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Volumn 52, Issue 4, 2012, Pages 984-995

Ligand aligning method for molecular docking: Alignment of property-weighted vectors

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT; COMPLEXATION; FREE ENERGY; PROTEINS; VECTOR SPACES; VECTORS;

EID: 84862010592     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci200501p     Document Type: Article
Times cited : (2)

References (42)
  • 1
    • 77953189302 scopus 로고    scopus 로고
    • A new Lamarckian genetic algorithm for flexible ligand-receptor docking
    • Fuhrmann, J.; Rurainski, A.; Lenhof, H. P.; Neumann, D. A new Lamarckian genetic algorithm for flexible ligand-receptor docking. J. Comput. Chem. 2010, 31, 1911-1918.
    • (2010) J. Comput. Chem. , vol.31 , pp. 1911-1918
    • Fuhrmann, J.1    Rurainski, A.2    Lenhof, H.P.3    Neumann, D.4
  • 2
    • 0030599010 scopus 로고    scopus 로고
    • A fast flexible docking method using an incremental construction algorithm
    • DOI 10.1006/jmbi.1996.0477
    • Rarey, M.; Kramer, B.; Lengauer, T.; Klebe, G. A fast flexible docking method using an incremental construction algorithm. J. Mol. Biol. 1996, 261, 470-489. (Pubitemid 26335901)
    • (1996) Journal of Molecular Biology , vol.261 , Issue.3 , pp. 470-489
    • Rarey, M.1    Kramer, B.2    Lengauer, T.3    Klebe, G.4
  • 3
    • 0031552362 scopus 로고    scopus 로고
    • Development and validation of a genetic algorithm for flexible docking
    • DOI 10.1006/jmbi.1996.0897
    • 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. (Pubitemid 27170693)
    • (1997) Journal of Molecular Biology , vol.267 , Issue.3 , pp. 727-748
    • Jones, G.1    Willett, P.2    Glen, R.C.3    Leach, A.R.4    Taylor, R.5
  • 6
    • 0035025191 scopus 로고    scopus 로고
    • DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases
    • DOI 10.1023/A:1011115820450
    • Ewing, T. J. A.; Makino, S.; Skillman, A. G.; Kuntz, I. D. DOCK 4.0: Search strategies for automated molecular docking of flexible molecule databases. J. Comput.-Aided Mol. Des. 2001, 15, 411-428. (Pubitemid 32452109)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.5 , pp. 411-428
    • Ewing, T.J.A.1    Makino, S.2    Skillman, A.G.3    Kuntz, I.D.4
  • 7
    • 0037212102 scopus 로고    scopus 로고
    • LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites
    • DOI 10.1016/S1093-3263(02)00164-X, PII S109332630200164X
    • Venkatachalam, C. M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graphics Modell. 2003, 21, 289-307. (Pubitemid 35441326)
    • (2003) Journal of Molecular Graphics and Modelling , vol.21 , Issue.4 , pp. 289-307
    • Venkatachalam, C.M.1    Jiang, X.2    Oldfield, T.3    Waldman, M.4
  • 8
    • 1642540577 scopus 로고    scopus 로고
    • Evaluation of docking performance: Comparative data on docking algorithms
    • DOI 10.1021/jm0302997
    • Kontoyianni, M.; McClellan, L. M.; Sokol, G. S. Evaluation of Docking Performance: Comparative Data on Docking Algorithms. J. Med. Chem. 2004, 47, 558-565. (Pubitemid 38129714)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.3 , pp. 558-565
    • Kontoyianni, M.1    McClellan, L.M.2    Sokol, G.S.3
  • 9
    • 5644287368 scopus 로고    scopus 로고
    • Free energy, entropy, and induced fit in host-guest recognition: Calculations with the second-generation mining minima algorithm
    • Chang, C.-E.; Gilson, M. K. Free Energy, Entropy, and Induced Fit in Host-Guest Recognition: Calculations with the Second-Generation Mining Minima Algorithm. J. Am. Chem. Soc. 2004, 126, 13156-13164. (Pubitemid 39372346)
    • (2004) Journal of the American Chemical Society , vol.126 , Issue.40 , pp. 13156-13164
    • Chang, C.-E.1    Gilson, M.K.2
  • 10
    • 0035144771 scopus 로고    scopus 로고
    • Ligand-receptor docking with the Mining Minima optimizer
    • DOI 10.1023/A:1008128723048
    • David, L.; Luo, R.; Gilson, M. K. Ligand-receptor docking with the Mining Minima optimizer. J. Comput.-Aided Mol. Des. 2001, 15, 157-171. (Pubitemid 32124508)
    • (2001) Journal of Computer-Aided Molecular Design , vol.15 , Issue.2 , pp. 157-171
    • David, L.1    Luo, R.2    Gilson, M.K.3
  • 14
    • 0035314043 scopus 로고    scopus 로고
    • Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions
    • DOI 10.1002/1097-0134(200104 01)43:1<12::AID-PROT 1013>3.0 .CO;2-7
    • Arora, N.; Bashford, D. Solvation energy density occlusion approximation for evaluation of desolvation penalties in biomolecular interactions. Proteins 2001, 43, 12-27. (Pubitemid 32194903)
    • (2001) Proteins: Structure, Function and Genetics , vol.43 , Issue.1 , pp. 12-27
    • Arora, N.1    Bashford, D.2
  • 15
    • 77649221514 scopus 로고    scopus 로고
    • Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions
    • Huang, S. Y.; Zou, X. Inclusion of solvation and entropy in the knowledge-based scoring function for protein-ligand interactions. J. Chem. Inf. Model. 2010, 50, 262-273.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 262-273
    • Huang, S.Y.1    Zou, X.2
  • 16
    • 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.
