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Volumn 44, Issue 4, 2010, Pages 648-654

GUI-BioPASED: A program for molecular dynamics simulations of biopolymers with a graphical user interface

Author keywords

graphical interface; molecular dynamics; molecular modeling

Indexed keywords


EID: 77955346639     PISSN: 00268933     EISSN: 16083245     Source Type: Journal    
DOI: 10.1134/S0026893310040217     Document Type: Article
Times cited : (19)

References (45)
  • 4
    • 4143116650 scopus 로고    scopus 로고
    • Computational studies of membrane channels
    • Roux B., Schulten K. 2004. Computational studies of membrane channels. Structure. 12, 1343-1351.
    • (2004) Structure. , vol.12 , pp. 1343-1351
    • Roux, B.1    Schulten, K.2
  • 6
  • 7
    • 7044239742 scopus 로고
    • Free energy calculations: Application to chemical and biochemical phenomena
    • Kollman P. A. 1993. Free energy calculations: Application to chemical and biochemical phenomena. Chem. Rev. 93, 2395-2417.
    • (1993) Chem. Rev. , vol.93 , pp. 2395-2417
    • Kollman, P.A.1
  • 8
    • 0242443692 scopus 로고    scopus 로고
    • Protein simulation and drug design
    • Wong C. F., McCammon A. J. 2003. Protein simulation and drug design. Adv. Protein Chem. 66, 87-121.
    • (2003) Adv. Protein Chem. , vol.66 , pp. 87-121
    • Wong, C.F.1    McCammon, A.J.2
  • 11
    • 35348911804 scopus 로고    scopus 로고
    • On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases
    • Faraldo-Gómez J. D., Roux B. 2007. On the importance of a funneled energy landscape for the assembly and regulation of multidomain Src tyrosine kinases. Proc. Natl. Acad. Sci. USA. 104, 13 643-13 648.
    • (2007) Proc. Natl. Acad. Sci. USA. , vol.104 , pp. 643-648
    • Faraldo-Gómez, J.D.1    Roux, B.2
  • 17
    • 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., 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
  • 20
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • Mackerell A. D., Jr., Feig M., Brooks C. L., III, 2004. Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J. Comput. Chem. 25, 1400-1415.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400-1415
    • Mackerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 21
    • 33748518255 scopus 로고    scopus 로고
    • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    • Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C. 2006. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins. 65, 712-725.
    • (2006) Proteins. , vol.65 , pp. 712-725
    • Hornak, V.1    Abel, R.2    Okur, A.3    Strockbine, B.4    Roitberg, A.5    Simmerling, C.6
  • 24
    • 30444448249 scopus 로고    scopus 로고
    • The GROMOS software for biomolecular simulation: GROMOS05
    • Christen M., Hünenberger P. H., Bakowies D., et al. 2005. The GROMOS software for biomolecular simulation: GROMOS05. J. Comput. Chem. 26, 1719-1751.
    • (2005) J. Comput. Chem. , vol.26 , pp. 1719-1751
    • Christen, M.1    Hünenberger, P.H.2    Bakowies, D.3
  • 25
    • 46249092554 scopus 로고    scopus 로고
    • GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation
    • Hess B., Kutzner C., Spoel D., Lindahl E. 2008. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J. Chem. Theory Comput. 4, 435-447.
    • (2008) J. Chem. Theory Comput. , vol.4 , pp. 435-447
    • Hess, B.1    Kutzner, C.2    Spoel, D.3    Lindahl, E.4
  • 27
    • 47149096704 scopus 로고    scopus 로고
    • CHARMM-GUI: A Web-based graphical user interface for CHARMM
    • Jo S., Kim T., Iyer V. G., Im W. 2008. CHARMM-GUI: A Web-based graphical user interface for CHARMM. J. Comput. Chem. 29, 1859-1865.
    • (2008) J. Comput. Chem. , vol.29 , pp. 1859-1865
    • Jo, S.1    Kim, T.2    Iyer, V.G.3    Im, W.4
  • 28
    • 0030793507 scopus 로고    scopus 로고
    • SIMS, Computation of smooth invariant molecular surface
    • Vorobjev Y. N., Hermans J. 1997. SIMS, Computation of smooth invariant molecular surface. Biophys. J. 73, 722-732.
    • (1997) Biophys. J. , vol.73 , pp. 722-732
    • Vorobjev, Y.N.1    Hermans, J.2
  • 29
    • 0001445346 scopus 로고    scopus 로고
    • A fast multigrid boundary element method for macromolecular electrostatis computations in solvent
    • Vorobjev Y. N., Scheraga H. A. 1997. A fast multigrid boundary element method for macromolecular electrostatis computations in solvent. J. Comp. Chem. 18, 569-583.
    • (1997) J. Comp. Chem. , vol.18 , pp. 569-583
    • Vorobjev, Y.N.1    Scheraga, H.A.2
  • 30
    • 0031872292 scopus 로고    scopus 로고
    • Discrimination between native and intentionally misfolded conformation of proteins: ES/IS, a new method for calculating conformational free energy
    • Vorobjev Y. N., Almagro J. C., Hermans J. 1998. Discrimination between native and intentionally misfolded conformation of proteins: ES/IS, a new method for calculating conformational free energy. Proteins. 32, 399-413.
    • (1998) Proteins. , vol.32 , pp. 399-413
    • Vorobjev, Y.N.1    Almagro, J.C.2    Hermans, J.3
