp. 965-973
    • Homeyer, N.1    Gohlke, H.2
  • 48
    • 84863304598 scopus 로고    scopus 로고
    • R Core Team, R Foundation for Statistical Computing: Vienna, Austria, (accessed date October 8, 2010).
    • R: A Language and Environment for Statistical Computing; R Core Team, R Foundation for Statistical Computing: Vienna, Austria, 2010, http://www.R-project.org (accessed date October 8, 2010).
    • (2010) R: A Language and Environment for Statistical Computing
  • 49
    • 0031637651 scopus 로고    scopus 로고
    • Ligand binding affinity prediction by linear interaction energy methods
    • Hansson, T.; Marelius, J.; Åqvist, J. Ligand binding affinity prediction by linear interaction energy methods J. Comput.-Aided Mol. Des. 1998, 12, 27-35
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 27-35
    • Hansson, T.1    Marelius, J.2    Åqvist, J.3
  • 50
    • 0033557303 scopus 로고    scopus 로고
    • What Determines the van der Waals Coefficient β in the LIE (Linear Interaction Energy) Method to Estimate Binding Free Energies Using Molecular Dynamics Simulations?
    • Wang, W.; Wang, J.; Kollman, P. A. What Determines the van der Waals Coefficient β in the LIE (Linear Interaction Energy) Method to Estimate Binding Free Energies Using Molecular Dynamics Simulations? Proteins: Struct., Funct., Bioinf. 1999, 34, 395-402
    • (1999) Proteins: Struct., Funct., Bioinf. , vol.34 , pp. 395-402
    • Wang, W.1    Wang, J.2    Kollman, P.A.3
  • 51
    • 78149423058 scopus 로고    scopus 로고
    • New Parameterization Approaches of the LIE Method to Improve Free Energy Calculations of PlmII-Inhibitors Complexes
    • Valiente, P. A.; Gil L, A.; Batista, P. R.; Caffarena, E. R.; Pons, T.; Pascutti, P. G. New Parameterization Approaches of the LIE Method to Improve Free Energy Calculations of PlmII-Inhibitors Complexes J. Comput. Chem. 2010, 31, 2723-2734
    • (2010) J. Comput. Chem. , vol.31 , pp. 2723-2734
    • Valiente, P.A.1    Gil, L.A.2    Batista, P.R.3    Caffarena, E.R.4    Pons, T.5    Pascutti, P.G.6
  • 52
    • 84906275041 scopus 로고    scopus 로고
    • version 3.1.1; OpenEye Scientific Software: Santa Fe, NM.
    • ROCS, version 3.1.1; OpenEye Scientific Software: Santa Fe, NM, http://www.eyesopen.com.
    • ROCS
  • 53
    • 33846212271 scopus 로고    scopus 로고
    • Comparison of Shape-Matching and Docking as Virtual Screening Tools
    • Hawkins, P. C.; Skillman, A. G.; Nicholls, A. Comparison of Shape-Matching and Docking as Virtual Screening Tools J. Med. Chem. 2007, 50, 74-82
    • (2007) J. Med. Chem. , vol.50 , pp. 74-82
    • Hawkins, P.C.1    Skillman, A.G.2    Nicholls, A.3
  • 54
    • 70350674995 scopus 로고
    • On the shortest spanning subtree of a graph and the traveling salesman problem
    • Kruskal, J. B. On the shortest spanning subtree of a graph and the traveling salesman problem Proc. Am. Math. Soc. 1956, 7, 48-50
    • (1956) Proc. Am. Math. Soc. , vol.7 , pp. 48-50
    • Kruskal, J.B.1
  • 55
    • 80053211021 scopus 로고    scopus 로고
    • Soft-Core Potentials in Thermodynamic Integration: Comparing One- and Two-step Transformations
    • Steinbrecher, T.; Joung, I.; Case, D. A. Soft-Core Potentials in Thermodynamic Integration: Comparing One- and Two-step Transformations J. Comput. Chem. 2011, 32, 3253-3263
    • (2011) J. Comput. Chem. , vol.32 , pp. 3253-3263
    • Steinbrecher, T.1    Joung, I.2    Case, D.A.3
  • 56
    • 79955462105 scopus 로고    scopus 로고
    • Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA
    • Genheden, S.; Nilsson, I.; Ryde, U. Binding Affinities of Factor Xa Inhibitors Estimated by Thermodynamic Integration and MM/GBSA J. Chem. Inf. Model. 2011, 51, 947-958
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 947-958
    • Genheden, S.1    Nilsson, I.2    Ryde, U.3
  • 57
    • 0000642138 scopus 로고    scopus 로고
    • Ionic charging free energies: Spherical versus periodic boundary conditions
    • Darden, T.; Pearlman, D. A.; Pedersen, L. G. Ionic charging free energies: Spherical versus periodic boundary conditions J. Chem. Phys. 1998, 109, 10921-10935
    • (1998) J. Chem. Phys. , vol.109 , pp. 10921-10935
    • Darden, T.1    Pearlman, D.A.2    Pedersen, L.G.3
  • 59
    • 52949088587 scopus 로고    scopus 로고
    • Statistically optimal analysis of samples from multiple equilibrium states
    • Shirts, M. R.; Chodera, J. D. Statistically optimal analysis of samples from multiple equilibrium states J. Chem. Phys. 2008, 129, 124105
    • (2008) J. Chem. Phys. , vol.129 , pp. 124105
    • Shirts, M.R.1    Chodera, J.D.2
  • 60
    • 0035846166 scopus 로고    scopus 로고
    • Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System
    • Pearlman, D. A.; Charifson, P. S. Are Free Energy Calculations Useful in Practice? A Comparison with Rapid Scoring Functions for the p38 MAP Kinase Protein System J. Med. Chem. 2001, 44, 3417-3423
    • (2001) J. Med. Chem. , vol.44 , pp. 3417-3423
    • Pearlman, D.A.1    Charifson, P.S.2
  • 61
    • 84965150247 scopus 로고    scopus 로고
    • version 1.3.9, 2013, (accessed date September 9).
