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barry's md_simulation [66 articles]

Recent papers added to barry's library classified by the tag md_simulation. You can also see everyone's md_simulation.
  • 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 md_simulation accelerated_md 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 replica_exchange md_simulation by barry on 2008-07-08 01:17:17 as ** along with 3 people and 3 groups loison sobolevnrm agrossfield McCammon structural_bioinformatics 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 md_simulation free_energy binding by barry on 2008-07-08 01:12:03 as ** along with 3 people and 3 groups sobolevnrm jmccammon biehl McCammon structural_bioinformatics baker-group
  • 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 solvation protein-ligand md_simulation free_energy by barry on 2008-07-08 01:11:30 as ** along with 2 people and 3 groups sobolevnrm jmccammon baker-group McCammon structural_bioinformatics
  • 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 protein-ligand md_simulation free_energy electrostatics binding 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 ras protein_structure protein_dynamics pca ntpases mine md_simulation by barry on 2008-06-10 22:34:01 as read along with 2 groups structural_bioinformatics 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 review protein_structure protein_dynamics pca nma md_simulation by barry on 2008-04-29 00:04:52 as ** along with 4 people and 1 group sobolevnrm choonpeng ttjoseph ffranca 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 review protein_structure protein_dynamics pca nma md_simulation 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 md_simulation allosteric by barry on 2008-04-27 22:02:29 as * along with 2 people and 2 groups skoddet sobolevnrm structural_bioinformatics baker-group
  • 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 md_simulation amber 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 md_simulation ff99sb amber by barry on 2008-04-25 20:56:25 as ** along with 5 people baaden lna allmensch choonpeng kazemi
  • 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 pka md_simulation bioinf_methods by barry on 2008-04-25 20:55:37 as ** along with 4 people and 1 group mschofie sunhwan bicko sim82 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 GermanErlenkamp allmensch daevans sobolevnrm LamBras 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 LamBras aqeel choonpeng sobolevnrm 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 1 person and 3 groups sobolevnrm 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 higueruelo ruvido 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
  • Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales
    The Journal Of Chemical Physics, Vol. 123, No. 14. (8 October 2005), pp. 144910-144910.
    by Burak Alakent, Mehmet C Camurdan, Pemra Doruker
    posted to md_simulation pca time_series_analysis by barry on 2005-12-05 19:15:31 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Comparative molecular dynamics--similar folds and similar motions?
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 809-822.
    by Andrew Pang, Yalini Arinaminpathy, Mark S Sansom, Philip C Biggin
    posted to md_simulation structural_bioinformatics structure_comparison by barry on 2005-11-29 23:22:16 as * along with 2 groups structural_bioinformatics Bioinformatics
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