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barrys md_simulation [68 articles]

Neue Publikationen in barrys Bibliothek eingetragen unter dem Bezeichner: md_simulation. You can also see everyone's md_simulation.
  • notes Rate of Loop Formation in Peptides: A Simulation Study
    Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 556-565.
    by Matthias J Feige, Emanuele Paci
    posted to md_simulation by barry on 2008-08-29 19:03:07 as ** along with 2 groups McCammon structural_bioinformatics
  • Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin
    Journal of Molecular Biology, Vol. 381, No. 5. (19 September 2008), pp. 1407-1420.
    by Yang Yang, Haibo Yu, Qiang Cui
    posted to md_simulation molecular_motors motor_model myosin qm by barry on 2008-08-18 20:21:10 as ** along with 2 groups Bioinformatics structural_bioinformatics
  • Accelerated Superposition State Molecular Dynamics for Condensed Phase Systems
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 560-568.
    by Michele Ceotto, Gary S Ayton, Gregory A Voth
    posted to accelerated_md md_simulation by barry on 2008-07-08 01:21:07 as ** along with 1 group McCammon
  • 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 md_simulation replica_exchange by barry on 2008-07-08 01:17:17 as ** along with 3 people and 3 groups agrossfield sobolevnrm loison baker-group structural_bioinformatics McCammon
  • 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 binding free_energy md_simulation protein-ligand by barry on 2008-07-08 01:12:03 as ** along with 3 people and 3 groups jmccammon biehl sobolevnrm baker-group structural_bioinformatics McCammon
  • From the Cover: A dry ligand-binding cavity in a solvated protein
    Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301.
    by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle
    posted to free_energy md_simulation protein-ligand solvation by barry on 2008-07-08 01:11:30 as ** along with 2 people and 3 groups jmccammon sobolevnrm structural_bioinformatics McCammon baker-group
  • Pathway and Endpoint Free Energy Calculations for Cyclic Nucleotide Binding to HCN Channels
    Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. L90-92.
    by Lei Zhou, Steven A Siegelbaum
    posted to binding electrostatics free_energy md_simulation protein-ligand by barry on 2008-07-08 00:49:17 as ** along with 1 person and 1 group jmccammon McCammon
  • notes Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins
    Structure, Vol. 16, No. 6. (11 June 2008), pp. 885-896.
    by Alemayehu A Gorfe, Barry J Grant, Andrew J Mccammon
    posted to md_simulation mine ntpases pca protein_dynamics protein_structure ras by barry on 2008-06-10 22:34:01 as read along with 2 groups Bioinformatics structural_bioinformatics
  • notes Investigating protein dynamics in collective coordinate space.
    Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 164-169.
    by A Kitao, N Go
    posted to md_simulation nma pca protein_dynamics protein_structure review by barry on 2008-04-29 00:04:52 as ** along with 4 people and 1 group ttjoseph ffranca choonpeng sobolevnrm baker-group
  • notes Collective protein dynamics in relation to function
    Current Opinion in Structural Biology, Vol. 10, No. 2. (1 April 2000), pp. 165-169.
    by Herman JC Berendsen, Steven Hayward
    posted to md_simulation nma pca protein_dynamics protein_structure review by barry on 2008-04-29 00:03:09 as **
  • 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 allosteric md_simulation by barry on 2008-04-27 22:02:29 as * along with 2 people and 2 groups sobolevnrm skoddet baker-group structural_bioinformatics
  • Development of polyphosphate parameters for use with the AMBER force field
    Journal of Computational Chemistry, Vol. 24, No. 9. (2003), pp. 1016-1025.
    by Kristin L Meagher, Luke T Redman, Heather A Carlson
    posted to amber md_simulation by barry on 2008-04-25 20:57:25 as ** along with 1 person blackbart
  • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (2006), pp. 712-725.
    by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling
    posted to amber ff99sb md_simulation by barry on 2008-04-25 20:56:25 as ** along with 7 people baaden lna allmensch choonpeng kazemi GermanErlenkamp RamuAnandakrishnan
  • Very fast empirical prediction and rationalization of protein pKa values.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 704-721.
    by H Li, AD Robertson, JH Jensen
    posted to bioinf_methods md_simulation pka by barry on 2008-04-25 20:55:37 as ** along with 4 people and 1 group bicko sim82 sunhwan mschofie Bioinformatics
  • notes 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 coarse-grained domain_motions md_simulation nma by barry on 2008-03-20 01:18:55 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Nucleotide-Mediated Conformational Changes of Monomeric Actin and Arp3 Studied by Molecular Dynamics Simulations.