    • Canty, A.; Ripley, B. boot: Bootstrap Functions, version 1.3.9, 2013, http://cran.r-project.org/web/packages/boot/index.html (accessed date September 9, 2013).
    • (2013) Boot: Bootstrap Functions
    • Canty, A.1    Ripley, B.2
  • 62
    • 0037198807 scopus 로고    scopus 로고
    • Predictions of Binding of a Diverse Set of Ligands to Gelatinase-A by a Combination of Molecular Dynamics and Continuum Solvent Models
    • Hou, T.; Guo, S.; Xu, X. Predictions of Binding of a Diverse Set of Ligands to Gelatinase-A by a Combination of Molecular Dynamics and Continuum Solvent Models J. Phys. Chem. B 2002, 106, 5527-5535
    • (2002) J. Phys. Chem. B , vol.106 , pp. 5527-5535
    • Hou, T.1    Guo, S.2    Xu, X.3
  • 63
    • 0037187412 scopus 로고    scopus 로고
    • Molecular dynamics and Free Energy Analyses of Cathepsin D-inhibitor Interactions: Insight into Structure-Based Ligand Design
    • Huo, S.; Wang, J.; Cieplak, P.; Kollman, P. A.; Kuntz, I. D. Molecular dynamics and Free Energy Analyses of Cathepsin D-inhibitor Interactions: Insight into Structure-Based Ligand Design J. Med. Chem. 2002, 45, 1412-1419
    • (2002) J. Med. Chem. , vol.45 , pp. 1412-1419
    • Huo, S.1    Wang, J.2    Cieplak, P.3    Kollman, P.A.4    Kuntz, I.D.5
  • 64
    • 76249112547 scopus 로고    scopus 로고
    • Fast and Accurate Predictions of Binding Free Energies using MM-PBSA and MM-GBSA
    • Rastelli, G.; Del Rio, A.; Degliesposti, G.; Sgobba, M. Fast and Accurate Predictions of Binding Free Energies using MM-PBSA and MM-GBSA J. Comput. Chem. 2010, 31, 797-810
    • (2010) J. Comput. Chem. , vol.31 , pp. 797-810
    • Rastelli, G.1    Del Rio, A.2    Degliesposti, G.3    Sgobba, M.4
  • 65
    • 77951997162 scopus 로고    scopus 로고
    • Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
    • Guimarães, C. R. W.; Mathiowetz, A. M. Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations J. Chem. Inf. Model. 2010, 50, 547-559
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 547-559
    • Guimarães, C.R.W.1    Mathiowetz, A.M.2
  • 67
    • 84859438966 scopus 로고    scopus 로고
    • Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies
    • Genheden, S.; Ryde, U. Comparison of end-point continuum-solvation methods for the calculation of protein-ligand binding free energies Proteins: Struct., Funct., Bioinf. 2012, 80, 1326-1342
    • (2012) Proteins: Struct., Funct., Bioinf. , vol.80 , pp. 1326-1342
    • Genheden, S.1    Ryde, U.2
  • 68
    • 78649747478 scopus 로고    scopus 로고
    • Dispersion dominated halogen-π interactions: Energies and locations of minima
    • Wallnoefer, H. G.; Fox, T.; Liedl, K. R.; Tautermann, C. S. Dispersion dominated halogen-π interactions: energies and locations of minima Phys. Chem. Chem. Phys. 2010, 12, 14941-14949
    • (2010) Phys. Chem. Chem. Phys. , vol.12 , pp. 14941-14949
    • Wallnoefer, H.G.1    Fox, T.2    Liedl, K.R.3    Tautermann, C.S.4
  • 69
    • 84866682261 scopus 로고    scopus 로고
    • Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents
    • Jorgensen, W. L.; Schyman, P. Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents J. Chem. Theory Comput. 2011, 8, 3895-3901
    • (2011) J. Chem. Theory Comput. , vol.8 , pp. 3895-3901
    • Jorgensen, W.L.1    Schyman, P.2
  • 70
    • 79959739959 scopus 로고    scopus 로고
    • Molecular mechanical study of halogen bonding in drug discovery
    • Ibrahim, M. A. Molecular mechanical study of halogen bonding in drug discovery J. Comput. Chem. 2011, 32, 2564-2574
    • (2011) J. Comput. Chem. , vol.32 , pp. 2564-2574
