메뉴 건너뛰기




Volumn 5, Issue 9, 2009, Pages 2465-2471

Coarse-grained MD simulations and protein-protein interactions: The cohesin-dockerin system

Author keywords

[No Author keywords available]

Indexed keywords


EID: 72749104760     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct900140w     Document Type: Article
Times cited : (23)

References (36)
  • 2
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink, S.J.; de Vries, A.H.; Mark, A.E. Coarse grained model for semiquantitative lipid simulations. J. Phys. Chem. B 2004, 108, 750-760.
    • (2004) J. Phys. Chem. B , vol.108 , pp. 750-760
    • Marrink, S.J.1    de Vries, A.H.2    Mark, A.E.3
  • 4
    • 11044233935 scopus 로고    scopus 로고
    • Coarse-grained simulations of lipid bilayers
    • Stevens, M.J. Coarse-grained simulations of lipid bilayers. J. Chem. Phys. 2004, 121, 11942-11948.
    • (2004) J. Chem. Phys. , vol.121 , pp. 11942-11948
    • Stevens, M.J.1
  • 5
    • 49549083949 scopus 로고    scopus 로고
    • Membrane proteins: molecular dynamics simulations
    • Lindahl, E.; Sansom, M.S.P. Membrane proteins: molecular dynamics simulations. Curr. Opin. Struct. Biol. 2008, 18, 425-431.
    • (2008) Curr. Opin. Struct. Biol. , vol.18 , pp. 425-431
    • Lindahl, E.1    Sansom, M.S.P.2
  • 6
    • 33847242278 scopus 로고    scopus 로고
    • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    • Bond, P.J.; Holyoake, J.; Ivetac, A.; Khalid, S.; Sansom, M.S.P. Coarse-grained molecular dynamics simulations of membrane proteins and peptides. J. Struct. Biol. 2007, 157, 593-605.
    • (2007) J. Struct. Biol. , vol.157 , pp. 593-605
    • Bond, P.J.1    Holyoake, J.2    Ivetac, A.3    Khalid, S.4    Sansom, M.S.P.5
  • 7
    • 34548146523 scopus 로고    scopus 로고
    • G protein-coupled receptors self-assemble in dynamics simulations of model bilayers
    • Periole, X.; Huber, T.; Marrink, S.J.; Sakmar, T.P. G protein-coupled receptors self-assemble in dynamics simulations of model bilayers. J. Am. Chem. Soc. 2007, 129, 10126-10132.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 10126-10132
    • Periole, X.1    Huber, T.2    Marrink, S.J.3    Sakmar, T.P.4
  • 8
    • 53249119350 scopus 로고    scopus 로고
    • Helix-helix interactions in membrane proteins: coarse grained simulations of glycophorin helix dimerization
    • Psachoulia, E.; Bond, P.J.; Fowler, P.W.; Sansom, M.S.P. Helix-helix interactions in membrane proteins: coarse grained simulations of glycophorin helix dimerization. Biochemistry 2008, 47, 10503-105012.
    • (2008) Biochemistry , vol.47 , pp. 10503-105012
    • Psachoulia, E.1    Bond, P.J.2    Fowler, P.W.3    Sansom, M.S.P.4
  • 10
    • 33646472024 scopus 로고    scopus 로고
    • High-resolution protein-protein docking
    • Gray, J.J. High-resolution protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 183-193.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 183-193
    • Gray, J.J.1
  • 11
    • 33645961330 scopus 로고    scopus 로고
    • Flexible protein-protein docking
    • Bonvin, A.M.J. J. Flexible protein-protein docking. Curr. Opin. Struct. Biol. 2006, 16, 194-200.
    • (2006) Curr. Opin. Struct. Biol. , vol.16 , pp. 194-200
    • Bonvin, A.M.J.J.1
  • 12
    • 14544291957 scopus 로고    scopus 로고
    • A multiscale coarse-graining method for biomolecular systems
    • Izvekov, S.; Voth, G.A. A multiscale coarse-graining method for biomolecular systems. J. Phys. Chem. B 2005, 109, 2469-2473.
    • (2005) J. Phys. Chem. B , vol.109 , pp. 2469-2473
    • Izvekov, S.1    Voth, G.A.2
  • 13