    J Mol Biol (28 November 2007)
    by Paul Dalhaimer, Thomas D D Pollard, Brad J J Nolen
    posted to actin arp3 md_simulation protein_structure subfamily by barry on 2008-01-14 19:48:54 as ****
  • Wordom: a program for efficient analysis of molecular dynamics simulations
    Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627.
    by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch
    posted to bioinf_methods md_simulation by barry on 2007-11-27 23:33:00 as ** along with 6 people and 2 groups jyuh tmmurali choonpeng hmk sobolevnrm LamBras structural_bioinformatics baker-group
  • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    Proceedings of the National Academy of Sciences (13 November 2007), 0706443104.
    by Karunesh Arora, Charles L Brooks
    posted to allosteric kinases md_simulation by barry on 2007-11-27 23:23:58 as ** along with 5 people and 2 groups allmensch cactus sobolevnrm jlh64 karunesh structural_bioinformatics baker-group
  • Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms
    J. Chem. Theory Comput. (6 October 2007)
    by J Shao, SW Tanner, N Thompson, TE Cheatham
    posted to clustering md_simulation protein_structure by barry on 2007-10-26 22:44:54 as **** along with 5 people and 2 groups daevans sobolevnrm LamBras allmensch GermanErlenkamp structural_bioinformatics baker-group
  • How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: A theoretical study.
    Protein Sci (7 March 2006)
    by Yuhui Cheng, Yingkai Zhang, J Andrew A McCammon
    posted to correlated_motions kinases md_simulation pca phosphorylation by barry on 2007-10-12 01:11:45 as * along with 1 person and 1 group nknii TCR_Signaling
  • Insights into Correlated Motions and Long-Range Interactions in CheY Derived from Molecular Dynamics Simulations.
    Biophys J, Vol. 92, No. 6. (15 March 2007), pp. 2062-2079.
    by MH Knaggs, FR Salsbury, MH Edgell, JS Fetrow
    posted to contacts correlated_motions md_simulation by barry on 2007-10-12 01:04:36 as * along with 1 person choonpeng
  • Complementarity of Structure Ensembles in Protein-Protein Binding
    Structure, Vol. 12, No. 12. (December 2004), pp. 2125-2136.
    by Raik Gruenberg, Johan Leckner, Michael Nilges
    posted to md_simulation protein_dynamics protein_protein by barry on 2007-10-02 03:05:14 as read along with 3 people and 3 groups lna allmensch cursonivel1 structural_bioinformatics Bioinformatics cursonivel1
  • Dihedral angle principal component analysis of molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 126, No. 24. (2007)
    by Alexandros Altis, Phuong H Nguyen, Rainer Hegger, Gerhard Stock
    posted to md_simulation pca torsion_angles by barry on 2007-09-27 20:06:59 as *** along with 2 people and 1 group ruvido nh structural_bioinformatics
  • Full correlation analysis of conformational protein dynamics
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Oliver F Lange, Helmut Grubmüller
    posted to md_simulation nma pca by barry on 2007-09-27 19:39:10 as read along with 3 people and 1 group choonpeng sobolevnrm LamBras baker-group
  • Sampling of near-native protein conformations during protein structure refinement using a coarse-grained model, normal modes, and molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Andrew W Stumpff-Kane, Katarzyna Maksimiak, Michael S Lee, Michael Feig
    posted to comparative_model md_simulation nma protein_structure structure_refinement by barry on 2007-09-27 18:43:03 as read along with 1 person and 2 groups sobolevnrm structural_bioinformatics baker-group
  • Dihedral angle principal component analysis of molecular dynamics simulations
    Journal of Chemical Physics, Vol. 126 (2007)
    by A Altis, PH Nguyen, R Hegger, G Stock
    posted to md_simulation pca torsion_angles by barry on 2007-08-28 02:10:54 as ** along with 1 person and 3 groups sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • Coarse-grained molecular dynamics simulations of membrane proteins and peptides
    Journal of Structural Biology, Vol. 157, No. 3. (2007), pp. 593-605.
