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Group: baker-group - with tag molecular_simulation [351 articles]

グループ baker-group のメンバーが最近追加した論文の一覧 with tag molecular_simulation
  • United-Atom Acyl Chains for CHARMM Phospholipids
    J. Phys. Chem. B, Vol. 112, No. 23. (12 June 2008), pp. 7008-7015.
    by Jérôme Hénin, Wataru Shinoda, Michael L Klein
    posted to biomembranes molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-07-09 11:35:53 as read
  • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method
    Journal of Computational Chemistry, Vol. 21, No. 2. (2000), pp. 132-146.
    by Araz Jakalian, Bruce L Bush, David B Jack, Christopher I Bayly
    posted to electrostatics molecular_dynamics molecular_simulation quantum_mechanics by sobolevnrm to the group baker-group on 2008-07-01 02:49:19 as read
  • Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
    J Comput Chem, Vol. 23, No. 16. (December 2002), pp. 1623-1641.
    by A Jakalian, DB Jack, CI Bayly
    posted to electrostatics molecular_dynamics molecular_simulation quantum_mechanics by sobolevnrm to the group baker-group on 2008-07-01 02:46:11 as read along with 2 people lillekatt patricia
  • Solvation Free Energies of the Nucleic Acid Bases
    J. Phys. Chem., Vol. 100, No. 20. (16 May 1996), pp. 8587-8594.
    by JL Miller, PA Kollman
    posted to molecular_simulation nucleic_acids solvation by sobolevnrm to the group baker-group on 2008-06-30 12:15:23 as read
  • Solvation Free Energy of Biomacromolecules: Parameters for a Modified Generalized Born Model Consistent with the AMBER Force Field
    J. Phys. Chem. B, Vol. 102, No. 47. (19 November 1998), pp. 9571-9576.
    by B Jayaram, D Sprous, DL Beveridge
    posted to generalized_born molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-06-30 12:10:27 as read
  • Efficient and precise solvation free energies via alchemical adiabatic molecular dynamics
    The Journal of Chemical Physics, Vol. 125, No. 7. (2006)
    by Jerry B Abrams, Lula Rosso, Mark E Tuckerman
    posted to molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-06-29 21:13:31 as read
  • Electrostatic potentials in systems periodic in one, two, and three dimensions
    The Journal of Chemical Physics, Vol. 128, No. 17. (2008)
    by ER Smith
    posted to electrostatics molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-06-18 11:50:09 as read
  • Calculation of protein-ligand binding free energy by using a polarizable potential
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295.
    by Dian Jiao, Pavel A Golubkov, Thomas A Darden, Pengyu Ren
    posted to electrostatics molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2008-06-13 11:49:09 as read along with 3 people and 2 groups jmccammon biehl barry structural_bioinformatics McCammon
  • Simulation approaches to soft matter: Generic statistical properties vs. chemical details
    Computer Physics Communications, Vol. 179, No. 1-3. (July 2008), pp. 51-60.
    by Matej Praprotnik, Christoph Junghans, Luigi Delle Site, Kurt Kremer
    posted to molecular_simulation multiscale by sobolevnrm to the group baker-group on 2008-06-07 15:37:58 as read
  • The Block-P3M algorithm
    Computer Physics Communications, Vol. 179, No. 1-3. (July 2008), pp. 46-50.
    by JW Eastwood
    posted to electrostatics mathematics molecular_simulation by sobolevnrm to the group baker-group on 2008-06-07 15:27:27 as read
  • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Proteins, Vol. 65, No. 3. (2006), pp. 712-725.
    by V Hornak, R Abel, A Okur, B Strockbine, A Roitberg, C Simmerling
    posted to molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-06-06 11:28:06 as read
  • Molecular dynamics simulations of the acyl-enzyme and the tetrahedral intermediate in the deacylation step of serine proteases
    Proteins, Vol. 47, No. 3. (2002), pp. 357-369.
