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Group: Bioinformatics - with tag md_simulation [45 articles]

グループ Bioinformatics のメンバーが最近追加した論文の一覧 with tag md_simulation
  • 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 to the group Bioinformatics on 2008-06-10 22:34:01 as read along with 1 group structural_bioinformatics
  • 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 to the group Bioinformatics on 2008-04-25 20:55:37 as ** along with 4 people mschofie sunhwan bicko sim82
  • 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 to the group Bioinformatics on 2007-10-02 03:05:14 as read along with 3 people and 2 groups lna allmensch cursonivel1 structural_bioinformatics cursonivel1
  • 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 torsion_angles pca md_simulation by barry to the group Bioinformatics on 2007-08-28 02:10:54 as ** along with 1 person and 2 groups sobolevnrm structural_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 md_simulation ion_channels coarse-grained by barry to the group Bioinformatics on 2007-08-28 01:58:49 as *** along with 1 person and 2 groups sobolevnrm structural_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 protein_structure pca nma md_simulation clustering by barry to the group Bioinformatics on 2007-08-27 19:15:41 as **** along with 4 people and 2 groups LamBras aqeel choonpeng sobolevnrm structural_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 protein_structure protein_folding md_simulation contacts clustering by barry to the group Bioinformatics on 2007-08-10 18:38:42 as ** along with 1 group structural_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 protein_structure protein_folding md_simulation contacts clustering by barry to the group Bioinformatics on 2007-08-10 18:36:13 as ** along with 1 person and 1 group choonpeng structural_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 protein_sequence md_simulation distance_matrices correlated_motions by barry to the group Bioinformatics on 2007-07-26 02:46:16 as ** along with 1 group structural_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 to the group Bioinformatics on 2007-04-27 17:36:16 as ** along with 1 group structural_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 nma md_simulation by barry to the group Bioinformatics on 2007-04-27 17:32:57 as ** along with 1 group structural_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 pca md_simulation clustering by barry to the group Bioinformatics on 2007-03-27 00:20:10 as ** along with 1 group structural_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 to the group Bioinformatics on 2007-02-12 23:41:33 as * along with 1 group structural_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 to the group Bioinformatics on 2007-01-30 20:09:59 as **** along with 3 people and 2 groups lna choonpeng sobolevnrm structural_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 to the group Bioinformatics on 2006-12-08 18:58:04 as * along with 1 group structural_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 to the group Bioinformatics on 2006-12-08 18:52:33 as ** along with 1 group structural_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 to the group Bioinformatics on 2006-12-08 18:50:17 as ** along with 1 group structural_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 to the group Bioinformatics on 2006-12-08 18:46:14 as * along with 2 people and 2 groups ibuch sobolevnrm structural_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 to the group Bioinformatics on 2006-12-08 18:42:44 as ** along with 1 group structural_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 to the group Bioinformatics on 2006-09-07 20:06:11 as ** along with 4 people and 2 groups blackbart kazemi sobolevnrm LamBras structural_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 to the group Bioinformatics on 2006-07-22 18:38:37 as * along with 1 group structural_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 to the group Bioinformatics on 2006-05-22 19:20:49 as ** along with 4 people and 1 group pansapiens lna aqeel allmensch structural_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 to the group Bioinformatics on 2006-05-08 20:05:12 as *** along with 1 person and 4 groups joergkurtwegner structural_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 to the group Bioinformatics on 2006-03-17 20:07:25 as read along with 1 group structural_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 to the group Bioinformatics on 2006-03-15 07:47:21 as * along with 1 person and 1 group RamuAnandakrishnan structural_bioinformatics
  • 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 to the group Bioinformatics on 2006-01-24 18:24:55 as **** along with 3 people and 1 group pansapiens lna choonpeng structural_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 to the group Bioinformatics on 2006-01-16 20:34:23 as ** along with 2 people and 1 group higueruelo ruvido structural_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 to the group Bioinformatics on 2006-01-09 21:03:10 as read along with 1 group structural_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 to the group Bioinformatics on 2005-12-05 19:15:31 as ** along with 1 group structural_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 to the group Bioinformatics on 2005-11-29 23:22:16 as * along with 1 group structural_bioinformatics
  • Ligand binding affinities from MD simulations.
    Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365.
    by J Aqvist, VB Luzhkov, BO Brandsdal
    posted to free_energy md_simulation by barry to the group Bioinformatics on 2005-10-26 00:14:13 as * along with 3 people and 1 group baaden dimka superpyrin structural_bioinformatics
  • Analysis methods for comparison of multiple molecular dynamics trajectories: applications to protein unfolding pathways and denatured ensembles.
    J Mol Biol, Vol. 290, No. 1. (2 July 1999), pp. 283-304.
    by SL Kazmirski, A Li, V Daggett
    posted to md_simulation protein_folding by barry to the group Bioinformatics on 2005-10-26 00:12:22 as ** along with 2 people and 1 group lillekatt choonpeng structural_bioinformatics
  • Functional Plasticity in the Substrate Binding Site of [beta]-Secretase
    Structure, Vol. 13, No. 10. (October 2005), pp. 1487-1498.
    by Alemayehu A Gorfe, Amedeo Caflisch
    posted to inhibitor_design md_simulation protein_dynamics by barry to the group Bioinformatics on 2005-10-17 19:23:01 as ** along with 1 group structural_bioinformatics
  • Simulation methods for protein structure fluctuations.
