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Group: baker-group - with tag molecular_dynamics [436 articles]

Neue Artikel von Mitliedern der Gruppe baker-group Gruppe with tag 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 bioinformatics database molecular_dynamics by sobolevnrm to the group baker-group on 2008-07-10 11:58:23 as read
  • 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 bioinformatics database molecular_dynamics by sobolevnrm to the group baker-group on 2008-07-10 11:56:38 as read
  • 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 bioinformatics database molecular_dynamics protein_folding by sobolevnrm to the group baker-group on 2008-07-10 11:55:39 as read
  • 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
  • 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 allostery diffusion molecular_dynamics by sobolevnrm to the group baker-group on 2008-07-09 02:31:01 as read
  • 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 kinetics mathematics molecular_dynamics by sobolevnrm to the group baker-group on 2008-07-01 03:10:54 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
  • 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
  • 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
  • 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 biomembranes molecular_dynamics protein-membrane_interactions by sobolevnrm to the group baker-group on 2008-05-22 12:06:08 as read
  • 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 biomembranes molecular_dynamics multiscale by sobolevnrm to the group baker-group on 2008-05-19 11:39:49 as read along with 6 people and 1 group Marine middledomain Ema aqeel DanielParton softsimu Molecular dynamics in MSU
  • 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
  • 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 biomembranes electrostatics molecular_dynamics by sobolevnrm to the group baker-group on 2008-05-13 11:45:02 as read along with 2 people paulschlesinger softsimu
  • 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 molecular_dynamics multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-12 11:53:54 as read along with 2 people paulschlesinger aqeel
  • 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
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins (in press)
    by M Machuqueiro, AM Baptista
    posted to molecular_dynamics pka solvation by sobolevnrm to the group baker-group on 2008-04-30 11:14:29 as read
  • 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 electrostatics molecular_dynamics nucleic_acids solvation by sobolevnrm to the group baker-group on 2008-04-29 19:38:40 as read
  • 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 allostery metalloregulation molecular_dynamics by sobolevnrm to the group baker-group on 2008-04-26 14:52:57 as read along with 2 people and 1 group skoddet barry structural_bioinformatics
  • 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
  • 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
  • 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 to the group baker-group on 2008-04-18 11:25:59 as read along with 1 person onufriev
  • 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
  • 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
  • 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 molecular_dynamics solvation statistical_mechanics by sobolevnrm to the group baker-group on 2008-04-15 11:53:50 as read
  • 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 to the group baker-group on 2008-03-28 10:50:31 as read along with 3 people 6rheology RamuAnandakrishnan dmobley
  • 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
  • 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
  • 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 to the group baker-group on 2008-03-12 11:29:44 as read
  • 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 to the group baker-group on 2008-03-12 11:07:09 as read along with 1 person jlh64
  • 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 to the group baker-group on 2008-03-05 17:33:29 as read along with 1 person sunnytov
  • 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 to the group baker-group on 2008-02-29 12:24:22 as read along with 7 people jwm daevans mmuecke r2s2 middledomain OndrejMarsalek loison
  • 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 to the group baker-group on 2008-02-29 12:20:31 as read along with 1 person dmobley
  • 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 to the group baker-group on 2008-02-27 12:28:57 as read
  • 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 to the group baker-group on 2008-02-27 12:22:48 as read
  • 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 to the group baker-group on 2008-02-25 12:09:47 as read along with 2 people sunhwan skoddet
  • 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 to the group baker-group on 2008-02-22 12:09:51 as read
  • 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 to the group baker-group on 2008-02-21 12:30:30 as read along with 1 person cactus
  • 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 to the group baker-group on 2008-02-13 12:55:12 as read
  • 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 to the group baker-group on 2008-02-13 12:52:10 as read along with 1 person r2s2
  • 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 to the group baker-group on 2008-02-13 12:45:30 as read
  • 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 to the group baker-group on 2008-02-01 12:50:34 as read
  • 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 to the group baker-group on 2008-01-31 12:59:41 as read along with 1 person choonpeng
  • 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 to the group baker-group on 2008-01-31 12:58:11 as read along with 1 person paulschlesinger
  • 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 to the group baker-group on 2008-01-30 12:46:07 as read along with 2 people choonpeng nh
  • 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 to the group baker-group on 2008-01-30 12:42:58 as read
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