    • (2009) J. Chem. Inf. Model. , vol.49 , pp. 84-96
    • Korb, O.1    Stutzle, T.2    Exner, T.E.3
  • 19
    • 0026209427 scopus 로고
    • An integrated approach to three-dimensional information management with MACCS-3D
    • Guner, O. F.; Hughes, D. W.; Dumont, L. M. An integrated approach to three-dimensional information management with MACCS-3D. J. Chem. Inf. Comput. Sci. 1991, 31, 408-414.
    • (1991) J. Chem. Inf. Comput. Sci. , vol.31 , pp. 408-414
    • Guner, O.F.1    Hughes, D.W.2    Dumont, L.M.3
  • 20
    • 0026110673 scopus 로고
    • The inclusion of electrostatic hydration energies in molecular mechanics calculations
    • Gilson, M. K.; Honig, B. The inclusion of electrostatic hydration energies in molecular mechanics calculations. J. Comput.-Aided Mol. Des. 1991, 5, 5-20.
    • (1991) J. Comput.-Aided Mol. Des. , vol.5 , pp. 5-20
    • Gilson, M.K.1    Honig, B.2
  • 21
    • 18344371385 scopus 로고    scopus 로고
    • A partition coefficient calculation method with the SFED model
    • DOI 10.1021/ci0498564
    • In, Y.; Chai, H. H.; No, K. T. A partition coefficient calculation method with the SFED model. J. Chem. Inf. Model. 2005, 45, 254-263. (Pubitemid 40635329)
    • (2005) Journal of Chemical Information and Modeling , vol.45 , Issue.2 , pp. 254-263
    • In, Y.1    Chai, H.H.2    No, K.T.3
  • 22
    • 84962441167 scopus 로고    scopus 로고
    • Description of hydration free energy density as a function of molecular physical properties
    • DOI 10.1016/S0301-4622(98)00225-7, PII S0301462298002257
    • No, K. T.; Kim, S. G.; Cho, K. H.; Scheraga, H. A. Description of hydration free energy density as a function of molecular physical properties. Biophys. Chem. 1999, 78, 127-145. (Pubitemid 29206662)
    • (1999) Biophysical Chemistry , vol.78 , Issue.1-2 , pp. 127-145
    • No, K.T.1    Kim, S.G.2    Cho, K.-H.3    Scheraga, H.A.4
  • 23
    • 0346951125 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 1. Application to neutral molecules as models for polypeptides
    • No, K. T.; Grant, J. A.; Scheraga, H. A. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 1. Application to neutral molecules as models for polypeptides. J. Phys. Chem. 1990, 94, 4732-4739.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4732-4739
    • No, K.T.1    Grant, J.A.2    Scheraga, H.A.3
  • 24
    • 33751553791 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 2. Application to ionic and aromatic molecules as models for polypeptides
    • No, K. T.; Grant, J. A.; Jhon, M. S.; Scheraga, H. A. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. 2. Application to ionic and aromatic molecules as models for polypeptides. J. Phys. Chem. 1990, 94, 4740-4746.
    • (1990) J. Phys. Chem. , vol.94 , pp. 4740-4746
    • No, K.T.1    Grant, J.A.2    Jhon, M.S.3    Scheraga, H.A.4
  • 25
    • 0001544247 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules
    • Park, J. M.; No, K. T.; Jhon, M. S.; Scheraga, H. A. Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. III. Application to halogenated and aromatic molecules. J. Comput. Chem. 1993, 14, 1482-1490.
