메뉴 건너뛰기




Volumn 10, Issue 7, 2014, Pages

Web-Based Computational Chemistry Education with CHARMMing I: Lessons and Tutorial

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; E-LEARNING; EDUCATION COMPUTING; PYTHON; TEACHING; WEB BROWSERS; WEBSITES;

EID: 84905457391     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003719     Document Type: Article
Times cited : (11)

References (57)
  • 1
    • 48849112218 scopus 로고    scopus 로고
    • Using Molecular Dynamics Simulation To Reinforce Student Understanding of Intermolecular Forces
    • Burkholder PR, Purser GH, Cole RS, (2008) Using Molecular Dynamics Simulation To Reinforce Student Understanding of Intermolecular Forces. J Chem Ed 85: 1071-1077.
    • (2008) J Chem Ed , vol.85 , pp. 1071-1077
    • Burkholder, P.R.1    Purser, G.H.2    Cole, R.S.3
  • 2
    • 0038583386 scopus 로고    scopus 로고
    • Integration of Computational Chemistry into the Chemistry Curriculum
    • Martin NH, (1998) Integration of Computational Chemistry into the Chemistry Curriculum. J Chem Ed 75: 241-243.
    • (1998) J Chem Ed , vol.75 , pp. 241-243
    • Martin, N.H.1
  • 5
    • 47149096704 scopus 로고    scopus 로고
    • CHARMM-GUI: A web-based graphical user interface for CHARMM
    • Jo S, Kim T, Iyer VG, 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
  • 6
    • 84905448151 scopus 로고    scopus 로고
    • Woods research group, Complex Carboyhdrate Research Center, University of Georgia Available: Accessed 25 June 2014
    • Woods research group, Complex Carboyhdrate Research Center, University of Georgia (2005-2014). Glycam Biomolecule Builder. Available: http://www.glycam.com Accessed 25 June 2014.
    • (2005) Glycam Biomolecule Builder
  • 7
    • 67849122319 scopus 로고    scopus 로고
    • Web 3DNA - A web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures
    • Zheng G, Lu XJ, Olson WK, (2009) Web 3DNA- A web server for the analysis, reconstruction, and visualization of three-dimensional nucleic-acid structures. Nucleic Acids Res 37: W240-W246.
    • (2009) Nucleic Acids Res , vol.37
    • Zheng, G.1    Lu, X.J.2    Olson, W.K.3
  • 8
    • 3242875210 scopus 로고    scopus 로고
    • ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement
    • Suhre K, Sanejouand YH, (2004) ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res 32: W610-W614.
    • (2004) Nucleic Acids Res , vol.32
    • Suhre, K.1    Sanejouand, Y.H.2
  • 9
    • 79952525037 scopus 로고    scopus 로고
    • Available: Accessed 25 June 2014
    • Zheng W (2007-2014). AD-ENM Web Server. Available: http://enm.lobos.nih.gov Accessed 25 June 2014.
    • (2007) AD-ENM Web Server
    • Zheng, W.1
  • 17
    • 66149092693 scopus 로고    scopus 로고
    • Binding and release of cholesterol in the OSH4 protein of yeast
    • Singh RP, Brooks BR, Klauda JB, (2009) Binding and release of cholesterol in the OSH4 protein of yeast. Proteins 75: 468-477.
    • (2009) Proteins , vol.75 , pp. 468-477
    • Singh, R.P.1    Brooks, B.R.2    Klauda, J.B.3
  • 19
    • 24344455560 scopus 로고    scopus 로고
    • Structural mechanism for sterol sensing and transport by OSBP-related proteins
    • Im YJ, Raychaudhuri S, Prinz WA, Hurley JH, (2005) Structural mechanism for sterol sensing and transport by OSBP-related proteins. Nature 437: 154-158.
