Registrer deg | Logg på | FAQ      [?] 
Recent | Unread | Search | Authors | Tags | Export

sobolevnrms molecular_dynamics [439 articles]

Artikler nylig sendt til sobolevnrms bibliotek klassifisert med nøkkelordet molecular_dynamics. You can also see everyone's molecular_dynamics.
  • Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data
    Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 379-386.
    by Catherine Kehl, Andrew M Simms, Rudesh D Toofanny, Valerie Daggett
    posted to molecular_dynamics database bioinformatics by sobolevnrm on 2008-07-10 11:58:23 as read along with 1 group baker-group
  • Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations
    Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 369-377.
    by Andrew M Simms, Rudesh D Toofanny, Catherine Kehl, Noah C Benson, Valerie Daggett
    posted to molecular_dynamics database bioinformatics by sobolevnrm on 2008-07-10 11:56:38 as read along with 1 group baker-group
  • Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations
    Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 353-368.
    by David A Beck, Amanda L Jonsson, Dustin R Schaeffer, Kathryn A Scott, Ryan Day, Rudesh D Toofanny, Darwin O Alonso, Valerie Daggett
    posted to protein_folding molecular_dynamics database bioinformatics by sobolevnrm on 2008-07-10 11:55:38 as read along with 1 group baker-group
  • 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 molecular_simulation molecular_dynamics biomembranes by sobolevnrm on 2008-07-09 11:35:52 as read along with 1 group baker-group
  • Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
    Proceedings of the National Academy of Sciences, Vol. 105, No. 27. (2008), pp. 9204-9209.
    by JZ Ruscio, D Kumar, M Shukla, MG Prisant, TM Murali, AV Onufriev
    posted to molecular_dynamics diffusion allostery by sobolevnrm on 2008-07-09 02:31:00 as read along with 1 group baker-group
  • Local spectral time splitting method for first- and second-order partial differential equations
    Journal of Computational Physics, Vol. 206, No. 2. (1 July 2005), pp. 727-780.
    by Sining Yu, Shan Zhao, GW Wei
    posted to molecular_dynamics mathematics kinetics by sobolevnrm on 2008-07-01 03:10:54 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
  • 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
  • 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
  • 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_simulation molecular_dynamics by sobolevnrm on 2008-06-06 11:28:06 as read along with 1 group baker-group
  • Role of Hydrogen Bonding and Helix−Lipid Interactions in Transmembrane Helix Association
    J. Am. Chem. Soc., Vol. 130, No. 20. (21 May 2008), pp. 6456-6462.
    by Jinhyuk Lee, Wonpil Im
    posted to protein-membrane_interactions molecular_dynamics biomembranes by sobolevnrm on 2008-05-22 12:06:08 as read along with 1 group baker-group
  • The MARTINI Coarse-Grained Force Field: Extension to Proteins
    J. Chem. Theory Comput. (16 April 2008)
    by Luca Monticelli, Senthil K Kandasamy, Xavier Periole, Ronald G Larson, Peter D Tieleman, Siewert-Jan Marrink
    posted to multiscale molecular_dynamics biomembranes by sobolevnrm on 2008-05-19 11:39:48 as read along with 5 people and 1 group softsimu Ema aqeel DanielParton middledomain 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
  • The Implementation of Slab Geometry for Membrane-Channel Molecular Dynamics Simulations
    Biophys. J., Vol. 85, No. 1. (1 July 2003), pp. 97-107.
    by David Bostick, Max L Berkowitz
    posted to molecular_dynamics electrostatics biomembranes by sobolevnrm on 2008-05-13 11:45:01 as read along with 2 people and 1 group paulschlesinger softsimu baker-group
  • Normal mode partitioning of Langevin dynamics for biomolecules
    The Journal of Chemical Physics, Vol. 128, No. 14. (2008)
    by Christopher R Sweet, Paula Petrone, Vijay S Pande, Jesús A Izaguirre
    posted to quasiharmonic-models_elastic-network_gnm_nma_pca_etc multiscale molecular_dynamics by sobolevnrm on 2008-05-12 11:53:54 as read along with 2 people and 1 group aqeel paulschlesinger 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
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins (in press)
    by M Machuqueiro, AM Baptista
    posted to solvation pka molecular_dynamics by sobolevnrm on 2008-04-30 11:14:29 as read along with 1 group baker-group
  • Molecular dynamics simulation of nucleic acids: Successes, limitations, and promise
    Biopolymers, Vol. 56, No. 4. (2001), pp. 232-256.