    • Ibrahim, M.A.1
  • 71
    • 80055038428 scopus 로고    scopus 로고
    • Halogen bonding in ligand-receptor systems in the framework of classical force fields
    • Rendine, S.; Pieraccini, S.; Forni, A.; Sironi, M. Halogen bonding in ligand-receptor systems in the framework of classical force fields Phys. Chem. Chem. Phys. 2011, 13, 19508-19516
    • (2011) Phys. Chem. Chem. Phys. , vol.13 , pp. 19508-19516
    • Rendine, S.1    Pieraccini, S.2    Forni, A.3    Sironi, M.4
  • 73
    • 33748637571 scopus 로고    scopus 로고
    • Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models
    • Wang, J.; Hou, T.; Yu, X. Recent Advances in Free Energy Calculations with a Combination of Molecular Mechanics and Continuum Models Curr. Comput.-Aided Drug Des. 2006, 2, 95-103
    • (2006) Curr. Comput.-Aided Drug Des. , vol.2 , pp. 95-103
    • Wang, J.1    Hou, T.2    Yu, X.3
  • 74
    • 8644224855 scopus 로고    scopus 로고
    • Molecular mechanisms of indirubine and its derivatives: Novel anticancer molecules with their origin in traditional Chinese phytomedicine
    • Eisenbrand, G.; Hippe, F.; Jakobs, S.; Muehlbeyer, S. Molecular mechanisms of indirubine and its derivatives: novel anticancer molecules with their origin in traditional Chinese phytomedicine J. Cancer Res. Clin. Oncol. 2004, 130, 627-635
    • (2004) J. Cancer Res. Clin. Oncol. , vol.130 , pp. 627-635
    • Eisenbrand, G.1    Hippe, F.2    Jakobs, S.3    Muehlbeyer, S.4
  • 75
    • 33750288698 scopus 로고    scopus 로고
    • Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method
    • Stjernschantz, E.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N. P. E.; Oostenbrink, C. Are Automated Molecular Dynamics Simulations and Binding Free Energy Calculations Realistic Tools in Lead Optimization? An Evaluation of the Linear Interaction Energy (LIE) Method J. Chem. Inf. Model. 2006, 46, 1972-1983
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1972-1983
    • Stjernschantz, E.1    Marelius, J.2    Medina, C.3    Jacobsson, M.4    Vermeulen, N.P.E.5    Oostenbrink, C.6
  • 76
    • 84859444429 scopus 로고    scopus 로고
    • Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods
    • Mikulskis, P.; Genheden, S.; Rydberg, P.; Sandberg, L.; Olsen, L.; Ryde, U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods J. Comput.-Aided Mol. Des. 2011, 26, 527-541
    • (2011) J. Comput.-Aided Mol. Des. , vol.26 , pp. 527-541
    • Mikulskis, P.1    Genheden, S.2    Rydberg, P.3    Sandberg, L.4    Olsen, L.5    Ryde, U.6
  • 77
    • 84855205990 scopus 로고    scopus 로고
    • MM/GBSA and LIE estimates of host-guest affinities: Dependence on charges and solvation model
    • Genheden, S. MM/GBSA and LIE estimates of host-guest affinities: dependence on charges and solvation model J. Comput.-Aided Mol. Des. 2011, 25, 1085-1093
    • (2011) J. Comput.-Aided Mol. Des. , vol.25 , pp. 1085-1093
    • Genheden, S.1
  • 78
    • 79953005073 scopus 로고    scopus 로고
    • Efficiency of Alchemical Free Energy Simulations. I. A Practical Comparison of the Exponential Formula, Thermodynamic Integration, and Bennett"s Acceptance Ratio Method
    • Bruckner, S.; Boresch, S. Efficiency of Alchemical Free Energy Simulations. I. A Practical Comparison of the Exponential Formula, Thermodynamic Integration, and Bennett"s Acceptance Ratio Method J. Comput. Chem. 2011, 32, 1303-1319
    • (2011) J. Comput. Chem. , vol.32 , pp. 1303-1319
    • Bruckner, S.1    Boresch, S.2
  • 79
    • 79953020995 scopus 로고    scopus 로고
