메뉴 건너뛰기




Volumn 57, Issue 2, 2017, Pages 127-132

SQM/COSMO Scoring Function at the DFTB3-D3H4 Level: Unique Identification of Native Protein-Ligand Poses

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEXATION; IONS; LIGANDS; QUANTUM THEORY;

EID: 85014303363     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.6b00513     Document Type: Article
Times cited : (38)

References (65)
  • 1
    • 77950503976 scopus 로고    scopus 로고
    • Virtual Screening: An Endless Staircase?
    • Schneider, G. Virtual Screening: An Endless Staircase? Nat. Rev. Drug Discovery 2010, 9, 273-276 10.1038/nrd3139
    • (2010) Nat. Rev. Drug Discovery , vol.9 , pp. 273-276
    • Schneider, G.1
  • 2
    • 84969545588 scopus 로고    scopus 로고
    • Docking Screens for Novel Ligands Conferring New Biology
    • Irwin, J. J.; Shoichet, B. K. Docking Screens for Novel Ligands Conferring New Biology J. Med. Chem. 2016, 59, 4103-4120 10.1021/acs.jmedchem.5b02008
    • (2016) J. Med. Chem. , vol.59 , pp. 4103-4120
    • Irwin, J.J.1    Shoichet, B.K.2
  • 3
    • 66149103553 scopus 로고    scopus 로고
    • Comparative Assessment of Scoring Functions on a Diverse Test Set
    • Cheng, T. J.; Li, X.; Li, Y.; Liu, Z. H.; Wang, R. X. Comparative Assessment of Scoring Functions on a Diverse Test Set J. Chem. Inf. Model. 2009, 49, 1079-1093 10.1021/ci9000053
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 1079-1093
    • Cheng, T.J.1    Li, X.2    Li, Y.3    Liu, Z.H.4    Wang, R.X.5
  • 4
    • 84973574825 scopus 로고    scopus 로고
    • Comprehensive Evaluation of Ten Docking Programs on a Diverse Set of Protein-Ligand Complexes: The Prediction Accuracy of Sampling Power and Scoring Power
    • Wang, Z.; Sun, H. Y.; Yao, X. J.; Li, D.; Xu, L.; Li, Y. Y.; Tian, S.; Hou, T. J. Comprehensive Evaluation of Ten Docking Programs on a Diverse Set of Protein-Ligand Complexes: The Prediction Accuracy of Sampling Power and Scoring Power Phys. Chem. Chem. Phys. 2016, 18, 12964-12975 10.1039/C6CP01555G
    • (2016) Phys. Chem. Chem. Phys. , vol.18 , pp. 12964-12975
    • Wang, Z.1    Sun, H.Y.2    Yao, X.J.3    Li, D.4    Xu, L.5    Li, Y.Y.6    Tian, S.7    Hou, T.J.8
  • 5
    • 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, 149-164 10.1002/jmr.1077
    • (2011) J. Mol. Recognit. , vol.24 , pp. 149-164
    • Yuriev, E.1    Agostino, M.2    Ramsland, P.A.3
  • 6
    • 41349106542 scopus 로고    scopus 로고
    • Recommendations for Evaluation of Computational Methods
    • Jain, A. N.; Nicholls, A. Recommendations for Evaluation of Computational Methods J. Comput.-Aided Mol. Des. 2008, 22, 133-139 10.1007/s10822-008-9196-5
    • (2008) J. Comput.-Aided Mol. Des. , vol.22 , pp. 133-139
    • Jain, A.N.1    Nicholls, A.2
  • 7
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of Docking Performance: Comparative Data on Docking Algorithms
    • Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of Docking Performance: Comparative Data on Docking Algorithms J. Med. Chem. 2004, 47, 558-565 10.1021/jm0302997
    • (2004) J. Med. Chem. , vol.47 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 8
    • 0034645763 scopus 로고    scopus 로고
    • Knowledge-based Scoring Function to Predict Protein-Ligand Interactions
    • Gohlke, H.; Hendlich, M.; Klebe, G. Knowledge-based Scoring Function to Predict Protein-Ligand Interactions J. Mol. Biol. 2000, 295, 337-356 10.1006/jmbi.1999.3371
    • (2000) J. Mol. Biol. , vol.295 , pp. 337-356
    • Gohlke, H.1    Hendlich, M.2    Klebe, G.3
  • 10
    • 84904819424 scopus 로고    scopus 로고
    • Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design
    • Grinter, S. Z.; Zou, X. Q. Challenges, Applications, and Recent Advances of Protein-Ligand Docking in Structure-Based Drug Design Molecules 2014, 19, 10150-10176 10.3390/molecules190710150
    • (2014) Molecules , vol.19 , pp. 10150-10176
    • Grinter, S.Z.1    Zou, X.Q.2
  • 11
    • 77952337364 scopus 로고    scopus 로고
    • Ligand Affinities Estimated by Quantum Chemical Calculations
    • Soderhjelm, P.; Kongsted, J.; Ryde, U. Ligand Affinities Estimated by Quantum Chemical Calculations J. Chem. Theory Comput. 2010, 6, 1726-1737 10.1021/ct9006986
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 1726-1737
    • Soderhjelm, P.1    Kongsted, J.2    Ryde, U.3
  • 12
    • 77957954013 scopus 로고    scopus 로고
    • Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein-Ligand Binding Affinity
    • Hayik, S. A.; Dunbrack, R.; Merz, K. M. Mixed Quantum Mechanics/Molecular Mechanics Scoring Function To Predict Protein-Ligand Binding Affinity J. Chem. Theory Comput. 2010, 6, 3079-3091 10.1021/ct100315g
    • (2010) J. Chem. Theory Comput. , vol.6 , pp. 3079-3091
    • Hayik, S.A.1    Dunbrack, R.2    Merz, K.M.3
  • 13
    • 84969818173 scopus 로고    scopus 로고
    • The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes
    • Berg, L.; Mishra, B. K.; Andersson, C. D.; Ekstrom, F.; Linusson, A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes Chem.-Eur. J. 2016, 22, 2672-2681 10.1002/chem.201503973
    • (2016) Chem. - Eur. J. , vol.22 , pp. 2672-2681
    • Berg, L.1    Mishra, B.K.2    Andersson, C.D.3    Ekstrom, F.4    Linusson, A.5
  • 14
    • 84912569558 scopus 로고    scopus 로고
    • Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function
    • Chaskar, P.; Zoete, V.; Rohrig, U. F. Toward On-The-Fly Quantum Mechanical/Molecular Mechanical (QM/MM) Docking: Development and Benchmark of a Scoring Function J. Chem. Inf. Model. 2014, 54, 3137-3152 10.1021/ci5004152
    • (2014) J. Chem. Inf. Model. , vol.54 , pp. 3137-3152
    • Chaskar, P.1    Zoete, V.2    Rohrig, U.F.3
  • 15
    • 79952582249 scopus 로고    scopus 로고
    • Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase
    • Burger, S. K.; Thompson, D. C.; Ayers, P. W. Quantum Mechanics/Molecular Mechanics Strategies for Docking Pose Refinement: Distinguishing between Binders and Decoys in Cytochrome c Peroxidase J. Chem. Inf. Model. 2011, 51, 93-101 10.1021/ci100329z
    • (2011) J. Chem. Inf. Model. , vol.51 , pp. 93-101
    • Burger, S.K.1    Thompson, D.C.2    Ayers, P.W.3
  • 16
    • 80054712743 scopus 로고    scopus 로고
    • Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods
    • Antony, J.; Grimme, S.; Liakos, D. G.; Neese, F. Protein-Ligand Interaction Energies with Dispersion Corrected Density Functional Theory and High-Level Wave Function Based Methods J. Phys. Chem. A 2011, 115, 11210-11220 10.1021/jp203963f
    • (2011) J. Phys. Chem. A , vol.115 , pp. 11210-11220
    • Antony, J.1    Grimme, S.2    Liakos, D.G.3    Neese, F.4
  • 17
    • 0942276314 scopus 로고    scopus 로고
    • A Quantum Mechanics-based Scoring Function: Study of Zinc Ion-mediated Ligand Binding
    • Raha, K.; Merz, K. M. A Quantum Mechanics-based Scoring Function: Study of Zinc Ion-mediated Ligand Binding J. Am. Chem. Soc. 2004, 126, 1020-1021 10.1021/ja038496i
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 1020-1021
    • Raha, K.1    Merz, K.M.2
  • 18
    • 22244451417 scopus 로고    scopus 로고
    • Large-scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein-Ligand Complexes