    by Iii Cheatham, MA Young
    posted to solvation nucleic_acids molecular_dynamics electrostatics by sobolevnrm on 2008-04-29 19:38:40 as read along with 1 group baker-group
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to molecular_dynamics metalloregulation allostery by sobolevnrm on 2008-04-26 14:52:57 as read along with 2 people and 2 groups barry skoddet structural_bioinformatics baker-group
  • 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 solvation molecular_simulation molecular_dynamics by sobolevnrm on 2008-04-26 14:43:02 as read along with 1 person and 1 group dmobley 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
  • Implementation and testing of stable, fast implicit solvation in molecular dynamics using the smooth-permittivity finite difference Poisson-Boltzmann method
    Journal of Computational Chemistry, Vol. 25, No. 16. (2004), pp. 2049-2064.
    by Ninad V Prabhu, Peijuan Zhu, Kim A Sharp
    posted to electrostatics molecular_dynamics solvation by sobolevnrm on 2008-04-18 11:25:59 as read along with 1 person and 1 group onufriev 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
  • 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 on 2008-04-16 11:29:21 as read along with 1 person and 1 group paulschlesinger 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
  • Combination of molecular dynamics method and 3D-RISM theory for conformational sampling of large flexible molecules in solution
    Journal of Computational Chemistry, Vol. 29, No. 6. (2008), pp. 871-882.
    by Tatsuhiko Miyata, Fumio Hirata
    posted to statistical_mechanics solvation molecular_dynamics integral_equation by sobolevnrm on 2008-04-15 11:53:50 as read along with 1 group baker-group
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to electrostatics molecular_dynamics pka solvation by sobolevnrm on 2008-03-28 10:50:31 as read along with 2 people and 1 group RamuAnandakrishnan dmobley baker-group
  • 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 on 2008-03-27 11:18:16 as read along with 1 person and 1 group dmobley baker-group
  • 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 on 2008-03-27 10:52:18 as read along with 1 person and 1 group dmobley baker-group
  • 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 on 2008-03-27 10:49:38 as read along with 1 group baker-group
  • 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 on 2008-03-14 11:18:27 as read along with 1 person and 1 group barry baker-group
  • 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 on 2008-03-14 11:15:30 as read along with 3 people and 1 group ruvido zwang phoenixzxl 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
  • 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
  • A molecular dynamics study of the packing structures in monolayers of partially fluorinated amphiphiles
    The Journal of Chemical Physics, Vol. 96, No. 2. (1992), pp. 1352-1366.
    by Seokmin Shin, Nancy Collazo, Stuart A Rice
    posted to interfaces molecular_dynamics by sobolevnrm on 2008-03-05 17:33:29 as read along with 1 person and 1 group sunnytov baker-group
  • GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation
    J. Chem. Theory Comput. (2 February 2008)
    by B Hess, C Kutzner, D Vanderspoel, E Lindahl
    posted to molecular_dynamics software by sobolevnrm on 2008-02-29 12:24:21 as read along with 6 people and 1 group loison daevans mmuecke r2s2 middledomain OndrejMarsalek baker-group
  • Theory for an order-driven disruption of the liquid state in water
    The Journal of Chemical Physics, Vol. 128, No. 4. (2008)
    by Jeremy L England, Sanghyun Park, Vijay S Pande
    posted to molecular_dynamics solvation by sobolevnrm on 2008-02-29 12:20:30 as read along with 1 person and 1 group dmobley baker-group
  • Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method
    The Journal of Chemical Physics, Vol. 128, No. 4. (2008)
    by Ilja V Khavrutskii, Joachim Dzubiella, Andrew J Mccammon
    posted to electrostatics molecular_dynamics molecular_simulation solvation by sobolevnrm on 2008-02-27 12:28:57 as read along with 1 group baker-group
  • A DMPA Langmuir Monolayer Study: From Gas to Solid Phase. An Atomistic Description by Molecular Dynamics Simulation
    Langmuir, Vol. 24, No. 5. (4 March 2008), pp. 1823-1828.
