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Volumn 20, Issue 3, 2013, Pages 188-198

Charge group partitioning in biomolecular simulation

Author keywords

atomic force fields; biomolecular simulation; charge groups; dynamic programming; grooms; tree decomposition

Indexed keywords

ADENOSINE TRIPHOSPHATE; AMINO ACID; WATER;

EID: 84874705707     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2012.0239     Document Type: Article
Times cited : (149)

References (29)
  • 1
    • 8344271208 scopus 로고    scopus 로고
    • Experimental evaluation of a tree decomposition-based algorithm for vertex cover on planar graphs
    • Alber, J., Dorn, F., and Niedermeier R. 2005. Experimental evaluation of a tree decomposition-based algorithm for vertex cover on planar graphs. Discrete Appl. Math. 145, 219-231.
    • (2005) Discrete Appl. Math. , vol.145 , pp. 219-231
    • Alber, J.1    Dorn, F.2    Niedermeier, R.3
  • 4
    • 0029633168 scopus 로고
    • GROMACS: A message-passing parallel molecular dynamics implementation
    • Berendsen, H.J.C., van der Spoel, D., and Van Drunen, R. 1995. GROMACS: a message-passing parallel molecular dynamics implementation. Com. Phys. Comm. 91, 43-56.
    • (1995) Com. Phys. Comm. , vol.91 , pp. 43-56
    • Berendsen, H.J.C.1    Van Der Spoel, D.2    Van Drunen, R.3
  • 5
    • 0024578173 scopus 로고
    • Free energy via molecular simulation: Applications to chemical and biomolecular systems
    • Beveridge, D.L., and DiCapua, F.M. 1989. Free energy via molecular simulation: applications to chemical and biomolecular systems. Annu. Rev. Biophys. Biophys. Chem. 18, 431-492.
    • (1989) Annu. Rev. Biophys. Biophys. Chem. , vol.18 , pp. 431-492
    • Beveridge, D.L.1    Dicapua, F.M.2
  • 7
    • 0002981945 scopus 로고    scopus 로고
    • A partial k-arboretum of graphs with bounded treewidth
    • Bodlaender, H.L. 1998. A partial k-arboretum of graphs with bounded treewidth. Theor. Comput. Sci., 209, 1-45.
    • (1998) Theor. Comput. Sci. , vol.209 , pp. 1-45
    • Bodlaender, H.L.1
  • 8
    • 77953805203 scopus 로고    scopus 로고
    • Effect of pH and ibuprofen on the phospholipid bilayer bending modulus
    • Boggara, M.B.B., Faraone, A., and Krishnamoorti, R. 2010. Effect of pH and ibuprofen on the phospholipid bilayer bending modulus. J. Phys. Chem. B 114, 8061-8066.
    • (2010) J. Phys. Chem. B , vol.114 , pp. 8061-8066
    • Boggara, M.B.B.1    Faraone, A.2    Krishnamoorti, R.3
  • 9
    • 67650500988 scopus 로고    scopus 로고
    • CHARMM: The biomolecular simulation program
    • Sp. Iss. SI
    • Brooks, B.R., Brooks III, C.L., and Mackerell Jr., et al. 2009. CHARMM: The Biomolecular Simulation Program. J. Comput. Chem. 30(10, Sp. Iss. SI), 1545-1614.
    • (2009) J. Comput. Chem. , vol.30 , Issue.10 , pp. 1545-1614
    • Brooks, B.R.1    Brooks III, C.L.2    Mackerell, J.R.3
  • 10
    • 0029011701 scopus 로고    scopus 로고
    • A second generation force field for the simulation of proteins, nucleic acids, and organic molecules
    • Cornell, W.D., Cieplak, P., Bayly, C.I., et al. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J. Am. Chem. Soc. 117, 5179-5197.
    • J. Am. Chem. Soc. , vol.117 , pp. 5179-5197
    • Cornell, W.D.1    Cieplak, P.2    Bayly, C.I.3
  • 11
    • 79951989026 scopus 로고    scopus 로고
    • Automated bond order assignment as an optimization problem