    • (1993) J. Comput. Chem. , vol.14 , pp. 1482-1490
    • Park, J.M.1    No, K.T.2    Jhon, M.S.3    Scheraga, H.A.4
  • 26
    • 84986469616 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method. IV. Application to hypervalent sulfur-and phosphorus-containing molecules
    • Park, J. M.; Kwon, O. Y.; No, K. T.; Jhon, M. S. Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method. IV. Application to Hypervalent Sulfur-and Phosphorus-Containing Molecules. J. Comput. Chem. 1995, 16, 1011.
    • (1995) J. Comput. Chem. , vol.16 , pp. 1011
    • Park, J.M.1    Kwon, O.Y.2    No, K.T.3    Jhon, M.S.4
  • 27
    • 0345925003 scopus 로고
    • Determination of net atomic charges using a modified partial equalization of orbital electronegativity method: V. Application to silicon-containing organic molecules and zeolites
    • Suk, J. E.; No, K. T. Determination of Net Atomic Charges Using a Modified Partial Equalization of Orbital Electronegativity Method: V. Application to Silicon-Containing Organic Molecules and Zeolites. Bull. Korean Chem. Soc. 1995, 16, 915.
    • (1995) Bull. Korean Chem. Soc. , vol.16 , pp. 915
    • Suk, J.E.1    No, K.T.2
  • 28
    • 0000596576 scopus 로고
    • An empirical method to calculate average molecular polarizabilities from the dependence of effective atomic polarizabilities on net atomic charge
    • No, K. T.; Cho, K. H.; Jhon, M. S.; Scheraga, H. A. An Empirical Method To Calculate Average Molecular Polarizabilities from the Dependence of Effective Atomic Polarizabilities on Net Atomic Charge. J. Am. Chem. Soc. 1993, 115, 2005.
    • (1993) J. Am. Chem. Soc. , vol.115 , pp. 2005
    • No, K.T.1    Cho, K.H.2    Jhon, M.S.3    Scheraga, H.A.4
  • 29
    • 0028063257 scopus 로고
    • Polar and nonpolar atomic environments in the protein core: Implications for folding and binding
    • DOI 10.1002/prot.340200307
    • Koehl, P.; Delarue, M. Polar and nonpolar atomic environments in the protein core: Implications for folding and binding. Proteins 1994, 20, 264-278. (Pubitemid 24378917)
    • (1994) Proteins: Structure, Function and Genetics , vol.20 , Issue.3 , pp. 264-278
    • Koehl, P.1    Delarue, M.2
  • 30
    • 0033127030 scopus 로고    scopus 로고
    • Development of three-dimensional descriptors represented by tensors: Free energy of hydration density tensor
    • Son, S. H.; Han, C. K.; Ahn, S. K.; Yoon, J. H.; No, K. T. Development of three-dimensional descriptors represented by tensors: Free energy of hydration density tensor. J. Chem. Inf. Comput. Sci. 1999, 39, 601-609. (Pubitemid 129539221)
    • (1999) Journal of Chemical Information and Computer Sciences , vol.39 , Issue.3 , pp. 601-609
    • Son, S.H.1    Han, C.K.2    Ahn, S.K.3    Yoon, J.H.4    No, K.T.5
  • 31
    • 0030934104 scopus 로고    scopus 로고
    • 3D-modelling and prediction by WHIM descriptors. Part 5. Theory development and chemical meaning of WHIM descriptors
    • Todeschini, R.; Gramatica, P. 3D-modelling and prediction by WHIM descriptors. Part 5. Theory development and chemical meaning of WHIM descriptors. Quant. Struct.-Act. Relat. 1997, 16, 113-119. (Pubitemid 27182829)
    • (1997) Quantitative Structure-Activity Relationships , vol.16 , Issue.2 , pp. 113-119
    • Todeschini, R.1    Gramatica, P.2
  • 32
    • 51649181712 scopus 로고
    • Point and interval estimations especially of point errors, in multidimensional least-squares adjustment
    • Grafarend, E.; Kelm, R. Point and interval estimations especially of point errors, in multidimensional least-squares adjustment. Bulletin Geod. 1972, 104, 165-184.