    by JJ Giner-Casares, L Camacho, MT Martin-Romero, JJ Lopezcascales
    posted to biomembranes molecular_dynamics by sobolevnrm on 2008-02-27 12:22:48 as read along with 1 group baker-group
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Miguel Machuqueiro, António M Baptista
    posted to molecular_dynamics pka by sobolevnrm on 2008-02-25 12:09:47 as read along with 2 people and 1 group skoddet sunhwan baker-group
  • Dynamics of the Acetylcholinesterase Tetramer
    Biophys. J., Vol. 94, No. 4. (15 February 2008), pp. 1144-1154.
    by Alemayehu A Gorfe, Chia-En A Chang, Ivaylo Ivanov, Andrew J Mccammon
    posted to acetylcholinesterase diffusion kinetics molecular_dynamics quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-02-22 12:09:50 as read along with 1 group baker-group
  • Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design
    Proceedings of the National Academy of Sciences, Vol. 105, No. 3. (22 January 2008), pp. 901-906.
    by Jin Liu, Ruth Nussinov
    posted to allostery molecular_dynamics by sobolevnrm on 2008-02-21 12:30:30 as read along with 1 person and 1 group cactus 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
  • A Proposed Time-Resolved X-Ray Scattering Approach to Track Local and Global Conformational Changes in Membrane Transport Proteins
    Structure, Vol. 16, No. 1. (8 January 2008), pp. 21-28.
    by Magnus Andersson, Jonathan Vincent, David van der Spoel, Jan Davidsson, Richard Neutze
    posted to allostery experimental_methodology molecular_dynamics by sobolevnrm on 2008-02-13 12:52:10 as read along with 1 group baker-group
  • Transmembrane Helix Tilting: Insights from Calculating the Potential of Mean Force
    Physical Review Letters, Vol. 100, No. 1. (2008)
    by Jinhyuk Lee, Wonpil Im
    posted to biomembranes molecular_dynamics protein-membrane_interactions by sobolevnrm on 2008-02-13 12:45:29 as read along with 1 group baker-group
  • Structure and Dynamics of Poly(T) Single-Strand DNA: Implications toward CPD Formation
    J. Phys. Chem. B, Vol. 111, No. 51. (27 December 2007), pp. 14398-14404.
    by AT Johnson, O Wiest
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm on 2008-02-01 12:50:34 as read along with 1 group baker-group
  • An extended dynamical hydration shell around proteins.
    Proc Natl Acad Sci U S A, Vol. 104, No. 52. (26 December 2007), pp. 20749-20752.
    by S Ebbinghaus, SJ Kim, M Heyden, X Yu, U Heugen, M Gruebele, DM Leitner, M Havenith
    posted to diffusion experimental_methodology kinetics molecular_dynamics solvation by sobolevnrm on 2008-01-31 12:59:41 as read along with 1 person and 1 group choonpeng baker-group
  • Effect of Local Anesthetic Lidocaine on Electrostatic Properties of a Lipid Bilayer
    Biophys. J., Vol. 94, No. 2. (15 January 2008), pp. 525-531.
    by Carl-Johan Hogberg, Alexander P Lyubartsev
    posted to biomembranes electrostatics molecular_dynamics molecular_simulation by sobolevnrm on 2008-01-31 12:58:11 as read along with 1 person and 1 group paulschlesinger baker-group
  • Coarse-grained models of protein folding: toy models or predictive tools?
    Curr Opin Struct Biol (19 December 2007)
    by Cecilia Clementi
    posted to molecular_dynamics molecular_simulation multiscale by sobolevnrm on 2008-01-30 12:46:07 as read along with 2 people and 1 group choonpeng nh baker-group
  • Simulation of the Pressure and Temperature Folding/Unfolding Equilibrium of a Small RNA Hairpin
    J. Am. Chem. Soc., Vol. 130, No. 3. (23 January 2008), pp. 815-817.
    by AE Garcia, D Paschek
    posted to molecular_dynamics molecular_simulation nucleic_acids by sobolevnrm on 2008-01-30 12:42:58 as read along with 1 group baker-group
    • NB: Du kan sitere denne siden som: http://www.citeulike.org/user/sobolevnrm/tag/molecular_dynamics

    Result page: 1 2 3 4 5 6 7 8 9 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.