    • (2005) Nature , vol.437 , pp. 154-158
    • Im, Y.J.1    Raychaudhuri, S.2    Prinz, W.A.3    Hurley, J.H.4
  • 20
    • 77953377650 scopus 로고    scopus 로고
    • Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types
    • Klauda JB, Venable RM, Freites JA, O'Connor JW, Tobias DJ, et al. (2010) Update of the CHARMM all-atom additive force field for lipids: Validation on six lipid types. J Phys Chem B 114: 7830-7843.
    • (2010) J Phys Chem B , vol.114 , pp. 7830-7843
    • Klauda, J.B.1    Venable, R.M.2    Freites, J.A.3    O'Connor, J.W.4    Tobias, D.J.5
  • 21
    • 33846823909 scopus 로고
    • Particle mesh Ewald: An N{dot operator}log(N) method for Ewald sums in large systems
    • Darden T, York D, Pedersen L, (1993) Particle mesh Ewald: An N{dot operator}log(N) method for Ewald sums in large systems. J Chem Phys 98: 10089-10092.
    • (1993) J Chem Phys , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 22
    • 0000123071 scopus 로고    scopus 로고
    • Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential
    • Bogusz S, Cheatam TE III, Brooks BR, (1998) Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential. J Chem Phys 108: 7070-7084.
    • (1998) J Chem Phys , vol.108 , pp. 7070-7084
    • Bogusz, S.1    Cheatam III, T.E.2    Brooks, B.R.3
  • 24
    • 84868155171 scopus 로고    scopus 로고
    • Protein folding kinetics and thermodynamics from atomistic simulation
    • Piana S, Lindorff-Larsen K, Shaw DE, (2012) Protein folding kinetics and thermodynamics from atomistic simulation. Proc Natl Acad Sci U S A 109: 17845-17850.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 17845-17850
    • Piana, S.1    Lindorff-Larsen, K.2    Shaw, D.E.3
  • 25
    • 84886701765 scopus 로고    scopus 로고
    • Atomistic description of the folding of a dimeric protein
    • Piana S, Lindorff-Larsen K, Shaw DE, (2013) Atomistic description of the folding of a dimeric protein. J Phys Chem B 117: 12935-12942.
    • (2013) J Phys Chem B , vol.117 , pp. 12935-12942
    • Piana, S.1    Lindorff-Larsen, K.2    Shaw, D.E.3
  • 27
  • 28
    • 0242509772 scopus 로고    scopus 로고
    • Self-guided Langevin dynamics simulation method
    • Wu X, Brooks BR, (2003) Self-guided Langevin dynamics simulation method. Chem Phys Lett 381: 512-518.
    • (2003) Chem Phys Lett , vol.381 , pp. 512-518
    • Wu, X.1    Brooks, B.R.2
  • 29
    • 0017100947 scopus 로고
    • Theoretical Studies of Enzymic Reactions - Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme
    • Warshel A, Levitt M, (1976) Theoretical Studies of Enzymic Reactions- Dielectric, Electrostatic and Steric Stabilization of Carbonium-Ion in Reaction of Lysozyme. J Mol Biol 103: 227-249.
    • (1976) J Mol Biol , vol.103 , pp. 227-249
    • Warshel, A.1    Levitt, M.2
  • 30
    • 84988053595 scopus 로고
    • A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the exchange reaction and gas phase protonation of polyethers
    • Singh UC, Kollman PA, (1986) A combined ab initio quantum mechanical and molecular mechanical method for carrying out simulations on complex molecular systems: Applications to the exchange reaction and gas phase protonation of polyethers. J Comput Chem 7: 718-730.
    • (1986) J Comput Chem , vol.7 , pp. 718-730
    • Singh, U.C.1    Kollman, P.A.2
  • 31
    • 84986513644 scopus 로고
    • A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations
    • Field MJ, Bash PA, Karplus M, (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J Comput Chem 11: 700-733.