    • Raha, K.; Merz, K. M. Large-scale Validation of a Quantum Mechanics Based Scoring Function: Predicting the Binding Affinity and the Binding Mode of a Diverse Set of Protein-Ligand Complexes J. Med. Chem. 2005, 48, 4558-4575 10.1021/jm048973n
    • (2005) J. Med. Chem. , vol.48 , pp. 4558-4575
    • Raha, K.1    Merz, K.M.2
  • 19
    • 35448937584 scopus 로고    scopus 로고
    • Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements
    • Stewart, J. J. P. Optimization of Parameters for Semiempirical Methods V: Modification of NDDO Approximations and Application to 70 Elements J. Mol. Model. 2007, 13, 1173-1213 10.1007/s00894-007-0233-4
    • (2007) J. Mol. Model. , vol.13 , pp. 1173-1213
    • Stewart, J.J.P.1
  • 20
    • 67849101722 scopus 로고    scopus 로고
    • Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes
    • Rezac, J.; Fanfrlik, J.; Salahub, D.; Hobza, P. Semiempirical Quantum Chemical PM6 Method Augmented by Dispersion and H-Bonding Correction Terms Reliably Describes Various Types of Noncovalent Complexes J. Chem. Theory Comput. 2009, 5, 1749-1760 10.1021/ct9000922
    • (2009) J. Chem. Theory Comput. , vol.5 , pp. 1749-1760
    • Rezac, J.1    Fanfrlik, J.2    Salahub, D.3    Hobza, P.4
  • 21
    • 84855668199 scopus 로고    scopus 로고
    • Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods
    • Rezac, J.; Hobza, P. Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods J. Chem. Theory Comput. 2012, 8, 141-151 10.1021/ct200751e
    • (2012) J. Chem. Theory Comput. , vol.8 , pp. 141-151
    • Rezac, J.1    Hobza, P.2
  • 22
    • 79954583073 scopus 로고    scopus 로고
    • A Halogen-bonding Correction for the Semiempirical PM6 Method
    • Rezac, J.; Hobza, P. A Halogen-bonding Correction for the Semiempirical PM6 Method Chem. Phys. Lett. 2011, 506, 286-289 10.1016/j.cplett.2011.03.009
    • (2011) Chem. Phys. Lett. , vol.506 , pp. 286-289
    • Rezac, J.1    Hobza, P.2
  • 23
    • 84962478542 scopus 로고    scopus 로고
    • Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications
    • Rezac, J.; Hobza, P. Benchmark Calculations of Interaction Energies in Noncovalent Complexes and Their Applications Chem. Rev. 2016, 116, 5038-5071 10.1021/acs.chemrev.5b00526
    • (2016) Chem. Rev. , vol.116 , pp. 5038-5071
    • Rezac, J.1    Hobza, P.2
  • 24
    • 77957291978 scopus 로고    scopus 로고
    • A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands
    • Fanfrlik, J.; Bronowska, A. K.; Rezac, J.; Prenosil, O.; Konvalinka, J.; Hobza, P. A Reliable Docking/Scoring Scheme Based on the Semiempirical Quantum Mechanical PM6-DH2 Method Accurately Covering Dispersion and H-Bonding: HIV-1 Protease with 22 Ligands J. Phys. Chem. B 2010, 114, 12666-12678 10.1021/jp1032965
    • (2010) J. Phys. Chem. B , vol.114 , pp. 12666-12678
    • Fanfrlik, J.1    Bronowska, A.K.2    Rezac, J.3    Prenosil, O.4    Konvalinka, J.5    Hobza, P.6
  • 25
    • 84883853834 scopus 로고    scopus 로고
    • The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design
    • Lepsik, M.; Rezac, J.; Kolar, M.; Pecina, A.; Hobza, P.; Fanfrlik, J. The Semiempirical Quantum Mechanical Scoring Function for In Silico Drug Design ChemPlusChem 2013, 78, 921-931 10.1002/cplu.201300199
    • (2013) ChemPlusChem , vol.78 , pp. 921-931
    • Lepsik, M.1    Rezac, J.2    Kolar, M.3    Pecina, A.4    Hobza, P.5    Fanfrlik, J.6
  • 30
    • 84890040875 scopus 로고    scopus 로고
    • Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors
    • Fanfrlik, J.; Brahmkshatriya, P. S.; Rezac, J.; Jilkova, A.; Horn, M.; Mares, M.; Hobza, P.; Lepsik, M. Quantum Mechanics-Based Scoring Rationalizes the Irreversible Inactivation of Parasitic Schistosoma mansoni Cysteine Peptidase by Vinyl Sulfone Inhibitors J. Phys. Chem. B 2013, 117, 14973-14982 10.1021/jp409604n
    • (2013) J. Phys. Chem. B , vol.117 , pp. 14973-14982
    • Fanfrlik, J.1    Brahmkshatriya, P.S.2    Rezac, J.3    Jilkova, A.4    Horn, M.5    Mares, M.6    Hobza, P.7    Lepsik, M.8
  • 31
    • 84958817901 scopus 로고    scopus 로고
    • The SQM/COSMO Filter: Reliable Native Pose Identification Based on the Quantum-Mechanical Description of Protein-Ligand Interactions and Implicit COSMO Solvation
    • Pecina, A.; Meier, R.; Fanfrlik, J.; Lepsik, M.; Rezac, J.; Hobza, P.; Baldauf, C. The SQM/COSMO Filter: Reliable Native Pose Identification Based on the Quantum-Mechanical Description of Protein-Ligand Interactions and Implicit COSMO Solvation Chem. Commun. 2016, 52, 3312-3315 10.1039/C5CC09499B
    • (2016) Chem. Commun. , vol.52 , pp. 3312-3315
    • Pecina, A.1    Meier, R.2    Fanfrlik, J.3    Lepsik, M.4    Rezac, J.5    Hobza, P.6    Baldauf, C.7
  • 33
    • 0035932162 scopus 로고    scopus 로고
    • Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs: A Density-Functional-Theory Based Treatment
    • Elstner, M.; Hobza, P.; Frauenheim, T.; Suhai, S.; Kaxiras, E. Hydrogen Bonding and Stacking Interactions of Nucleic Acid Base Pairs: A Density-Functional-Theory Based Treatment J. Chem. Phys. 2001, 114, 5149-5155 10.1063/1.1329889
    • (2001) J. Chem. Phys. , vol.114 , pp. 5149-5155
    • Elstner, M.1    Hobza, P.2    Frauenheim, T.3    Suhai, S.4    Kaxiras, E.5
  • 34
    • 34447127776 scopus 로고    scopus 로고
    • DFTB+, A Sparse Matrix-based Implementation of the DFTB Method
    • Aradi, B.; Hourahine, B.; Frauenheim, T. DFTB+, A Sparse Matrix-based Implementation of the DFTB Method J. Phys. Chem. A 2007, 111, 5678-5684 10.1021/jp070186p
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5678-5684
    • Aradi, B.1    Hourahine, B.2    Frauenheim, T.3
  • 35
    • 84976605400 scopus 로고    scopus 로고
    • Stewart Computational Chemistry: Colorado Springs, CO
    • Stewart, J. J. P. MOPAC2016; Stewart Computational Chemistry: Colorado Springs, CO, 2016.
    • (2016) MOPAC2016
    • Stewart, J.J.P.1
  • 36
    • 67349218843 scopus 로고    scopus 로고
    • Application of the PM6 Method to Modeling Proteins
    • Stewart, J. J. P. Application of the PM6 Method to Modeling Proteins J. Mol. Model. 2009, 15, 765-805 10.1007/s00894-008-0420-y
    • (2009) J. Mol. Model. , vol.15 , pp. 765-805
    • Stewart, J.J.P.1
  • 37
    • 84976641914 scopus 로고    scopus 로고
    • Three Pillars for Achieving Quantum Mechanical Molecular Dynamics Simulations of Huge Systems: Divide-and-conquer, Density-functional Tight-binding, and Massively Parallel Computation
    • Nishizawa, H.; Nishimura, Y.; Kobayashi, M.; Irle, S.; Nakai, H. Three Pillars for Achieving Quantum Mechanical Molecular Dynamics Simulations of Huge Systems: Divide-and-conquer, Density-functional Tight-binding, and Massively Parallel Computation J. Comput. Chem. 2016, 37, 1983-1992 10.1002/jcc.24419
    • (2016) J. Comput. Chem. , vol.37 , pp. 1983-1992
    • Nishizawa, H.1    Nishimura, Y.2    Kobayashi, M.3    Irle, S.4    Nakai, H.5
  • 38
    • 85010651895 scopus 로고    scopus 로고
    • Description of Non-Covalent Interactions in SCC-DFTB Methods
    • Rezac, J.; Miriyala, V. M. Description of Non-Covalent Interactions in SCC-DFTB Methods J. Comput. Chem. 2017, 10.1002/jcc.24725
    • (2017) J. Comput. Chem.
