Register | Log in | FAQ      [?] 

Tag molecular_simulation [147 articles]

Recent papers classified by the tag molecular_simulation.
  • Setting up and running molecular dynamics simulations of membrane proteins.
    Methods, Vol. 41, No. 4. (April 2007), pp. 475-488.
    by C Kandt, WL Ash, D Peter Tieleman
    posted to biomembranes molecular_dynamics molecular_simulation by sobolevnrm on 2008-01-09 17:36:22 as read along with 1 person and 2 groups xdeupi LabCompMed baker-group
  • 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 solvation molecular_simulation by sobolevnrm on 2008-06-29 21:13:30 as read along with 1 group baker-group
  • Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations
    J. Chem. Theory Comput., Vol. 4, No. 2. (12 February 2008), pp. 217-221.
    by A Heyden, DG Truhlar
    posted to molecular_simulation multiscale by sobolevnrm on 2008-02-27 12:18:27 as read along with 1 group baker-group
  • Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels
    Biophysical Chemistry, Vol. 124, No. 3. (1 December 2006), pp. 251-267.
    by Toby W Allen, Olaf S Andersen, Benoit Roux
    posted to biomembranes electrostatics molecular_dynamics molecular_simulation solvation by sobolevnrm on 2007-09-18 22:11:10 as read along with 2 people and 3 groups ibuch barry structural_bioinformatics Bioinformatics baker-group
  • Perturbation of Local Solvent Structure by a Small Dication: A Theoretical Study on Structural, Vibrational, and Reactive Properties of Beryllium Ion in Water
    J. Phys. Chem. B, Vol. 112, No. 10. (13 March 2008), pp. 2958-2963.
    by S Gnanakaran, B Scott, TM Mccleskey, AE Garcia
    posted to electrostatics molecular_dynamics molecular_simulation solvation by sobolevnrm on 2008-03-12 11:29:44 as read along with 1 group baker-group
  • Polarizable Force Fields: History, Test Cases, and Prospects
    J. Chem. Theory Comput. (25 September 2007)
    by A Warshel, M Kato, AV Pisliakov
    posted to electrostatics molecular_dynamics molecular_simulation by sobolevnrm on 2007-09-25 12:56:39 as read along with 1 person and 1 group middledomain baker-group
  • Molecular Modeling and Simulation
    (19 August 2002)
    by Tamar Schlick
    posted to molecular_simulation teaching by sobolevnrm on 2008-04-19 21:08:50 as read along with 1 group baker-group
  • Molecular Modelling: Principles and Applications (2nd Edition)
    (30 March 2001)
    by Andrew Leach
    posted to molecular_simulation teaching by sobolevnrm on 2008-04-19 21:07:03 as read along with 4 people and 1 group dimka yoel_rf choonpeng samtam baker-group
  • Protein-protein docking by simulating the process of association subject to biochemical constraints
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Domantas Motiejunas, Razif Gabdoulline, Ting Wang, Anna Feldman-Salit, Tim Johann, Peter J Winn, Rebecca C Wade
    posted to molecular_simulation protein-protein_interactions by sobolevnrm on 2008-02-18 12:22:20 as read along with 1 group baker-group
  • 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 quantum_mechanics molecular_simulation molecular_dynamics electrostatics by sobolevnrm on 2008-07-01 02:49:19 as read along with 1 group baker-group
  • Control of Membrane Fusion Mechanism by Lipid Composition: Predictions from Ensemble Molecular Dynamics
    PLoS Computational Biology, Vol. 3, No. 11. (1 November 2007), e220.
    by Peter M Kasson, Vijay S Pande
    posted to biomembranes molecular_simulation by sobolevnrm on 2007-12-27 12:45:22 as read along with 1 person and 1 group Ema baker-group
  • A Computational Investigation of Allostery in the Catabolite Activator Protein
    J. Am. Chem. Soc., Vol. 129, No. 50. (19 December 2007), pp. 15668-15676.
    by L Li, VN Uversky, AK Dunker, SO Meroueh
    posted to allostery electrostatics molecular_simulation solvation by sobolevnrm on 2007-12-27 12:44:54 as read along with 1 person and 1 group ruvido baker-group
  • Calculation of local and average pressure tensors in molecular simulations
    Molecular Simulation, Vol. 33, No. 9. (2007), pp. 747-758.