    by M Topf, P Várnai, CJ Schofield, WG Richards
    posted to kinetics molecular_simulation thrombin by sobolevnrm to the group baker-group on 2008-06-04 11:58:07 as read
  • Tension-induced vesicle fusion: pathways and pore dynamics
    Soft Matter, Vol. 4 (2008), pp. 1208-1214.
    by L Gao, R Lipowsky, J Shillcock
    posted to biomembranes molecular_simulation multiscale by sobolevnrm to the group baker-group on 2008-06-04 11:43:25 as read
  • Redox entropy of plastocyanin: Developing a microscopic view of mesoscopic polar solvation
    The Journal of Chemical Physics, Vol. 128, No. 15. (2008)
    by David N Lebard, Dmitry V Matyushov
    posted to molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-22 12:03:41 as read
  • A novel algorithm for creating coarse-grained, density dependent implicit solvent models
    The Journal of Chemical Physics, Vol. 128, No. 15. (2008)
    by Erik C Allen, Gregory C Rutledge
    posted to electrostatics molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-22 11:54:29 as read along with 1 person agrossfield
  • Concurrent triple-scale simulation of molecular liquids
    The Journal of Chemical Physics, Vol. 128, No. 11. (2008)
    by Rafael D Buscalioni, Kurt Kremer, Matej Praprotnik
    posted to molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-05-20 11:35:10 as read
  • Improved Sampling for Simulations of Interfacial Membrane Proteins: Application of Generalized Shadow Hybrid Monte Carlo to a Peptide Toxin/Bilayer System
    J. Phys. Chem. B, Vol. 112, No. 18. (8 May 2008), pp. 5710-5717.
    by CL Wee, MSP Sansom, S Reich, E Akhmatskaya
    posted to biomembranes enhanced_sampling molecular_dynamics molecular_simulation protein-membrane_interactions by sobolevnrm to the group baker-group on 2008-05-19 11:38:23 as read
  • Rapid approximation to molecular surface area via the use of Boolean logic and look-up tables
    Journal of Computational Chemistry, Vol. 14, No. 3. (1993), pp. 349-352.
    by SM Le Grand, Jr Merz
    posted to electrostatics mathematics molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-05-12 17:54:03 as read
  • MolAxis: Efficient and accurate identification of channels in macromolecules
    Proteins (in press)
    by E Yaffe, D Fishelovitch, HJ Wolfson, D Halperin, R Nussinov
    posted to molecular_simulation structure by sobolevnrm to the group baker-group on 2008-05-09 11:24:52 as read
  • Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics
    The Journal of Chemical Physics, Vol. 124, No. 23. (2006)
    by Christopher J Fennell, Daniel J Gezelter
    posted to electrostatics molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-05-09 11:02:47 as read along with 3 people mikaellund OndrejMarsalek michaelbussmann
  • Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method
    Chemical Physics Letters, Vol. 454, No. 4-6. (20 March 2008), pp. 391-395.
    by Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang
    posted to electrostatics molecular_simulation nucleic_acids statistical_mechanics by sobolevnrm to the group baker-group on 2008-05-08 11:41:20 as read
  • Src Kinase Conformational Activation: Thermodynamics, Pathways, and Mechanisms
    PLoS Computational Biology, Vol. 4, No. 3. (2008), e1000047.
    by S Yang, B Roux
    posted to allostery molecular_simulation by sobolevnrm to the group baker-group on 2008-05-06 11:21:24 as read
  • A new approach for efficient simulation of Coulomb interactions in ionic fluids
    The Journal of Chemical Physics, Vol. 128, No. 12. (2008)
    by Natalia A Denesyuk, John D Weeks
    posted to electrostatics molecular_simulation by sobolevnrm to the group baker-group on 2008-05-06 11:05:56 as read along with 1 person sunhwan
  • Efficient free energy calculation of water across lipid membranes
    Journal of Computational Chemistry (in press)
    by K Shinoda, W Shinoda, M Mikami
    posted to biomembranes molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-30 11:07:08 as read
  • Reassessing a sparse energetic network within a single protein domain
    Proceedings of the National Academy of Sciences (13 March 2008), 0711732105.
    by Celestine N Chi, Lisa Elfstrom, Yao Shi, Tord Snall, Ake Engstrom, Per Jemth
    posted to allostery molecular_simulation by sobolevnrm to the group baker-group on 2008-04-30 11:02:56 as read along with 4 people apaydin cjeans cactus sunhwan
  • van der Waals volumes and radii
    Journal of Physical Chemistry, Vol. 68, No. 3. (1964), pp. 441-451.
    by A Bondi
    posted to molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-28 14:58:38 as read
  • The packing density in proteins: standard radii and volumes.