    Biopolymers, Vol. 19, No. 5. (May 1980), pp. 1001-1016.
    by SH Northrup, JA McCammon
    posted to bd_simulation md_simulation review by barry to the group Bioinformatics on 2005-10-11 23:35:50 as ** along with 1 person and 1 group lyongu structural_bioinformatics
  • Application of torsion angle molecular dynamics for efficient sampling of protein conformations
    Journal Of Computational Chemistry, Vol. 26, No. 15. (30 November 2005), pp. 1565-1578.
    by Jianhan Chen, Wonpil Im, Charles L Brooks
    posted to bioinf_methods md_simulation torsion_angles by barry to the group Bioinformatics on 2005-10-03 19:29:19 as ** along with 1 group structural_bioinformatics
  • Steered molecular dynamics and mechanical functions of proteins
    Current Opinion in Structural Biology, Vol. 11, No. 2. (1 April 2001), pp. 224-230.
    by Barry Isralewitz, Mu Gao, Klaus Schulten
    posted to md_simulation review smd by barry to the group Bioinformatics on 2005-09-28 01:04:14 as ** along with 2 people and 1 group LamBras ttjoseph structural_bioinformatics
  • Identifying and engineering ion pairs in adenylate kinases. Insights from molecular dynamics simulations of thermophilic and mesophilic homologues
    The Journal Of Biological Chemistry, Vol. 280, No. 35. (2 September 2005), pp. 30943-30948.
    by Euiyoung Bae, George N Phillips
    posted to ion_pairs kinases md_simulation protein_design by barry to the group Bioinformatics on 2005-09-20 18:56:31 as * along with 1 group structural_bioinformatics
  • Molecular dynamics simulations of evolved collective motions of atoms in the myosin motor domain upon perturbation of the ATPase pocket
    Biophysical Chemistry, Vol. 115, No. 1. (1 May 2005), pp. 77-85.
    by Tatsuyuki Kawakubo, Okimasa Okada, Tomoyuki Minami
    posted to allosteric md_simulation myosin pca protein_dynamics by barry to the group Bioinformatics on 2005-09-20 18:41:52 as ***** along with 1 person and 1 group julien_lv structural_bioinformatics
  • Thermodynamic calculations in biological systems
    Biophysical Chemistry, Vol. In Press, Corrected Proof
    by Mario L Amzel, Xavier Siebert, Anthony Armstrong, German Pabon
    posted to md_simulation protein_dynamics by barry to the group Bioinformatics on 2005-06-27 19:38:32 as ** along with 5 people and 2 groups pansapiens shuns imouthesmp ttjoseph nknii structural_bioinformatics TCR_Signaling
  • Force probe molecular dynamics simulations.
    Methods Mol Biol, Vol. 305 (2005), pp. 493-515.
    by H Grubmüller
    posted to md_simulation protein_dynamics smd by barry to the group Bioinformatics on 2005-06-24 00:42:13 as ** along with 2 people and 1 group baaden choonpeng structural_bioinformatics
  • Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation.
    J Biomol NMR, Vol. 29, No. 3. (July 2004), pp. 243-257.
    by J Chen, CL Brooks, PE Wright
    posted to md_simulation nmr protein_dynamics by barry to the group Bioinformatics on 2005-05-25 18:32:42 as ** along with 1 person and 1 group allmensch structural_bioinformatics
  • Generation of native-like protein structures from limited NMR data, modern force fields and advanced conformational sampling
    Journal of Biomolecular NMR, Vol. 31, No. 1. (January 2005), pp. 59-64.
    by Jianhan Chen, Hyung-Sik Won, Wonpil Im, H Dyson, Charles Brooks
    posted to md_simulation nmr protein_dynamics replica_exchange by barry to the group Bioinformatics on 2005-05-25 18:28:59 as ** along with 1 person and 1 group bilab structural_bioinformatics
  • Change in protein flexibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 322-337.
    by H Gohlke, LA Kuhn, DA Case
    posted to md_simulation protein_protein protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-03-16 03:52:20 as ***** along with 3 people and 1 group lna aqeel blackbart structural_bioinformatics
  • Simultaneous determination of protein structure and dynamics
    Nature, Vol. 433, No. 7022. (13 January 2005), pp. 128-132.
    by Kresten Lindorff-Larsen, Robert B Best, Mark A Depristo, Christopher M Dobson, Michele Vendruscolo
    posted to md_simulation protein_dynamics protein_structure structural_bioinformatics by barry to the group Bioinformatics on 2005-03-16 03:27:40 as ***** along with 12 people and 1 group rph karbak apaydin lillekatt baaden lna dgront allmensch daevans rsantana jlh64 biehl structural_bioinformatics
  • Biomolecular motors: the F1-ATPase paradigm.
    Curr Opin Struct Biol, Vol. 14, No. 2. (April 2004), pp. 250-259.
    by M Karplus, YQ Gao
    posted to md_simulation molecular_motors by barry to the group Bioinformatics on 2005-03-03 06:45:40 as read along with 1 group structural_bioinformatics
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