    by H Heinz
    posted to molecular_dynamics molecular_simulation statistical_mechanics by sobolevnrm on 2007-08-23 13:27:52 as read along with 1 group baker-group
  • 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 quantum_mechanics molecular_simulation molecular_dynamics electrostatics by sobolevnrm on 2008-07-01 02:46:11 as read along with 2 people and 1 group lillekatt patricia baker-group
  • 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 on 2008-04-17 11:47:12 as read along with 1 group baker-group
  • Application of Ewald summations to long-range dispersion forces
    The Journal of Chemical Physics, Vol. 127, No. 14. (2007)
    by Pieter, Ahmed E Ismail, Gary S Grest
    posted to molecular_dynamics molecular_simulation nonpolar by sobolevnrm on 2007-10-30 11:36:05 as read along with 1 group baker-group
  • Local electrostatics algorithm for classical molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 127, No. 13. (2007)
    by Jörg Rottler
    posted to electrostatics molecular_simulation by sobolevnrm on 2007-10-11 12:27:54 as read along with 5 people and 1 group afenley softsimu mikaellund OndrejMarsalek michaelbussmann baker-group
  • Molecular-Scale Structure in Fluid-Gel Patterned Bilayers: Stability of Interfaces and Transmembrane Distribution
    Langmuir, Vol. 23, No. 25. (4 December 2007), pp. 12465-12468.
    by SV Bennun, ML Longo, R Faller
    posted to biomembranes molecular_simulation by sobolevnrm on 2008-01-08 12:55:49 as read along with 1 group baker-group
  • Coarse-Grained Protein Model Coupled with a Coarse-Grained Water Model: Molecular Dynamics Study of Polyalanine-Based Peptides
    J. Chem. Theory Comput. (2 October 2007)
    by W Han, YD Wu
    posted to molecular_simulation multiscale protein_folding by sobolevnrm on 2007-10-08 12:22:48 as read along with 1 group baker-group
  • Molecular simulation as an aid to experimentalists
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Wilfred F van Gunsteren, Jozica Dolenc, Alan E Mark
    posted to experimental_methodology molecular_dynamics molecular_simulation by sobolevnrm on 2008-03-12 11:07:09 as read along with 1 person and 1 group jlh64 baker-group
  • Structure and dynamics of phospholipid bilayers using recently developed general all-atom force fields
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Lula Rosso, Ian R Gould
    posted to biomembranes molecular_simulation by sobolevnrm on 2007-10-08 12:22:05 as read along with 2 people and 1 group daevans easybakemuffin baker-group
  • Solvent reaction field potential inside an uncharged globular protein: A bridge between implicit and explicit solvent models?
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007), 155101.
    by DS Cerutti, NA Baker, JA Mccammon
    posted to electrostatics molecular_simulation nonpolar solvation by sobolevnrm on 2007-10-16 12:13:55 as read along with 1 person and 1 group onufriev baker-group
  • Accelerated entropy estimates with accelerated dynamics
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by David DL Minh, Donald Hamelberg, Andrew J Mccammon
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm on 2007-11-02 11:13:50 as read along with 2 people and 1 group afenley dmobley baker-group
  • Evaluation of Configurational Entropy Methods from Peptide Folding-Unfolding Simulation
    J. Phys. Chem. B, Vol. 111, No. 49. (13 December 2007), pp. 13807-13813.
    by DW Li, M Khanlarzadeh, J Wang, S Huo, R Bruschweiler
    posted to molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-01-22 12:59:16 as read
  • Metal-Coupled Folding of Cys2His2 Zinc-Finger
    J. Am. Chem. Soc., Vol. 130, No. 3. (23 January 2008), pp. 892-900.
    by W Li, J Zhang, J Wang, W Wang
    posted to metalloregulation molecular_simulation protein_folding by sobolevnrm on 2008-02-20 12:47:57 as read along with 1 group baker-group
  • Flexible ligand-flexible protein docking in protein kinase systems
    Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1784, No. 1. (January 2008), pp. 244-251.