    • Rezac, J.1    Miriyala, V.M.2
  • 39
    • 84969622308 scopus 로고    scopus 로고
    • Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications
    • Christensen, A. S.; Kubar, T.; Cui, Q.; Elstner, M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications Chem. Rev. 2016, 116, 5301-5337 10.1021/acs.chemrev.5b00584
    • (2016) Chem. Rev. , vol.116 , pp. 5301-5337
    • Christensen, A.S.1    Kubar, T.2    Cui, Q.3    Elstner, M.4
  • 40
    • 79954547473 scopus 로고    scopus 로고
    • DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)
    • Gaus, M.; Cui, Q. A.; Elstner, M. DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) J. Chem. Theory Comput. 2011, 7, 931-948 10.1021/ct100684s
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 931-948
    • Gaus, M.1    Cui, Q.A.2    Elstner, M.3
  • 41
    • 84872145856 scopus 로고    scopus 로고
    • Parametrization and Benchmark of DFTB3 for Organic Molecules
    • Gaus, M.; Goez, A.; Elstner, M. Parametrization and Benchmark of DFTB3 for Organic Molecules J. Chem. Theory Comput. 2013, 9, 338-354 10.1021/ct300849w
    • (2013) J. Chem. Theory Comput. , vol.9 , pp. 338-354
    • Gaus, M.1    Goez, A.2    Elstner, M.3
  • 42
    • 84898462014 scopus 로고    scopus 로고
    • Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications
    • Gaus, M.; Lu, X. Y.; Elstner, M.; Cui, Q. Parameterization of DFTB3/3OB for Sulfur and Phosphorus for Chemical and Biological Applications J. Chem. Theory Comput. 2014, 10, 1518-1537 10.1021/ct401002w
    • (2014) J. Chem. Theory Comput. , vol.10 , pp. 1518-1537
    • Gaus, M.1    Lu, X.Y.2    Elstner, M.3    Cui, Q.4
  • 43
    • 84921507266 scopus 로고    scopus 로고
    • Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications
    • Lu, X. Y.; Gaus, M.; Elstner, M.; Cui, Q. Parametrization of DFTB3/3OB for Magnesium and Zinc for Chemical and Biological Applications J. Phys. Chem. B 2015, 119, 1062-1082 10.1021/jp506557r
    • (2015) J. Phys. Chem. B , vol.119 , pp. 1062-1082
    • Lu, X.Y.1    Gaus, M.2    Elstner, M.3    Cui, Q.4
  • 44
    • 84921342469 scopus 로고    scopus 로고
    • Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems
    • Kubillus, M.; Kubar, T.; Gaus, M.; Rezac, J.; Elstner, M. Parameterization of the DFTB3 Method for Br, Ca, Cl, F, I, K, and Na in Organic and Biological Systems J. Chem. Theory Comput. 2015, 11, 332-342 10.1021/ct5009137
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 332-342
    • Kubillus, M.1    Kubar, T.2    Gaus, M.3    Rezac, J.4    Elstner, M.5
  • 45
    • 84941313380 scopus 로고    scopus 로고
    • DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters
    • Gaus, M.; Jin, H. Y.; Demapan, D.; Christensen, A. S.; Goyal, P.; Elstner, M.; Cui, Q. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters J. Chem. Theory Comput. 2015, 11, 4205-4219 10.1021/acs.jctc.5b00600
    • (2015) J. Chem. Theory Comput. , vol.11 , pp. 4205-4219
    • Gaus, M.1    Jin, H.Y.2    Demapan, D.3    Christensen, A.S.4    Goyal, P.5    Elstner, M.6    Cui, Q.7
  • 46
    • 80051662513 scopus 로고    scopus 로고
    • S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures
    • Rezac, J.; Riley, K. E.; Hobza, P. S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular Structures J. Chem. Theory Comput. 2011, 7, 2427-2438 10.1021/ct2002946
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2427-2438
    • Rezac, J.1    Riley, K.E.2    Hobza, P.3
  • 47