    by PJ Bond, J Holyoake, A Ivetac, S Khalid, MSP Sansom
    posted to coarse-grained ion_channels md_simulation by barry on 2007-08-28 01:58:49 as *** along with 1 person and 3 groups sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • Characterization of Protein Conformational States by Normal-Mode Frequencies
    J. Am. Chem. Soc. (23 August 2007)
    by BA Hall, SL Kaye, A Pang, R Perera, PC Biggin
    posted to clustering md_simulation nma pca protein_structure by barry on 2007-08-27 19:15:41 as **** along with 4 people and 3 groups aqeel choonpeng sobolevnrm LamBras structural_bioinformatics Bioinformatics baker-group
  • Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.
    Proc Natl Acad Sci U S A, Vol. 101, No. 51. (21 December 2004), pp. 17658-17663.
    by M Ota, M Ikeguchi, A Kidera
    posted to clustering contacts md_simulation protein_folding protein_structure by barry on 2007-08-10 18:38:42 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Unfolding Pathways of Goat [alpha]-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories
    Journal of Molecular Biology, Vol. 371, No. 5. (31 August 2007), pp. 1354-1364.
    by Tomotaka Oroguchi, Mitsunori Ikeguchi, Motonori Ota, Kunihiro Kuwajima, Akinori Kidera
    posted to clustering contacts md_simulation protein_folding protein_structure by barry on 2007-08-10 18:36:13 as ** along with 1 person and 2 groups choonpeng structural_bioinformatics Bioinformatics
  • Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3.
    Biophys. J., Vol. 73, No. 3. (1 September 1997), pp. 1147-1159.
    by GE Arnold, RL Ornstein
    posted to correlated_motions distance_matrices md_simulation protein_sequence by barry on 2007-07-26 02:46:16 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Ensemble-Based Convergence Analysis of Biomolecular Trajectories
    Biophys. J., Vol. 91, No. 1. (1 July 2006), pp. 164-172.
    by Edward Lyman, Daniel M Zuckerman
    posted to md_simulation by barry on 2007-04-27 17:36:16 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Equilibration of experimentally determined protein structures for molecular dynamics simulation
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 6. (2006)
    by Emily B Walton, Krystyn J Vanvliet
    posted to md_simulation nma by barry on 2007-04-27 17:32:57 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping.
    Proteins, Vol. 64, No. 1. (1 July 2006), pp. 210-218.
    by S Mesentean, S Fischer, JC Smith
    posted to clustering md_simulation pca by barry on 2007-03-27 00:20:10 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations
    PLoS Computational Biology, Vol. 3, No. 2. (1 February 2007), e21.
    by Haibo Yu, Liang Ma, Yang Yang, Qiang Cui
    posted to md_simulation molecular_motors myosin pmf by barry on 2007-02-12 23:41:33 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 2. (2006), pp. 347-361.
    by Kim Sharp, John J Skinner
    posted to protein_structure protein_dynamics md_simulation bioinf_methods allosteric by barry on 2007-01-30 20:09:59 as **** along with 3 people and 3 groups lna choonpeng sobolevnrm structural_bioinformatics Bioinformatics baker-group
  • Exploration of the conformational space of myosin recovery stroke via molecular dynamics
    Biophysical Chemistry, Vol. 125, No. 1. (January 2007), pp. 127-137.
    by Hyung-June Woo
    posted to md_simulation myosin by barry on 2006-12-08 18:58:04 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Can MM-PBSA calculations predict the specificities of protein kinase inhibitors?