  • 31
    • 52349088763 scopus 로고    scopus 로고
    • FAMBE-pH: A fast and accurate method to compute the total solvation free energies of proteins
    • Vorobjev Y. N., Vila J. A., Scheraga H. A. 2008. FAMBE-pH: A fast and accurate method to compute the total solvation free energies of proteins. J. Phys. Chem. B. 112. 11122-11136.
    • (2008) J. Phys. Chem. B. , vol.112 , pp. 11122-11136
    • Vorobjev, Y.N.1    Vila, J.A.2    Scheraga, H.A.3
  • 32
    • 0033135638 scopus 로고    scopus 로고
    • Effective energy function for proteins in solution
    • Lazaridis T., Karplus M. 1999. Effective energy function for proteins in solution. Proteins. 35, 133-152.
    • (1999) Proteins. , vol.35 , pp. 133-152
    • Lazaridis, T.1    Karplus, M.2
  • 34
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J., Cieplak P., Kollman P. A. 2000. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049-1074.
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 35
    • 77953039644 scopus 로고    scopus 로고
    • Vorobjev Y. N. 2009. Blind docking method combining search of low-resolution binding sites with ligand pose refinement by molecular dynamics-based global optimization J. Comput. Chem. Published online: Oct. 9, 2009. DOI: 10. 1002/jcc. 21394.
  • 36
    • 0001024425 scopus 로고
    • Pair correlations in a sodium chloride-SPC water model: Simulations versus extended-RISM computations
    • Hummer G., Soumpasis D. M., Neuman M. 1992. Pair correlations in a sodium chloride-SPC water model: Simulations versus extended-RISM computations. Mol. Phys. 77, 769-785.
    • (1992) Mol. Phys. , vol.77 , pp. 769-785
    • Hummer, G.1    Soumpasis, D.M.2    Neuman, M.3
  • 37
    • 4544369164 scopus 로고
    • A generalized reaction field method for molecular-dynamics simulations
    • Tironi I. G., Sperb P., Smith P. E., van Gunsteren W. F. 1995. A generalized reaction field method for molecular-dynamics simulations. J. Phys. Chem. 102, 5451-5459.
    • (1995) J. Phys. Chem. , vol.102 , pp. 5451-5459
    • Tironi, I.G.1    Sperb, P.2    Smith, P.E.3    van Gunsteren, W.F.4
  • 38
    • 17144471008 scopus 로고    scopus 로고
    • Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal
    • Walser R., Hunenberger P. H., van Gunsteren W. F. 2001. Comparison of different schemes to treat long-range electrostatic interactions in molecular dynamics simulations of a protein crystal. Proteins. 43, 509-519.
    • (2001) Proteins. , vol.43 , pp. 509-519
    • Walser, R.1    Hunenberger, P.H.2    van Gunsteren, W.F.3
  • 39
    • 0036679837 scopus 로고    scopus 로고
    • Distance and exposure dependent effective dielectric function
    • Mallik B., Masunov A., Lazaridis T. 2002. Distance and exposure dependent effective dielectric function. J. Comput. Chem. 23, 1090-1099.
    • (2002) J. Comput. Chem. , vol.23 , pp. 1090-1099
    • Mallik, B.1    Masunov, A.2    Lazaridis, T.3
  • 40
    • 0037470581 scopus 로고    scopus 로고
    • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes
    • Kortemme T., Morozov A. V., Baker D. 2003. An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes. J. Mol. Biol. 326, 1239-1259.
    • (2003) J. Mol. Biol. , vol.326 , pp. 1239-1259
    • Kortemme, T.1    Morozov, A.V.2    Baker, D.3
  • 41
    • 0029987862 scopus 로고    scopus 로고
    • Energy functions that discriminate X-ray and near native folds from well-constructed decoys
    • Park B. H., Levitt M. 1996. Energy functions that discriminate X-ray and near native folds from well-constructed decoys. J. Mol. Biol. 258, 367-392.
    • (1996) J. Mol. Biol. , vol.258 , pp. 367-392
    • Park, B.H.1    Levitt, M.2
  • 42
    • 0034610354 scopus 로고    scopus 로고
    • Role for lysine 142 in the excision of adenine from A:G mispairs by MutY DNA glycosylase of Escherichia coli
    • Zharkov D. O., Gilboa R., Yagil I., Kycia J. H., Gerchman S. E., Shoham G., Grollman A. P. 2000. Role for lysine 142 in the excision of adenine from A: G mispairs by MutY DNA glycosylase of Escherichia coli. Biochemistry. 39, 14768-14778.
    • (2000) Biochemistry. , vol.39 , pp. 14768-14778
    • Zharkov, D.O.1    Gilboa, R.2    Yagil, I.3    Kycia, J.H.4    Gerchman, S.E.5    Shoham, G.6    Grollman, A.P.7
  • 43
    • 35349026806 scopus 로고    scopus 로고
    • Structure and conformational dynamics of base excision repair DNA glycosylases
    • Zharkov D. O. 2007. Structure and conformational dynamics of base excision repair DNA glycosylases. Mol. Biol. 41, 702-716.
    • (2007) Mol. Biol. , vol.41 , pp. 702-716
    • Zharkov, D.O.1
  • 44
    • 77955394745 scopus 로고    scopus 로고
    • BioPASED Web: Information guide
    • BioPASED Web: Information guide. http://biopased. niboch. nsc. ru/index. php?a=manual.
  • 45
    • 77955409848 scopus 로고    scopus 로고
    • BioPASED Web: An example of typical task formulation
    • BioPASED Web: An example of typical task formulation. http://biopased. niboch. nsc. ru/index. php?a=usage.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.