    • 34247098754 scopus 로고    scopus 로고
    • Multiscale modeling of biomolecular systems: in serial and in parallel
    • Ayton, G.A.; Noid, W.G.; Voth, G.A. Multiscale modeling of biomolecular systems: in serial and in parallel. Curr. Opin. Struct. Biol. 2007, 17, 192-198.
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 192-198
    • Ayton, G.A.1    Noid, W.G.2    Voth, G.A.3
  • 17
    • 3142757398 scopus 로고    scopus 로고
    • Cellulosomes: plant-cell-wall-degrading enzyme complexes
    • Doi, R.H.; Kosugi, A. Cellulosomes: plant-cell-wall-degrading enzyme complexes. Nature Rev. Microbiol. 2004, 2, 541-551.
    • (2004) Nature Rev. Microbiol. , vol.2 , pp. 541-551
    • Doi, R.H.1    Kosugi, A.2
  • 18
    • 33644644163 scopus 로고    scopus 로고
    • Insertion assembly of membrane proteins via simulation
    • Bond, P.J.; Sansom, M.S.P. Insertion and assembly of membrane proteins via simulation. J. Am. Chem. Soc. 2006, 128, 2697-2704.
    • (2006) J. Am. Chem. Soc. , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 20
    • 0035789518 scopus 로고    scopus 로고
    • GROMACS 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl, E.; Hess, B.; van der Spoel, D. GROMACS 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 2001, 7, 306-317.
    • (2001) J. Mol. Model. , vol.7 , pp. 306-317
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 22
    • 0027136282 scopus 로고
    • Comparative protein modeling by satisfaction of spatial restraints
    • Sali, A.; Blundell, T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 1993, 234, 779-815.
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 24
    • 33846823909 scopus 로고
    • Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems
    • Darden, T.; York, D.; Pedersen, L. Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems. J. Chem. Phys. 1993, 98, 10089-10092.
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 27
    • 0037230970 scopus 로고    scopus 로고
    • Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation
    • Wang, T.; Wade, R.C. Implicit solvent models for flexible protein-protein docking by molecular dynamics simulation. Proteins: Struct., Funct., Bioinf. 2003, 50, 158-169.
    • (2003) Proteins: Struct., Funct., Bioinf. , vol.50 , pp. 158-169
    • Wang, T.1    Wade, R.C.2
  • 33
    • 21644477228 scopus 로고    scopus 로고
    • Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI
    • Smith, G.R.; Fitzjohn, P.W.; Page, C.S.; Bates, P.A. Incorporation of flexibility into rigid-body docking: Applications in rounds 3-5 of CAPRI. Proteins: Struct., Funct., Bioinf. 2005, 60, 263-268.
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.60 , pp. 263-268
    • Smith, G.R.1    Fitzjohn, P.W.2    Page, C.S.3    Bates, P.A.4
  • 34
    • 21644435306 scopus 로고    scopus 로고
    • ATTRACT: Protein-protein docking in CAPRI using a reduced protein model
    • Zacharias, M. ATTRACT: Protein-protein docking in CAPRI using a reduced protein model. Proteins: Struct., Funct., Bioinf. 2005, 60, 252-256.
    • (2005) Proteins: Struct., Funct., Bioinf. , vol.60 , pp. 252-256
    • Zacharias, M.1
  • 35
    • 34548020295 scopus 로고    scopus 로고
    • A coarse-grained protein-protein potential derived from an all-atom force field
    • Basdevant, N.; Borgis, D.; Ha-Doung, T. A coarse-grained protein-protein potential derived from an all-atom force field. J. Phys. Chem. B 2007, 111, 9390-9399.
    • (2007) J. Phys. Chem. B , vol.111 , pp. 9390-9399
    • Basdevant, N.1    Borgis, D.2    Ha-Doung, T.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.