    by Chung F Wong
    posted to drugdesign molecular_simulation protein-ligand_interactions by sobolevnrm on 2008-01-18 16:34:38 as read along with 1 group baker-group
  • A particle-particle, particle-density algorithm for the calculation of electrostatic interactions of particles with slablike geometry
    The Journal of Chemical Physics, Vol. 127, No. 22. (2007), 224102.
    by Alireza S Ghasemi, Alexey Neelov, Stefan Goedecker
    posted to electrostatics mathematics molecular_dynamics molecular_simulation by sobolevnrm on 2008-01-22 12:44:43 as read along with 1 person and 1 group softsimu baker-group
  • 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 protein-ligand_interactions molecular_simulation electrostatics by sobolevnrm on 2008-06-13 11:49:09 as read along with 3 people and 3 groups barry jmccammon biehl McCammon structural_bioinformatics baker-group
  • 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 on 2008-04-22 11:48:56 as read along with 8 people and 5 groups ibuch dimka jwm ttjoseph sangeetha yoel_rf bilab wilsoros Radiation_Damage Stressosome Bioinformatics insilicodrug baker-group
  • Charge Asymmetries in Hydration of Polar Solutes
    J. Phys. Chem. B (6 February 2008)
    by DL Mobley, AE Barber, CJ Fennell, KA Dill
    posted to electrostatics molecular_simulation solvation by sobolevnrm on 2008-03-03 12:35:35 as read along with 3 people and 1 group onufriev dmobley middledomain baker-group
  • Direct Comparisons of Experimental and Calculated Neutron Structure Factors of Pure Solvents as a Method for Force Field Validation
    J. Phys. Chem. B (24 October 2007)
    by JL Thomas, DJ Tobias, AD Mackerell
    posted to molecular_simulation by sobolevnrm on 2007-12-17 12:51:03 as read along with 1 person and 1 group dmobley baker-group
  • Rotation of Lipids in Membranes: MD Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics
    Biophys. J. (11 January 2008), biophysj.107.121806.
    by Jeffrey B Klauda, Mary F Roberts, Alfred G Redfield, Bernard R Brooks, Richard W Pastor
    posted to biomembranes molecular_simulation nmr by sobolevnrm on 2008-02-25 12:11:21 as read along with 2 people and 1 group paulschlesinger sunhwan baker-group
  • Structure of the first- and second-neighbor shells of simulated water: Quantitative relation to translational and orientational order
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 5. (2007)
    by Zhenyu Yan, Sergey V Buldyrev, Pradeep Kumar, Nicolas Giovambattista, Pablo G Debenedetti, Eugene H Stanley
    posted to molecular_simulation solvation by sobolevnrm on 2008-01-08 12:23:35 as read along with 1 group baker-group
  • 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 on 2008-04-15 16:59:38 as read along with 1 group baker-group
  • 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 on 2008-04-15 00:45:50 as read along with 2 people and 1 group paulschlesinger sunhwan baker-group
  • Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints
    The Journal of Chemical Physics, Vol. 127, No. 12. (2007)
    by Ilja V Khavrutskii, Andrew J Mccammon
    posted to biomembranes enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-19 12:31:32 as read along with 1 group baker-group
  • Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
    Biophys. J., Vol. 93, No. 10. (15 November 2007), pp. 3460-3469.
    by Kei Moritsugu, Jeremy C Smith
    posted to enhanced_sampling molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-11-01 11:59:51 as read along with 3 people and 1 group choonpeng aqeel hmk baker-group
  • 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 protein-membrane_interactions molecular_simulation molecular_dynamics enhanced_sampling biomembranes by sobolevnrm on 2008-05-19 11:38:22 as read along with 1 group baker-group
  • Local feature analysis: A statistical theory for reproducible essential dynamics of large macromolecules
    Proteins: Structure, Function, and Bioinformatics, Vol. 64, No. 2. (2006), pp. 391-403.