    • 84878077947 scopus 로고    scopus 로고
    • Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches
    • Kolar, M.; Fanfrlik, J.; Lepsik, M.; Forti, F.; Luque, F. J.; Hobza, P. Assessing the Accuracy and Performance of Implicit Solvent Models for Drug Molecules: Conformational Ensemble Approaches J. Phys. Chem. B 2013, 117, 5950-5962 10.1021/jp402117c
    • (2013) J. Phys. Chem. B , vol.117 , pp. 5950-5962
    • Kolar, M.1    Fanfrlik, J.2    Lepsik, M.3    Forti, F.4    Luque, F.J.5    Hobza, P.6
  • 48
    • 84961980743 scopus 로고
    • COSMO - A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient
    • Klamt, A.; Schuurmann, G. COSMO-A New Approach to Dielectric Screening in Solvents with Explicit Expressions for the Screening Energy and Its Gradient J. Chem. Soc., Perkin Trans. 2 1993, 2, 799-805 10.1039/P29930000799
    • (1993) J. Chem. Soc., Perkin Trans. 2 , vol.2 , pp. 799-805
    • Klamt, A.1    Schuurmann, G.2
  • 49
    • 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 2000, 56, 275-291 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E
    • (2000) Biopolymers , vol.56 , pp. 275-291
    • Tsui, V.1    Case, D.A.2
  • 51
    • 0037022789 scopus 로고    scopus 로고
    • 3D Structure of Torpedo Californica Acetylcholinesterase Complexed with Huprine X at 2.1 Angstrom Resolution: Kinetic and Molecular Dynamic Correlates
    • Dvir, H.; Wong, D. M.; Harel, M.; Barril, X.; Orozco, M.; Luque, F. J.; Munoz-Torrero, D.; Camps, P.; Rosenberry, T. L.; Silman, I.; Sussman, J. L. 3D Structure of Torpedo Californica Acetylcholinesterase Complexed with Huprine X at 2.1 Angstrom Resolution: Kinetic and Molecular Dynamic Correlates Biochemistry 2002, 41, 2970-2981 10.1021/bi011652i
    • (2002) Biochemistry , vol.41 , pp. 2970-2981
    • Dvir, H.1    Wong, D.M.2    Harel, M.3    Barril, X.4    Orozco, M.5    Luque, F.J.6    Munoz-Torrero, D.7    Camps, P.8    Rosenberry, T.L.9    Silman, I.10    Sussman, J.L.11
  • 52
    • 37549070327 scopus 로고    scopus 로고
    • Novel Thiol-based TACE Inhibitors. Part 2: Rational Design, Synthesis, and SAR of Thiol-containing Aryl Sulfones
    • Bandarage, U. K.; Wang, T.; Come, J. H.; Perola, E.; Wei, Y.; Rao, B. G. Novel Thiol-based TACE Inhibitors. Part 2: Rational Design, Synthesis, and SAR of Thiol-containing Aryl Sulfones Bioorg. Med. Chem. Lett. 2008, 18, 44-48 10.1016/j.bmcl.2007.11.014
    • (2008) Bioorg. Med. Chem. Lett. , vol.18 , pp. 44-48
    • Bandarage, U.K.1    Wang, T.2    Come, J.H.3    Perola, E.4    Wei, Y.5    Rao, B.G.6
  • 53
    • 34047134951 scopus 로고    scopus 로고
    • Structural and Thermodynamic Study on Aldose Reductase: Nitro-substituted Inhibitors with Strong Enthalpic Binding Contribution
    • Steuber, H.; Heine, A.; Klebe, G. Structural and Thermodynamic Study on Aldose Reductase: Nitro-substituted Inhibitors with Strong Enthalpic Binding Contribution J. Mol. Biol. 2007, 368, 618-638 10.1016/j.jmb.2006.12.004
    • (2007) J. Mol. Biol. , vol.368 , pp. 618-638
    • Steuber, H.1    Heine, A.2    Klebe, G.3
  • 54
    • 11144356514 scopus 로고    scopus 로고
    • A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation, and Subsite-pocket Interactions Analyzed at Atomic Resolution
    • Brynda, J.; Rezacova, P.; Fabry, M.; Horejsi, M.; Stouracova, R.; Sedlacek, J.; Soucek, M.; Hradilek, M.; Lepsik, M.; Konvalinka, J. A Phenylnorstatine Inhibitor Binding to HIV-1 Protease: Geometry, Protonation, and Subsite-pocket Interactions Analyzed at Atomic Resolution J. Med. Chem. 2004, 47, 2030-2036 10.1021/jm031105q