    • Dehof, A., Rurainski, A., Bui, Q.B.A., et al. 2011. Automated bond order assignment as an optimization problem. Bioinformatics, 27, 619-625.
    • (2011) Bioinformatics , vol.27 , pp. 619-625
    • Dehof, A.1    Rurainski, A.2    Bui, Q.B.A.3
  • 12
    • 0020709558 scopus 로고
    • On the complexity of partitioning graphs into connected subgraphs
    • Dyer, M., and Frieze, A. 1985. On the complexity of partitioning graphs into connected subgraphs. Discrete Appl. Math. 10, 139-153.
    • (1985) Discrete Appl. Math. , vol.10 , pp. 139-153
    • Dyer, M.1    Frieze, A.2
  • 13
    • 0031616705 scopus 로고    scopus 로고
    • Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field mab
    • Gerber, P.R. 1998. Charge distribution from a simple molecular orbital type calculation and non-bonding interaction terms in the force field mab. J. Comput.-Aided Mol. Des. 12, 37-51.
    • (1998) J. Comput.-Aided Mol. Des. , vol.12 , pp. 37-51
    • Gerber, P.R.1
  • 14
    • 0036081122 scopus 로고    scopus 로고
    • LIGAND: Database of chemical compounds and reactions in biological pathways
    • Goto, S., Okuno, Y., Hattori, M., et al. 2002. LIGAND: database of chemical compounds and reactions in biological pathways. Nucleic Acids Res. 30, 402-404.
    • (2002) Nucleic Acids Res , vol.30 , pp. 402-404
    • Goto, S.1    Okuno, Y.2    Hattori, M.3
  • 15
    • 77958077680 scopus 로고    scopus 로고
    • Frequent subgraph mining in outer planar graphs
    • Horva'th, T., Ramon, J., and Wrobel, S. 2010. Frequent subgraph mining in outer planar graphs. Data Min. Knowl. Discov. 21, 472-508.
    • (2010) Data Min. Knowl. Discov. , vol.21 , pp. 472-508
    • Horva'Th, T.1    Ramon, J.2    Wrobel, S.3
  • 16
    • 0029912748 scopus 로고    scopus 로고
    • Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids
    • Jorgensen, W.L., Maxwell, D.S., and Tirado-Rives, J. 1996. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J. Am. Chem. Soc. 118, 11225-11236.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11225-11236
    • Jorgensen, W.L.1    Maxwell, D.S.2    Tirado-Rives, J.3
  • 17
    • 78650680564 scopus 로고    scopus 로고
    • Practical considerations for building GROMOS-compatible smallmolecule topologies
    • Lemkul, J.A., Allen, W.J., and Bevan, D.R. 2010. Practical considerations for building GROMOS-compatible smallmolecule topologies. J. Chem. Inf. Model. 50, 2221-2235.
    • (2010) J. Chem. Inf. Model. , vol.50 , pp. 2221-2235
    • Lemkul, J.A.1    Allen, W.J.2    Bevan, D.R.3
  • 18
    • 84961981789 scopus 로고    scopus 로고
    • An automated force field topology builder (ATB) and repository: Version 1.0
    • Malde, A.K., Zuo, L., Breeze, M., et al. 2011. An automated force field topology builder (ATB) and repository: version 1.0. J. Chem. Theory Comput. 7, 4026-4037.
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 4026-4037
    • Malde, A.K.1    Zuo, L.2    Breeze, M.3
  • 19
    • 4444282928 scopus 로고    scopus 로고
    • A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
    • Oostenbrink, C., Villa, A., Mark, A.E., and van Gunsteren, W.F. 2004. A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6. J. Comp. Chem. 25, 1656-1676.
    • (2004) J. Comp. Chem. , vol.25 , pp. 1656-1676
    • Oostenbrink, C.1    Villa, A.2    Mark, A.E.3    Van Gunsteren, W.F.4
  • 20
    • 0000673493 scopus 로고
    • Graph minors. II. Algorithmic aspects of tree-width
    • Robertson, N., and Seymour, P.D. 1986. Graph minors. II. Algorithmic aspects of tree-width. J. Algorithms 7, 309-322.