    by Zhiyong Zhang, Willy Wriggers
    posted to molecular_dynamics molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-08-22 20:24:51 as read along with 1 group baker-group
  • 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 molecular_simulation molecular_dynamics electrostatics by sobolevnrm on 2008-06-18 11:50:09 as read along with 1 group baker-group
  • 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 molecular_simulation molecular_dynamics electrostatics by sobolevnrm on 2008-05-09 11:02:47 as read along with 3 people and 1 group mikaellund OndrejMarsalek michaelbussmann baker-group
  • Phase diagram of water in carbon nanotubes
    Proceedings of the National Academy of Sciences, Vol. 105, No. 1. (8 January 2008), pp. 39-43.
    by Daisuke Takaiwa, Itaru Hatano, Kenichiro Koga, Hideki Tanaka
    posted to molecular_dynamics molecular_simulation nanotech solvation by sobolevnrm on 2008-02-13 12:55:12 as read along with 1 group baker-group
  • Ion Pairing as a Possible Clue for Discriminating between Sodium and Potassium in Biological and Other Complex Environments
    J. Phys. Chem. B, Vol. 111, No. 51. (27 December 2007), pp. 14077-14079.
    by B Jagoda-Cwiklik, R Vacha, M Lund, M Srebro, P Jungwirth
    posted to electrostatics molecular_simulation solvation by sobolevnrm on 2008-01-10 12:54:04 as read along with 2 people and 1 group mikaellund robertvacha baker-group
  • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Anna CV Johansson, Erik Lindahl
    posted to biomembranes molecular_simulation by sobolevnrm on 2007-09-23 15:46:51 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • 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 structure solvation molecular_simulation by sobolevnrm on 2008-04-28 14:56:20 as read along with 5 people and 3 groups ana barry bicko blackbart medic0747 baker-group structural_bioinformatics Bioinformatics
  • Methodological problems in pressure profile calculations for lipid bilayers
    The Journal of Chemical Physics, Vol. 122, No. 12. (2005)
    by Jacob Sonne, Flemming Y Hansen, Günther H Peters
    posted to biomembranes molecular_dynamics molecular_simulation by sobolevnrm on 2007-12-18 13:06:36 as read along with 1 group baker-group
  • 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 solvation multiscale molecular_simulation by sobolevnrm on 2008-05-22 12:03:41 as read along with 1 group baker-group
  • Short range order and collective dynamics of DMPC bilayers. A comparison between molecular dynamics simulations, x-ray, and neutron scattering experiments
    Biophys. J. (13 July 2007), biophysj.107.104885.
    by Jochen S Hub, Tim Salditt, Maikel C Rheinstadter, Bert L de Groot
    posted to biomembranes experimental_methodology molecular_dynamics molecular_simulation by sobolevnrm on 2007-11-01 11:13:58 as read along with 3 people and 1 group dimka char paulschlesinger baker-group
  • Construction of effective free energy landscape from single-molecule time series
    Proceedings of the National Academy of Sciences, Vol. 104, No. 49. (4 December 2007), pp. 19297-19302.
    by Akinori Baba, Tamiki Komatsuzaki
    posted to mathematics molecular_simulation quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-01-10 12:46:56 as read along with 6 people and 1 group hsekiguc hmk zwang cactus Diego_Prada arnaudriegert baker-group
  • Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by D Hamelberg, CAF de Oliveira, JA Mccammon
    posted to diffusion enhanced_sampling molecular_simulation by sobolevnrm on 2007-11-01 11:10:19 as read along with 1 group baker-group
    • Note: You may cite this page as: http://www.citeulike.org/tag/molecular_simulation

    Result page: 1 2 3 Next RIS BibTeX
    CiteULike organises scholarly (or academic) papers or literature and provides bibliographic (which means it makes bibliographies) for universities and higher education establishments. It helps undergraduates and postgraduates. People studying for PhDs or in postdoctoral (postdoc) positions. The service is similar in scope to EndNote or RefWorks or any other reference manager like BibTeX, but it is a social bookmarking service for scientists and humanities researchers.