    J Mol Biol, Vol. 290, No. 1. (2 July 1999), pp. 253-266.
    by J Tsai, R Taylor, C Chothia, M Gerstein
    posted to molecular_simulation solvation structure by sobolevnrm to the group baker-group on 2008-04-28 14:56:20 as read along with 5 people and 2 groups ana barry bicko blackbart medic0747 structural_bioinformatics Bioinformatics
  • How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636.
    by Hugh Nymeyer
    posted to enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2008-04-28 11:43:27 as read along with 3 people and 2 groups agrossfield loison barry structural_bioinformatics McCammon
  • CHARMM-GUI: A web-based graphical user interface for CHARMM
    Journal of Computational Chemistry (in press)
    by S Jo, T Kim, VG Iyer, W Im
    posted to database electrostatics molecular_simulation software by sobolevnrm to the group baker-group on 2008-04-28 11:28:35 as read
  • Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations
    The Journal of Chemical Physics, Vol. 128, No. 11. (2008)
    by Yuqing Deng, Benoît Roux
    posted to molecular_dynamics molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-26 14:43:02 as read along with 1 person dmobley
  • Modeling Membranes under a Transmembrane Potential
    J. Phys. Chem. B (16 April 2008)
    by L Delemotte, F Dehez, W Treptow, M Tarek
    posted to biomembranes electrostatics ion_channels molecular_simulation nanotech solvation by sobolevnrm to the group baker-group on 2008-04-23 20:42:06 as read
  • Scalable molecular dynamics with NAMD.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1781-1802.
    by JC Phillips, R Braun, W Wang, J Gumbart, E Tajkhorshid, E Villa, C Chipot, RD Skeel, L Kalé, K Schulten
    posted to molecular_dynamics molecular_simulation software by sobolevnrm to the group baker-group on 2008-04-22 11:48:56 as read along with 10 people and 4 groups vahmurk gisle dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros ibuch Radiation_Damage Stressosome Bioinformatics insilicodrug
  • Molecular Modeling and Simulation
    (19 August 2002)
    by Tamar Schlick
    posted to molecular_simulation teaching by sobolevnrm to the group baker-group on 2008-04-19 21:08:50 as read
  • Molecular Modelling: Principles and Applications (2nd Edition)
    (30 March 2001)
    by Andrew Leach
    posted to molecular_simulation teaching by sobolevnrm to the group baker-group on 2008-04-19 21:07:03 as read along with 4 people dimka yoel_rf choonpeng samtam
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to allostery diffusion kinetics molecular_simulation by sobolevnrm to the group baker-group on 2008-04-18 11:47:00 as read along with 4 people and 2 groups aqeel barry paulschlesinger toerst structural_bioinformatics McCammon
  • How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
    J. Phys. Chem. B, Vol. 110, No. 37. (21 September 2006), pp. 18680-18687.
    by C Tan, L Yang, R Luo
    posted to electrostatics molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-18 11:27:21 as **
  • Surface Tension and Surface Orientation of Perfluorinated Alkanes
    J. Phys. Chem. C, Vol. 112, No. 13. (3 April 2008), pp. 5029-5035.
    by M Tsige, GS Grest
    posted to interfaces molecular_dynamics molecular_simulation perfluorocarbons by sobolevnrm to the group baker-group on 2008-04-17 11:47:12 as read
  • Secondary Structure Bias in Generalized Born Solvent Models: Comparison of Conformational Ensembles and Free Energy of Solvent Polarization from Explicit and Implicit Solvation
