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タグ: charmm [27 articles]

Recent papers classified by the tag charmm.
  • Experimental Validation of Molecular Dynamics Simulations of Lipid Bilayers: A New Approach
    Biophys. J., Vol. 88, No. 2. (1 February 2005), pp. 805-817.
    by Ryan W Benz, Francisco Castro-Roman, Douglas J Tobias, Stephen H White
    posted to charmm gromacs molecular-dynamics namd by softsimu on 2008-01-23 07:03:25 as **
  • Assessing Atomistic and Coarse-Grained Force Fields for Protein−Lipid Interactions: the Formidable Challenge of an Ionizable Side Chain in a Membrane
    J. Phys. Chem. B (18 July 2008)
    by Igor Vorobyov, Libo Li, Toby W Allen
    posted to coarse-graining charmm by softsimu on 2008-10-12 21:38:07 as ** along with 3 people A_Coletta_Thesis middledomain agrossfield
  • Electrostatic Characterization of Enzyme Complexes: Evaluation of the Mechanism of Catalysis of Dihydrofolate Reductase
    J. Am. Chem. Soc., Vol. 119, No. 10. (12 March 1997), pp. 2386-2395.
    by WR Cannon, BJ Garrison, SJ Benkovic
    posted to charmm dhfr by ruvido on 2007-04-23 14:40:36 as **
  • CHARMM: A program for macromolecular energy, minimization, and dynamics calculations
    Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217.
    by Bernard R Brooks, Robert E Bruccoleri, Barry D Olafson, David J States, S Swaminathan, Martin Karplus
    posted to charmm continuous_moodels force_field by rabio on 2007-02-28 13:00:38 as ** along with 4 people dgront mmuecke saravan gisle
  • Density of states simulations of proteins
    The Journal of Chemical Physics, Vol. 118, No. 9. (2003), pp. 4285-4290.
    by Nitin Rathore, Thomas A Knotts, Juan J de Pablo
    posted to charmm monte_carlo protein_thermodynamics wang-landau_sampling by rabio on 2007-02-27 14:03:44 as read
  • All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins
    J. Phys. Chem. B, Vol. 102, No. 18. (30 April 1998), pp. 3586-3616.
    by AD Mackerell, D Bashford, M Bellott, RL Dunbrack, JD Evanseck, MJ Field, S Fischer, J Gao, H Guo, S Ha, D Joseph-Mccarthy, L Kuchnir, K Kuczera, FTK Lau, C Mattos, S Michnick, T Ngo, DT Nguyen, B Prodhom, WE Reiher, B Roux, M Schlenkrich, JC Smith, R Stote, J Straub, M Watanabe, J Wiorkiewicz-Kuczera, D Yin, M Karplus
    posted to charmm field force model by papatonyhill on 2006-06-14 19:16:43 as **** along with 4 people timg dimka ttjoseph ssomani
  • Monte Carlo simulations of biomolecules: The MC module in CHARMM.
    J Comput Chem, Vol. 27, No. 2. (30 January 2006), pp. 203-216.
    by J Hu, A Ma, AR Dinner
    posted to charmm dynamics molecular monte-carlo by msuarezdiez on 2008-01-16 12:44:28 as **
  • Interfacing Q-Chem and CHARMM to perform QM/MM reaction path calculations
    Journal of Computational Chemistry, Vol. 28, No. 9. (2007), pp. 1485-1502.
    by Lee H Woodcock, Milan Hodo?ček, Andrew TB Gilbert, Peter MW Gill, Henry F Schaefer, Bernard R Brooks
    posted to charmm dynamics molecular by msuarezdiez on 2008-01-16 12:42:51 as **
  • Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm
    Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1549-1562.
    by Guosheng Wu, Daniel H Robertson, Charles L Brooks, Michal Vieth
    posted to charmm dynamics molecular by msuarezdiez on 2008-01-16 12:47:10 as ** along with 3 people apostola papatonyhill mmuecke
  • notes The development and integration of a distributed 3D FFT for a cluster of workstations
    (2000), pp. 26-26.
    by Christopher E Cramer, John A Board
    posted to charmm fft mpi by mmuecke on 2007-12-06 16:31:13 as **
  • On the performance of molecular dynamics applications on current high-end systems.
    Philos Transact A Math Phys Eng Sci, Vol. 363, No. 1833. (15 August 2005), pp. 1987-1998.
    by J Hein, F Reid, L Smith, I Bush, M Guest, P Sherwood
    posted to charmm high-performance_computing molecular_dynamics survey by mmuecke on 2008-01-21 12:24:25 as read along with 1 person hlwoodcock
  • Parallelizing Molecular Dynamics Programs for Distributed-Memory Machines
    IEEE Comput. Sci. Eng., Vol. 2, No. 2. (June 1995), pp. 18-29.