    • (1990) J Comput Chem , vol.11 , pp. 700-733
    • Field, M.J.1    Bash, P.A.2    Karplus, M.3
  • 32
    • 84905493547 scopus 로고    scopus 로고
    • Available: Accessed 25 June 2014
    • The Nobel Prize in Chemistry 2013. Available: http://www.nobelprize.org/nobel_prizes/chemistry/laureates/2013/ Accessed 25 June 2014.
    • The Nobel Prize in Chemistry 2013
  • 33
    • 0346726109 scopus 로고    scopus 로고
    • How enzymes work: analysis by modern rate theory and computer simulations
    • Garcia-Viloca M, Gao J, Karplus M, Truhlar DG, (2004) How enzymes work: analysis by modern rate theory and computer simulations. Science 303: 186-195.
    • (2004) Science , vol.303 , pp. 186-195
    • Garcia-Viloca, M.1    Gao, J.2    Karplus, M.3    Truhlar, D.G.4
  • 35
    • 60349127442 scopus 로고    scopus 로고
    • QM/MM methods for biomolecular systems
    • Senn HM, Thiel W, (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed Engl 48: 1198-1229.
    • (2009) Angew Chem Int Ed Engl , vol.48 , pp. 1198-1229
    • Senn, H.M.1    Thiel, W.2
  • 36
    • 75449116384 scopus 로고    scopus 로고
    • Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions
    • Acevedo O, Jorgensen WL, (2010) Advances in Quantum and Molecular Mechanical (QM/MM) Simulations for Organic and Enzymatic Reactions. Acc Chem Res 43: 142-151.
    • (2010) Acc Chem Res , vol.43 , pp. 142-151
    • Acevedo, O.1    Jorgensen, W.L.2
  • 37
    • 76249087938 scopus 로고    scopus 로고
    • CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields
    • Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, et al. (2010) CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31: 671-690.
    • (2010) J Comput Chem , vol.31 , pp. 671-690
    • Vanommeslaeghe, K.1    Hatcher, E.2    Acharya, C.3    Kundu, S.4    Zhong, S.5
  • 38
    • 84871545594 scopus 로고    scopus 로고
    • Automation of the CHARMM General Force Field (CGenFF) I: Bond and perception and atom typing
    • Vanommeslaeghe K, MacKerell J, (2012) Automation of the CHARMM General Force Field (CGenFF) I: Bond and perception and atom typing. J Chem Inf Mod 52: 3144-3154.
    • (2012) J Chem Inf Mod , vol.52 , pp. 3144-3154
    • Vanommeslaeghe, K.1    MacKerell, J.2
  • 39
    • 84871544678 scopus 로고    scopus 로고
    • Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges
    • Vanommeslaeghe K, Raman EP, MacKerell J, (2012) Automation of the CHARMM General Force Field (CGenFF) II: Assignment of bonded parameters and partial atomic charges. J Chem Inf Model 52: 3155-3168.
    • (2012) J Chem Inf Model , vol.52 , pp. 3155-3168
    • Vanommeslaeghe, K.1    Raman, E.P.2    MacKerell, J.3
  • 40
    • 33746563448 scopus 로고    scopus 로고
    • Advances in methods and algorithms in a modern quantum chemistry program package
    • Shao Y, Molnar LF, Jung Y, Kussmann J, Ochsenfeld C, et al. (2006) Advances in methods and algorithms in a modern quantum chemistry program package. Phys Chem Chem Phys 8: 3172-3191.