    Journal Of Computational Chemistry, Vol. 27, No. 16. (December 2006), pp. 1990-2007.
    by Christopher S Page, Paul A Bates
    posted to drug_design md_simulation mm-pbsa by barry on 2006-12-08 18:52:33 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Ion selectivity in potassium channels
    Biophysical Chemistry, Vol. 124, No. 3. (1 December 2006), pp. 279-291.
    by Sergei Y Noskov, Benoit Roux
    posted to ion_channels ksca md_simulation by barry on 2006-12-08 18:50:17 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • 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 ion_channels md_simulation pmf by barry on 2006-12-08 18:46:14 as * along with 2 people and 3 groups sobolevnrm ibuch structural_bioinformatics Bioinformatics baker-group
  • Can principal components yield a dimension reduced description of protein dynamics on long time scales?
    The Journal Of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Vol. 110, No. 45. (16 November 2006), pp. 22842-22852.
    by Oliver F Lange, Helmut Grubmuller
    posted to md_simulation pca by barry on 2006-12-08 18:42:44 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme.
    Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62.
    by JH Lin, AL Perryman, JR Schames, JA McCammon
    posted to bioinf_methods docking drug_design md_simulation protein_dynamics protein_structure by barry on 2006-09-07 20:06:11 as ** along with 4 people and 3 groups blackbart kazemi sobolevnrm LamBras structural_bioinformatics Bioinformatics baker-group
  • Dynamical properties of fasciculin-2
    Proteins: Structure, Function, and Genetics, Vol. 36, No. 4. (1999), pp. 447-453.
    by Nathan A Baker, Volkhard Helms, Andrew J Mccammon
    posted to md_simulation protein_dynamics protein_structure by barry on 2006-07-22 18:38:37 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Flexibility and conformational entropy in protein-protein binding.
    Structure, Vol. 14, No. 4. (April 2006), pp. 683-693.
    by R Grünberg, M Nilges, J Leckner
    posted to md_simulation protein_dynamics protein_protein by barry on 2006-05-22 19:20:49 as ** along with 4 people and 2 groups pansapiens lna aqeel allmensch structural_bioinformatics Bioinformatics
  • Flexibility and conformational entropy in protein-protein binding
    Structure (London, England: 1993), Vol. 14, No. 4. (April 2006), pp. 683-693.
    by Raik Grunberg, Michael Nilges, Johan Leckner
    posted to md_simulation protein_dynamics protein_protein protein_structure by barry on 2006-05-08 20:05:12 as *** along with 1 person and 5 groups joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water.
    Proteins, Vol. 22, No. 1. (May 1995), pp. 45-54.
    by DM van Aalten, A Amadei, AB Linssen, VG Eijsink, G Vriend, HJ Berendsen
    posted to md_simulation pca protein_dynamics protein_structure by barry on 2006-03-17 20:07:25 as read along with 2 groups structural_bioinformatics Bioinformatics
  • Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus
    Structure, Vol. 14, No. 3. (March 2006), pp. 437-449.
    by Peter L Freddolino, Anton S Arkhipov, Steven B Larson, Alexander Mcpherson, Klaus Schulten
    posted to md_simulation protein_structure by barry on 2006-03-15 07:47:21 as * along with 1 person and 2 groups RamuAnandakrishnan structural_bioinformatics Bioinformatics
  • notes Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion
    Journal of Molecular Biology, Vol. 351, No. 2. (12 August 2005), pp. 345-354.
    by Nobuyuki Ota, David A Agard
    posted to allosteric contacts correlated_motions correlated_mutations md_simulation by barry on 2006-01-24 18:24:55 as **** along with 3 people and 2 groups pansapiens lna choonpeng structural_bioinformatics Bioinformatics
  • The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis
    Journal of Molecular Biology, Vol. 356, No. 1. (10 February 2006), pp. 237-247.
    by Yifei Kong, Jianpeng Ma, Martin Karplus, William N Lipscomb
    posted to allosteric md_simulation protein_structure by barry on 2006-01-16 20:34:23 as ** along with 2 people and 2 groups ruvido higueruelo structural_bioinformatics Bioinformatics
  • Molecular dynamics studies of proteins
    Current Opinion in Structural Biology, Vol. 3, No. 2. (April 1993), pp. 277-281.
    by Wilfred F van Gunsteren
    posted to md_simulation nmr protein_dynamics review by barry on 2006-01-09 21:03:10 as read along with 2 groups structural_bioinformatics Bioinformatics
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