    • (1986) J. Algorithms , vol.7 , pp. 309-322
    • Robertson, N.1    Seymour, P.D.2
  • 21
    • 79959713919 scopus 로고    scopus 로고
    • Definition and testing of the GROMOS force-field versions 54A7 and 54B7
    • Schmid, N., Eichenberger, A., Choutko, A., et al. 2011. Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur. Biophys. J. 40, 843-856.
    • (2011) Eur. Biophys. J. , vol.40 , pp. 843-856
    • Schmid, N.1    Eichenberger, A.2    Choutko, A.3
  • 22
    • 7544226311 scopus 로고    scopus 로고
    • PRODRG: A tool for high-throughput crystallography of protein-ligand complexes
    • Schu?ttelkopf, A.W., and van Aalten, D.M. 2004. PRODRG: a tool for high-throughput crystallography of protein-ligand complexes. Acta Crystallogr. 60, 1355-1363.
    • (2004) Acta Crystallogr , vol.60 , pp. 1355-1363
    • Schuttelkopf, A.W.1    Van Aalten, D.M.2
  • 23
    • 0008819754 scopus 로고    scopus 로고
    • The GROMOS biomolecular simulation program package
    • Scott, W.R.P., Hu?nenberger, P.H., Tironi, I. G., et al. 1999. The GROMOS biomolecular simulation program package. J. Phys. Chem. A 103, 3596-3607.
    • (1999) J. Phys. Chem. A , vol.103 , pp. 3596-3607
    • Scott, W.R.P.1    Hunenberger, P.H.2    Tironi, I.G.3
  • 24
    • 58849122630 scopus 로고    scopus 로고
    • Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: A multifunctional target for antischistosomal therapy
    • Sharma, M., Khanna, S., Bulusu, G., and Mitra, A. 2009. Comparative modeling of thioredoxin glutathione reductase from Schistosoma mansoni: a multifunctional target for antischistosomal therapy. J. Mol. Graphics Model. 27, 665-675.
    • (2009) J. Mol. Graphics Model. , vol.27 , pp. 665-675
    • Sharma, M.1    Khanna, S.2    Bulusu, G.3    Mitra, A.4
  • 26
    • 33746271105 scopus 로고    scopus 로고
    • Biomolecular modeling: Goals, problems, perspectives
    • van Gunsteren, W. F., Bakowies, D., Baron, R., et al. 2006. Biomolecular modeling: Goals, problems, perspectives. Angew. Chem. Int. Ed. 45, 4064-4092.
    • (2006) Angew. Chem. Int. Ed. , vol.45 , pp. 4064-4092
    • Van Gunsteren, W.F.1    Bakowies, D.2    Baron, R.3
  • 27
    • 0037089015 scopus 로고    scopus 로고
    • Calculation of the free energy of solvation for neutral analogs of amino acid side chains
    • Villa, A., and Mark, A.E. 2002. Calculation of the free energy of solvation for neutral analogs of amino acid side chains. J. Comp. Chem. 2345, 548-553.
    • (2002) J. Comp. Chem. , vol.2345 , pp. 548-553
    • Villa, A.1    Mark, A.E.2
  • 28
    • 33645590327 scopus 로고    scopus 로고
    • Graph complexity of chemical compounds in biological pathways
    • Yamaguchi, A., Aoki, K.F., and Mamitsuka, H. 2003. Graph complexity of chemical compounds in biological pathways. Genome Inform. 14, 376-377.
    • (2003) Genome Inform. , vol.14 , pp. 376-377
    • Yamaguchi, A.1    Aoki, K.F.2    Mamitsuka, H.3
  • 29
    • 77954611371 scopus 로고    scopus 로고
    • Exploration of the mechanism for LPFFD inhibiting the formation of betasheet conformation of A beta(1-42) in water
    • Yang, C., Zhu, X., Li, J., and Shi, R. 2010. Exploration of the mechanism for LPFFD inhibiting the formation of betasheet conformation of A beta(1-42) in water. J. Mol. Model. 16, 813-21.
    • (2010) J. Mol. Model. , vol.16 , pp. 813-821
    • Yang, C.1    Zhu, X.2    Li, J.3    Shi, R.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.