    • (2004) J. Med. Chem. , vol.47 , pp. 2030-2036
    • Brynda, J.1    Rezacova, P.2    Fabry, M.3    Horejsi, M.4    Stouracova, R.5    Sedlacek, J.6    Soucek, M.7    Hradilek, M.8    Lepsik, M.9    Konvalinka, J.10
  • 55
  • 56
    • 62449330667 scopus 로고    scopus 로고
    • Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS
    • Korb, O.; Stutzle, T.; Exner, T. E. Empirical Scoring Functions for Advanced Protein-Ligand Docking with PLANTS J. Chem. Inf. Model. 2009, 49, 84-96 10.1021/ci800298z
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 84-96
    • Korb, O.1    Stutzle, T.2    Exner, T.E.3
  • 57
    • 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, 455-461 10.1002/jcc.21334
    • (2010) J. Comput. Chem. , vol.31 , pp. 455-461
    • Trott, O.1    Olson, A.J.2
  • 58
    • 0031226772 scopus 로고    scopus 로고
    • Empirical Scoring Functions 1. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes
    • Eldridge, M. D.; Murray, C. W.; Auton, T. R.; Paolini, G. V.; Mee, R. P. Empirical Scoring Functions 1. The Development of a Fast Empirical Scoring Function to Estimate the Binding Affinity of Ligands in Receptor Complexes J. Comput.-Aided Mol. Des. 1997, 11, 425-445 10.1023/A:1007996124545
    • (1997) J. Comput.-Aided Mol. Des. , vol.11 , pp. 425-445
    • Eldridge, M.D.1    Murray, C.W.2    Auton, T.R.3    Paolini, G.V.4    Mee, R.P.5
  • 59
    • 0031552362 scopus 로고    scopus 로고
    • Development and Validation of a Genetic Algorithm for Flexible Docking
    • Jones, G.; Willett, P.; Glen, R. C.; Leach, A. R.; Taylor, R. Development and Validation of a Genetic Algorithm for Flexible Docking J. Mol. Biol. 1997, 267, 727-748 10.1006/jmbi.1996.0897
    • (1997) J. Mol. Biol. , vol.267 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 60
    • 26444468103 scopus 로고    scopus 로고
    • General and Targeted Statistical Potentials for Protein-Ligand Interactions
    • Mooij, W. T. M.; Verdonk, M. L. General and Targeted Statistical Potentials for Protein-Ligand Interactions Proteins: Struct., Funct., Genet. 2005, 61, 272-287 10.1002/prot.20588
    • (2005) Proteins: Struct., Funct., Genet. , vol.61 , pp. 272-287
    • Mooij, W.T.M.1    Verdonk, M.L.2
  • 63
    • 33746921247 scopus 로고    scopus 로고
    • Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-scale Survey on the Retrieval of Protein-bound Ligand Conformations
    • Kirchmair, J.; Wolber, G.; Laggner, C.; Langer, T. Comparative Performance Assessment of the Conformational Model Generators Omega and Catalyst: A Large-scale Survey on the Retrieval of Protein-bound Ligand Conformations J. Chem. Inf. Model. 2006, 46, 1848-1861 10.1021/ci060084g
    • (2006) J. Chem. Inf. Model. , vol.46 , pp. 1848-1861
    • Kirchmair, J.1    Wolber, G.2    Laggner, C.3    Langer, T.4
  • 64
    • 84870308957 scopus 로고    scopus 로고
    • Essential Considerations for Using Protein-Ligand Structures in Drug Discovery
    • Warren, G. L.; Do, T. D.; Kelley, B. P.; Nicholls, A.; Warren, S. D. Essential Considerations for Using Protein-Ligand Structures in Drug Discovery Drug Discovery Today 2012, 17, 1270-1281 10.1016/j.drudis.2012.06.011
    • (2012) Drug Discovery Today , vol.17 , pp. 1270-1281
    • Warren, G.L.1    Do, T.D.2    Kelley, B.P.3    Nicholls, A.4    Warren, S.D.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.