    • Efficiency of Alchemical Free Energy Simulations. II. Improvements for Thermodynamic Integration
    • Bruckner, S.; Boresch, S. Efficiency of Alchemical Free Energy Simulations. II. Improvements for Thermodynamic Integration J. Comput. Chem. 2011, 32, 1320-1333
    • (2011) J. Comput. Chem. , vol.32 , pp. 1320-1333
    • Bruckner, S.1    Boresch, S.2
  • 80
    • 23944432199 scopus 로고    scopus 로고
    • Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration
    • Shirts, M. R.; Pande, V. S. Comparison of efficiency and bias of free energies computed by exponential averaging, the Bennett acceptance ratio, and thermodynamic integration J. Chem. Phys. 2005, 122, 144107
    • (2005) J. Chem. Phys. , vol.122 , pp. 144107
    • Shirts, M.R.1    Pande, V.S.2
  • 81
    • 84884170318 scopus 로고    scopus 로고
    • Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package
    • Kaus, J. W.; Pierce, L. T.; Walker, R. C.; McCammont, J. A. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package J. Chem. Theory Comput. 2013, 9, 4131-4139
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 4131-4139
    • Kaus, J.W.1    Pierce, L.T.2    Walker, R.C.3    McCammont, J.A.4
  • 82
    • 84881065022 scopus 로고    scopus 로고
    • Protonation and pK changes in protein-ligand binding
    • Onufriev, A. V.; Alexov, E. Protonation and pK changes in protein-ligand binding Q. Rev. Biophys. 2013, 46, 181-209
    • (2013) Q. Rev. Biophys. , vol.46 , pp. 181-209
    • Onufriev, A.V.1    Alexov, E.2
  • 83
    • 84873642828 scopus 로고    scopus 로고
    • Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors
    • Wang, L.; Deng, Y.; Knight, J. L.; Wu, Y.; Kim, B.; Sherman, W.; Shelley, J. C.; Lin, T.; Abel, R. Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors J. Chem. Theory Comput. 2013, 9, 1282-1293
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 1282-1293
    • Wang, L.1    Deng, Y.2    Knight, J.L.3    Wu, Y.4    Kim, B.5    Sherman, W.6    Shelley, J.C.7    Lin, T.8    Abel, R.9
  • 84
    • 34548297023 scopus 로고    scopus 로고
    • Structural Basis of Spirolactone Recognition by the Mineralocorticoid Receptor
    • Huyet, J.; Pinon, G. M.; Fay, M. R.; Fagart, J.; Rafestin-Oblin, M. E. Structural Basis of Spirolactone Recognition by the Mineralocorticoid Receptor Mol. Pharmacol. 2007, 72, 563-571
    • (2007) Mol. Pharmacol. , vol.72 , pp. 563-571
    • Huyet, J.1    Pinon, G.M.2    Fay, M.R.3    Fagart, J.4    Rafestin-Oblin, M.E.5
  • 85
    • 23044510503 scopus 로고    scopus 로고
    • Structural and Biochemical Mechanisms for the Specificity of Hormone Binding and Coactivator Assembly by Mineralocorticoid Receptor
    • Li, Y.; Suino, K.; Daugherty, J.; Xu, H. E. Structural and Biochemical Mechanisms for the Specificity of Hormone Binding and Coactivator Assembly by Mineralocorticoid Receptor Mol. Cell 2005, 19, 367-380
    • (2005) Mol. Cell , vol.19 , pp. 367-380
    • Li, Y.1    Suino, K.2    Daugherty, J.3    Xu, H.E.4
  • 86
    • 73249124826 scopus 로고    scopus 로고
    • Molecular Switch in the Glucocorticoid Receptor: Active and Passive Antagonist Conformations
    • Schoch, G. A.; D'Arcy, B.; Stihle, M.; Burger, D.; Bär, D.; Benz, J.; Thoma, R.; Ruf, A. Molecular Switch in the Glucocorticoid Receptor: Active and Passive Antagonist Conformations J. Mol. Biol. 2010, 395, 568-577
    • (2010) J. Mol. Biol. , vol.395 , pp. 568-577
    • Schoch, G.A.1    D'Arcy, B.2    Stihle, M.3    Burger, D.4    Bär, D.5    Benz, J.6    Thoma, R.7    Ruf, A.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.