    by Yuan-Shin Hwang, Raja Das, Joel H Saltz, Milan Hodoscek, Bernard R Brooks
    posted to charmm high-performance_computing by mmuecke on 2007-12-11 10:11:54 as ****
  • Improved Treatment of the Protein Backbone in Empirical Force Fields
    J. Am. Chem. Soc., Vol. 126, No. 3. (28 January 2004), pp. 698-699.
    by AD Mackerell, M Feig, CL Brooks
    posted to charmm dipeptides force_field torsion by middledomain on 2008-08-01 09:31:27 as read along with 1 person hlwoodcock
  • Methyl Group Dynamics and the Onset of Anharmonicity in Myoglobin
    J. Phys. Chem. B (10 April 2008)
    by M Krishnan, V Kurkal-Siebert, JC Smith
    posted to charmm md methyl_rotation rotation torsion_paper by middledomain on 2008-04-10 14:01:14 as ** along with 2 people and 1 group mkrishna r2s2 CMB
  • CHARMM-GUI: A web-based graphical user interface for CHARMM
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Sunhwan Jo, Taehoon Kim, Vidyashankara G Iyer, Wonpil Im
    posted to charmm force_field gui web_interface by middledomain on 2008-03-20 13:06:34 as **
  • Electrostatic Properties of Aqueous Salt Solution Interfaces: A Comparison of Polarizable and Nonpolarizable Ion Models
    J. Phys. Chem. B (20 August 2008)
    by Lee G Warren, Sandeep Patel
    posted to charmm drude force_field ion polarization water by middledomain on 2008-08-20 12:00:10 as ** along with 1 person paulschlesinger
  • Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field
    J. Phys. Chem. B (27 February 2008)
    by E Harder, VM Anisimov, T Whitfield, AD Mackerell, B Roux
    posted to charmm liquids polarization by middledomain on 2008-02-27 11:07:04 as **
  • Is Alanine Dipeptide a Good Model for Representing the Torsional Preferences of Protein Backbones?
    J. Chem. Theory Comput. (30 July 2008)
    by Michael Feig
    posted to charmm dipeptide force_field md tip3p torsion by middledomain on 2008-07-30 13:37:23 as read
  • CHARMMing: A New, Flexible Web Portal for CHARMM
    J. Chem. Inf. Model. (13 August 2008)
    by Benjamin T Miller, Rishi P Singh, Jeffery B Klauda, Milan Hodošček, Bernard R Brooks, Lee H Woodcock
    posted to charmm web_interface by middledomain on 2008-08-13 13:11:15 as ** along with 2 people and 1 group jmccammon reyez McCammon
  • Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes
    J. Chem. Theory Comput., Vol. 3, No. 6. (13 November 2007), pp. 1878-1889.
    by W Xie, J Pu, AD Mackerell, J Gao
    posted to force_field polarization charmm by middledomain on 2008-01-22 16:58:06 as **
  • Contribution of Charged Groups to the Enthalpic Stabilization of the Folded States of Globular Proteins
    J. Phys. Chem. B (28 February 2008)
    by VM Dadarlat, CB Post
    posted to charmm electrosatics enthalpy proteins solvation by middledomain on 2008-02-28 11:47:00 as **
  • Energetics of Infinite Homopolypeptide Chains: A New Look at Commonly Used Force Fields
    J. Phys. Chem. B (14 May 2008)
    by Evgeni Penev, Joel Ireta, Joan-Emma Shea
    posted to amber ameoba charmm comparison dft force_field opls by middledomain on 2008-05-14 09:46:35 as **
  • 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
    Journal of Computational Chemistry, Vol. 25, No. 11. (2004), pp. 1400-1415.
    by Alexander D Mackerell, Michael Feig, Charles L Brooks
    posted to ab_initio charmm dipeptides force_field by middledomain on 2008-08-01 09:30:33 as ** along with 2 people dgront hlwoodcock
  • Systematic Comparison of Empirical Forcefields for Molecular Dynamic Simulation of Insulin
    J. Phys. Chem. B (12 August 2008)
    by Nevena Todorova, Sue F Legge, Herbert Treutlein, Irene Yarovsky
    posted to amber charmm comparison force_field gromos by middledomain on 2008-08-12 15:09:51 as ** along with 1 person agrossfield
  • Effective energy function for proteins in solution.
    Proteins, Vol. 35, No. 2. (1 May 1999), pp. 133-152.
    by T Lazaridis, M Karplus
    posted to charmm eef1 by kgutwin on 2008-06-24 21:04:05 as *** along with 4 people and 2 groups marcius bluvsh1 choonpeng hmk BioinfoCIPF SGU-CIPF
  • Hydrogen Bonding and Binding of Polybasic Residues with Negatively Charged Mixed Lipid Monolayers.
    Langmuir (23 January 2008)
    by Christian D Lorenz, Jordi Faraudo, Alex Travesset
    posted to charmm dopc dops force-field lipid md membrane pip2 simulations by dimka on 2008-01-24 14:42:43 as **
  • Ligand affinities predicted with the MM/PBSA method: dependence on the simulation method and the force field.
    J Med Chem, Vol. 49, No. 22. (2 November 2006), pp. 6596-6606.
    by A Weis, K Katebzadeh, P Söderhjelm, I Nilsson, U Ryde
    posted to charmm mmpbsa by dimka on 2007-06-13 22:09:38 as **
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