    J. Phys. Chem. B, Vol. 111, No. 7. (22 February 2007), pp. 1846-1857.
    by DR Roe, A Okur, L Wickstrom, V Hornak, C Simmerling
    posted to molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-16 11:41:28 as read along with 3 people baaden choonpeng onufriev
  • Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 3. (2008)
    by Victor Vivcharuk, Bruno Tomberli, Igor S Tolokh, CG Gray
    posted to biomembranes molecular_dynamics molecular_simulation protein-membrane_interactions by sobolevnrm to the group baker-group on 2008-04-16 11:29:22 as read along with 1 person paulschlesinger
  • Poisson-Boltzmann Analytical Gradients for Molecular Modeling Calculations
    J. Phys. Chem. B, Vol. 103, No. 16. (22 April 1999), pp. 3057-3061.
    by M Friedrichs, R Zhou, SR Edinger, RA Friesner
    posted to electrostatics molecular_dynamics molecular_simulation solvation by sobolevnrm to the group baker-group on 2008-04-15 16:59:39 as read
  • Recent advances in the study of nucleic acid flexibility by molecular dynamics
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Modesto Orozco, Agnes Noy, Alberto Pérez
    posted to molecular_simulation nucleic_acids by sobolevnrm to the group baker-group on 2008-04-15 11:50:15 as read along with 2 people onufriev mazo
  • Biomolecular simulations of membranes: Physical properties from different force fields
    The Journal of Chemical Physics, Vol. 128, No. 12. (2008)
    by Shirley WI Siu, Robert Vácha, Pavel Jungwirth, Rainer A Böckmann
    posted to biomembranes molecular_simulation by sobolevnrm to the group baker-group on 2008-04-15 00:45:50 as read along with 3 people robertvacha paulschlesinger sunhwan
  • Accurate Structural Correlations from Maximum Likelihood Superpositions
    PLoS Computational Biology, Vol. 4, No. 2. (2008), e43.
    by DL Theobald, DS Wuttke
    posted to molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-04-14 12:25:45 as read along with 1 person zwang
  • Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Luca Monticelli, Eric J Sorin, Peter D Tieleman, Vijay S Pande, Giorgio Colombo
    posted to enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2008-04-03 12:01:59 as read
  • Finding Transition Pathways Using the String Method with Swarms of Trajectories
    J. Phys. Chem. B (22 February 2008)
    by AC Pan, D Sezer, B Roux
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-03-27 11:18:17 as read along with 1 person dmobley
  • Efficient calculation of configurational entropy from molecular simulations by combining the mutual-information expansion and nearest-neighbor methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Vladimir Hnizdo, Jun Tan, Benjamin J Killian, Michael K Gilson
    posted to molecular_simulation by sobolevnrm to the group baker-group on 2008-03-27 11:00:23 as read
  • Evaluation of Salt Bridge Structure and Energetics in Peptides Using Explicit, Implicit, and Hybrid Solvation Models
    J. Chem. Theory Comput. (21 February 2008)
    by A Okur, L Wickstrom, C Simmerling
    posted to molecular_dynamics molecular_simulation multiscale solvation by sobolevnrm to the group baker-group on 2008-03-27 10:52:18 as read along with 1 person dmobley
  • Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 2. (2008)
    by Matthew A Wyczalkowski, Rohit V Pappu
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-03-27 10:49:38 as read
  • Combining Elastic Network Analysis and Molecular Dynamics Simulations by Hamiltonian Replica Exchange
    J. Chem. Theory Comput., Vol. 4, No. 3. (11 March 2008), pp. 477-487.
    by M Zacharias
    posted to molecular_dynamics molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-03-14 11:18:27 as read along with 1 person barry
  • Molecular dynamics simulations of nucleic acid-protein complexes
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Mackerell, Lennart Nilsson
    posted to molecular_dynamics molecular_simulation protein-nucleic_acid_interactions by sobolevnrm to the group baker-group on 2008-03-14 11:15:30 as read along with 3 people ruvido zwang phoenixzxl
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