    • (1972) Bulletin Geod. , vol.104 , pp. 165-184
    • Grafarend, E.1    Kelm, R.2
  • 33
    • 2542530042 scopus 로고    scopus 로고
    • The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures
    • DOI 10.1021/jm030580l
    • Wang, R.; Fang, X.; Lu, Y.; Wang, S. The PDBbind database: Collection of binding affinities for protein-ligand complexes with known three-dimensional structures. J. Med. Chem. 2004, 47, 2977-2980. (Pubitemid 38702694)
    • (2004) Journal of Medicinal Chemistry , vol.47 , Issue.12 , pp. 2977-2980
    • Wang, R.1    Fang, X.2    Lu, Y.3    Wang, S.4
  • 34
    • 77952754227 scopus 로고    scopus 로고
    • ParaDockS: A framework for molecular docking with population-based metaheuristics
    • Meier, R.; Pippel, M.; Brandt, F.; Sippl, W.; Baldauf, C. ParaDockS: A framework for molecular docking with population-based metaheuristics. J. Chem. Inf. Model. 2010, 50, 879-889.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 879-889
    • Meier, R.1    Pippel, M.2    Brandt, F.3    Sippl, W.4    Baldauf, C.5
  • 35
    • 84986522856 scopus 로고
    • Poling: Promoting conformational variation
    • Smellie, A.; Teig, S. L.; Towbin, P. Poling: Promoting conformational variation. J. Comput. Chem. 1995, 16, 171-187.
    • (1995) J. Comput. Chem. , vol.16 , pp. 171-187
    • Smellie, A.1    Teig, S.L.2    Towbin, P.3
  • 36
    • 0242411477 scopus 로고    scopus 로고
    • Tork: Conformational analysis method for molecules and complexes
    • Chang, C. E.; Gilson, M. K. Tork: Conformational Analysis Method for Molecules and Complexes. J. Comput. Chem. 2003, 24, 1987-1998.
    • (2003) J. Comput. Chem. , vol.24 , pp. 1987-1998
    • Chang, C.E.1    Gilson, M.K.2
  • 37
    • 0037438461 scopus 로고    scopus 로고
    • The basis of the hydrophobic effect
    • DOI 10.1016/S0301-4622(02)00281-8, PII S0301462202002818
    • Kyte, J. The basis of the hydrophobic effect. Biophys. Chem. 2003, 100, 193-203. (Pubitemid 36338042)
    • (2003) Biophysical Chemistry , vol.100 , Issue.1-3 , pp. 193-203
    • Kyte, J.1
  • 38
    • 0036304021 scopus 로고    scopus 로고
    • An extension of the consistent valence force field (CVFF) with the aim to simulate the structures of vanadium phosphorus oxides and the adsorption of n-butane and of 1-butene on their crystal planes
    • Friedrich Ritschl, M. F.; Fiedler, K.; Khler, J. E. H.; Kubias, B.; Meisel, M. An Extension of the Consistent Valence Force Field (CVFF) with the Aim to Simulate the Structures of Vanadium Phosphorus Oxides and the Adsorption of n-Butane and of 1-Butene on their Crystal Planes. Z. Anorg. Allg. Chem. 2002, 628, 1385-1396.
    • (2002) Z. Anorg. Allg. Chem. , vol.628 , pp. 1385-1396
    • Friedrich Ritschl, M.F.1    Fiedler, K.2    Khler, J.E.H.3    Kubias, B.4    Meisel, M.5
  • 39
    • 0037020138 scopus 로고    scopus 로고
    • Investigation of some amino acids conformations at the interface of binary mixture using the solvation free energy density model
    • Nam, K.-Y.; Cho, D. H.; Paek, K.; No, K. T. Investigation of some amino acids conformations at the interface of binary mixture using the solvation free energy density model. Chem. Phys. Lett. 2002, 364, 267-272.
    • (2002) Chem. Phys. Lett. , vol.364 , pp. 267-272
    • Nam, K.-Y.1    Cho, D.H.2    Paek, K.3    No, K.T.4
  • 40
    • 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.; Abagyan, R. A. Protein Flexibility in Ligand Docking and Virtual Screening to Protein Kinases. J. Mol. Biol. 2004, 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
  • 41
    • 3142750620 scopus 로고
    • A theory of hydrogen bond directionality
    • Kollman, P. A. A theory of hydrogen bond directionality. J. Am. Chem. Soc. 1972, 94, 1837-1842.
    • (1972) J. Am. Chem. Soc. , vol.94 , pp. 1837-1842
    • Kollman, P.A.1
  • 42
    • 0026410002 scopus 로고
    • Structural aspects of metal liganding to functional groups in proteins
    • Academic Press: New York
    • Glusker, J. P. Structural Aspects of Metal Liganding to Functional Groups in Proteins. In Advances in Protein Chemistry; Academic Press: New York, 1991; Vol. 42, pp 1-76.
    • (1991) Advances in Protein Chemistry , vol.42 , pp. 1-76
    • Glusker, J.P.1


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