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Tag md_simulation [79 articles]

Recent papers classified by the tag md_simulation.
  • Hybrid Monte Carlo
    Physics Letters B, Vol. 195, No. 2. (3 September 1987), pp. 216-222.
    by Simon Duane, AD Kennedy, Brian J Pendleton, Duncan Roweth
    posted to md_simulation by ssomani on 2008-09-25 23:54:06 as ** along with 1 person fghorow
  • Membrane proteins: molecular dynamics simulations
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Erik Lindahl, Mark SP Sansom
    posted to coarse_grain ion_channel md md_simulation membrane membrane_proteins by rok on 2008-08-21 21:06:02 as ** along with 3 people and 1 group vahmurk cat_worth jmccammon McCammon
  • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    Current Opinion in Structural Biology, Vol. 17, No. 6. (December 2007), pp. 633-640.
    by Ivet Bahar, Chakra Chennubhotla, Dror Tobi
    posted to coarse_grain md_simulation protein-ligand by jmccammon on 2008-08-21 19:52:40 as read along with 8 people and 4 groups barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras structural_bioinformatics Bioinformatics baker-group McCammon
  • An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.
    J Comput Aided Mol Des (15 January 2008)
    by Rommie E Amaro, Riccardo Baron, J A McCammon
    posted to protein-ligand md_simulation drug-discovery by jmccammon on 2008-09-27 20:31:32 as read along with 4 people and 1 group rbaron higueruelo kazemi LamBras McCammon
  • The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations
    Biophys. J. (9 May 2008), biophysj.107.123190.
    by Chze-Ling Wee, Kia Balali-Mood, David Gavaghan, Mark S Sansom
    posted to coarse_grain md_simulation membrane by jmccammon on 2008-08-20 22:15:41 as *** along with 1 person and 1 group paulschlesinger 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 jmccammon on 2008-05-26 21:33:02 as read along with 2 people and 3 groups barry sobolevnrm structural_bioinformatics McCammon baker-group
  • Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations
    J. Chem. Theory Comput., Vol. 4 (13 August 2008), pp. 1516-1525.
    by CAF de Oliveira, D Hamelberg, JA Mccammon
    posted to md_simulation free_energy accelerated_md by jmccammon on 2008-09-27 23:51:04 as read along with 2 people and 1 group dmobley cesar McCammon
  • CHARMMing: A New, Flexible Web Portal for CHARMM
    J. Chem. Inf. Model. (13 August 2008)
    by Benjamin T Miller, Rishi P Singh, Jeffery B Klauda, Milan Hodošček, Bernard R Brooks, Lee H Woodcock
    posted to md_simulation drug-discovery by jmccammon on 2008-09-27 19:30:35 as ** along with 2 people and 1 group middledomain reyez McCammon
  • Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State
    J. Chem. Theory Comput., Vol. 4 (13 August 2008), pp. 1541-1554.
    by Ilja V Khavrutskii, Mikolai Fajer, JA Mccammon
    posted to md_simulation ion_channel free_energy by jmccammon on 2008-09-28 00:04:07 as read along with 1 person and 1 group dmobley McCammon
  • Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions
    Proceedings of the National Academy of Sciences, Vol. 105, No. 31. (2008), pp. 10659-10664.
    by Christopher K Materese, Christa C Goldmon, Garegin A Papoian
    posted to md_simulation by jmccammon on 2008-08-19 23:38:22 as **** along with 1 person and 1 group OriginalLurch McCammon
  • 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 jmccammon on 2008-07-03 00:57:58 as read along with 1 person and 1 group barry 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 jmccammon on 2008-05-26 21:31:42 as read along with 3 people and 3 groups biehl sobolevnrm barry baker-group structural_bioinformatics McCammon
  • REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
    Biophys. J. (9 May 2008), biophysj.108.131714.
    by Kei Moritsugu, Jeremy C Smith
    posted to coarse_grain md_simulation by jmccammon on 2008-08-20 22:13:17 as *** along with 5 people and 1 group A_Coletta_Thesis paulschlesinger choonpeng aqeel rok McCammon
  • 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
  • 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 6 people and 1 group hmk raik pansapiens lna aqeel allmensch 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
  • 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
  • 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
  • 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 to the group Bioinformatics on 2008-08-18 20:21:10 as ** along with 1 group structural_bioinformatics
  • 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
  • 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 to the group Bioinformatics on 2008-06-10 22:34:01 as read along with 1 group 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
  • 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 ruvido higueruelo 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
  • 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
  • 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
  • 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
  • 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 ttjoseph LamBras 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
  • 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
  • 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 karbak apaydin lillekatt baaden lna dgront allmensch daevans rsantana jlh64 biehl rph structural_bioinformatics
  • 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
  • Flexible ligand docking to multiple receptor conformations: a practical alternative.
    Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184.
    by M Totrov, R Abagyan
    posted to review md_simulation docking by barry to the group Bioinformatics on 2008-10-02 19:48:14 as ** along with 1 person and 2 groups aqeel structural_bioinformatics McCammon
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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 5 people and 2 groups ubcg08l aqeel choonpeng sobolevnrm LamBras structural_bioinformatics baker-group
  • 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
  • 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 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
  • 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 to the group Bioinformatics on 2008-04-25 20:55:37 as ** along with 6 people RamuAnandakrishnan gisle bicko sim82 sunhwan mschofie
  • 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
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