    • (2006) Phys Chem Chem Phys , vol.8 , pp. 3172-3191
    • Shao, Y.1    Molnar, L.F.2    Jung, Y.3    Kussmann, J.4    Ochsenfeld, C.5
  • 42
    • 0034646218 scopus 로고    scopus 로고
    • Mechanisms and kinetics of β-hairpin formation
    • Klimov DK, Thirumalai D, (2000) Mechanisms and kinetics of β-hairpin formation. Proc Natl Acad Sci USA 97: 2544-2549.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 2544-2549
    • Klimov, D.K.1    Thirumalai, D.2
  • 43
    • 1642485164 scopus 로고    scopus 로고
    • Coarse grained model for semiquantitative lipid simulations
    • Marrink SJ, de Vries AH, Mark AE, (2004) Coarse grained model for semiquantitative lipid simulations. J Phys Chem B 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
  • 44
    • 33644644163 scopus 로고    scopus 로고
    • Insertion and Assembly of Membrane Proteins via Simulation
    • Bond PJ, Sansom MSP, (2006) Insertion and Assembly of Membrane Proteins via Simulation. J Am Chem Soc 128: 2697-2704.
    • (2006) J Am Chem Soc , vol.128 , pp. 2697-2704
    • Bond, P.J.1    Sansom, M.S.P.2
  • 46
    • 77957959681 scopus 로고    scopus 로고
    • Fold versus sequence effects on the driving force for protein-mediated electron transfer
    • Perrin BS, Ichiye T, (2010) Fold versus sequence effects on the driving force for protein-mediated electron transfer. Proteins: Struct, Funct, Bioinf 78: 2798-2808.
    • (2010) Proteins: Struct, Funct, Bioinf , vol.78 , pp. 2798-2808
    • Perrin, B.S.1    Ichiye, T.2
  • 47
    • 84986534166 scopus 로고
    • New spherical-cutoff methods for long-range forces in macromolecular simulation
    • Steinbach PJ, Brooks BR, (1994) New spherical-cutoff methods for long-range forces in macromolecular simulation. J Comput Chem 15: 667-683.
    • (1994) J Comput Chem , vol.15 , pp. 667-683
    • Steinbach, P.J.1    Brooks, B.R.2
  • 48
    • 0027459475 scopus 로고
    • Atomic Resolution (0.83 Å) Crystal Structure of the Hydrophobic Protein Crambin at 130 K
    • Teeter MM, Roe S, Heo NH, (1993) Atomic Resolution (0.83 Å) Crystal Structure of the Hydrophobic Protein Crambin at 130 K. J Mol Biol 230: 292-311.
    • (1993) J Mol Biol , vol.230 , pp. 292-311
    • Teeter, M.M.1    Roe, S.2    Heo, N.H.3
  • 49
    • 84876239078 scopus 로고    scopus 로고
    • JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia
    • Hanson RM, Prilusky J, Renjian Z, Nakane T, Sussman JL, (2013) JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr J Chem 53: 207-216.
    • (2013) Isr J Chem , vol.53 , pp. 207-216
    • Hanson, R.M.1    Prilusky, J.2    Renjian, Z.3    Nakane, T.4    Sussman, J.L.5
  • 52
    • 84905472886 scopus 로고    scopus 로고
    • Department of Homeland Security: USCERT, Available Accessed 25 June 2014
    • Department of Homeland Security: USCERT (2013). Alert (TA13-010A): Oracle Java 7 Security Manager Bypass Vulnerability. Available http://www.us-cert.gov/ncas/alerts/ta13-010a Accessed 25 June 2014.
    • (2013) Alert (TA13-010A): Oracle Java 7 Security Manager Bypass Vulnerability
  • 54
    • 79954580509 scopus 로고    scopus 로고
    • Schrödinger LLC. Available: Accessed 25 June 2014
    • Schrödinger LLC (2010). The PyMOL Molecular Graphics System, Version 1.3r1. Available: http://www.pymol.org/ Accessed 25 June 2014.
    • (2010) The PyMOL Molecular Graphics System, Version 1.3r1
  • 57
    • 0023644679 scopus 로고
    • Structure of ubiquitin refined at 1.8 Å resolution
    • Vijay-Kumar S, Bugg CE, Cook WJ, (1987) Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol 194: 531-544.
    • (1987) J Mol Biol , vol.194 , pp. 531-544
    • Vijay-Kumar, S.1    Bugg, C.E.2    Cook, W.J.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.