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Tag protein_dynamics [253 articles]

Recent papers classified by the tag protein_dynamics.
  • A consensus view of protein dynamics
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (10 January 2007), pp. 796-801.
    by Manuel Rueda, Carles F Costa, Tim Meyer, Alberto Pérez, Jordi Camps, Adam Hospital, Josep, Modesto Orozco
    posted to force_field protein_dynamics by rabio on 2007-12-10 13:29:10 as read along with 13 people and 2 groups bmduggan lna dimka aqeel aswin grahamc hmk zwang biehl Ema phoenixzxl ras LamBras ParkinsonLab_at_MaRS The BMM Dome
  • Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima.
    Proteins, Vol. 67, No. 3. (15 May 2007), pp. 569-578.
    by GG Maisuradze, DM Leitner
    posted to protein_dynamics md by onufriev on 2008-11-17 01:39:36 as read
  • Linking folding with aggregation in Alzheimer's beta-amyloid peptides
    Proceedings of the National Academy of Sciences, Vol. 104, No. 43. (23 October 2007), pp. 16880-16885.
    by Jana Khandogin, Charles L Brooks
    posted to protein_folding protein_dynamics pka by onufriev on 2008-11-01 02:33:42 as ** along with 2 people and 1 group Diego_Prada sobolevnrm baker-group
  • Solvent mobility and the protein 'glass' transition.
    Nat Struct Biol, Vol. 7, No. 1. (January 2000), pp. 34-38.
    by D Vitkup, D Ringe, GA Petsko, M Karplus
    posted to myoglobin protein_dynamics by onufriev on 2008-01-25 02:22:48 as *** along with 2 people naitsabes jteyra
  • Convergence of sampling in protein simulations
    Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910.
    by Berk Hess
    posted to protein_dynamics md by onufriev on 2008-11-17 01:53:50 as ** along with 1 person softsimu
  • Similarities between principal components of protein dynamics and random diffusion
    Physical Review E, Vol. 62, No. 6. (1 December 2000), 8438.
    by Berk Hess
    posted to protein_dynamics md by onufriev on 2008-11-17 01:56:06 as **
  • Coupling Between Folding and Ionization Equilibria: Effects of pH on the Conformational Preferences of Polypeptides
    Journal of Molecular Biology (December 1996), pp. 770-783.
    by DR Ripoll, YN Vorobjev, A Liwo, JA Vila, HA Scheraga
    posted to protein_folding protein_dynamics ph by onufriev on 2008-11-08 22:48:34 as **
  • Toward quantitative simulations of carbon monoxide escape pathways in myoglobin.
    The journal of physical chemistry. B, Vol. 112, No. 19. (15 May 2008), pp. 6147-6154.
    by R Elber, QH Gibson
    posted to protein_dynamics myoglobin md by onufriev on 2008-11-18 02:01:48 as read
  • Physical aspects of protein dynamics
    Reports on Progress in Physics, Vol. 66, No. 2. (2003), pp. 103-129.
    by Fritz G Parak
    posted to protein_dynamics by medic0747 on 2007-02-10 13:56:24 as **
  • Electrostatics and dynamics of proteins
    Reports of Progress in Physics, Vol. 66 (May 2003), pp. 737-787.
    by T Simonson
    posted to protein_dynamics by medic0747 on 2007-02-10 13:55:22 as ** along with 2 people chiufanlee onufriev
  • Intrinsic dynamics of an enzyme underlies catalysis
    Nature, Vol. 438, No. 7064., pp. 117-121.
    by Elan Z Eisenmesser, Oscar Millet, Wladimir Labeikovsky, Dmitry M Korzhnev, Magnus Wolf-Watz, Daryl A Bosco, Jack J Skalicky, Lewis E Kay, Dorothee Kern
    posted to catalysis nmr protein_dynamics by karbak on 2006-02-12 08:00:06 as **** along with 7 people barry BragilMassoud lna dlr tny jlh64 rph
  • Direct evaluation of thermal fluctuations in proteins using a single-parameter harmonic potential
    Folding and Design, Vol. 2, No. 3. (June 1997), pp. 173-181.
    by Ivet Bahar, Ali R Atilgan, Burak Erman
    posted to protein_dynamics gnm by joseph_x_zhou on 2008-09-09 20:12:54 as read along with 1 group protein_Dyn
  • Statistical Prediction and Molecular Dynamics Simulation
    Biophys. J. (1 August 2008), biophysj.108.131623.
    by Ben Cooke, Scott Schmidler
    posted to statistical_prediction protein_dynamics journal by joseph_x_zhou on 2008-11-16 21:08:25 as ** along with 2 people agrossfield paulschlesinger
  • Journal club
    Nature, Vol. 454, No. 7200. (02 July 2008), pp. 5-5.
    by Peter Csermely
    posted to protein_design protein_dynamics by joseph_x_zhou on 2008-07-21 13:19:46 as **
  • Review: Protein Design--Where We Were, Where We Are, Where We're Going
    Journal of Structural Biology, Vol. 134, No. 2-3. (May 2001), pp. 269-281.
    by Navin Pokala, Tracy M Handel
    posted to protein_dynamics protein_strut_func by joseph_x_zhou on 2008-07-21 13:16:06 as ** along with 2 people medic0747 msuarezdiez
  • notes Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading.
    J Mol Biol, Vol. 256, No. 3. (1 March 1996), pp. 623-644.
    by S Miyazawa, RL Jernigan
    posted to potential protein_dynamics by joseph_x_zhou on 2008-08-27 14:42:03 as ** along with 2 people and 1 group choonpeng rabio protein_Dyn
  • Nonlinear relaxation dynamics in elastic networks and design principles of molecular machines
    PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8697-8702.
    by Yuichi Togashi, Alexander S Mikhailov
    posted to protein_dynamics by joseph_x_zhou on 2008-05-08 16:29:26 as **** along with 2 people aqeel cactus
  • Toward a molecular understanding of the anisotropic response of proteins to external forces: Insights from elastic network models.
    Biophys J (25 January 2008)
    by Eran Eyal, Ivet Bahar
    posted to coarse_model protein_dynamics single_molecule_experiment by joseph_x_zhou on 2008-06-08 22:41:07 as ***** along with 2 people choonpeng jennifermbui
  • EXPLORING THE SUITABILITY OF COARSE-GRAINED TECHNIQUES FOR THE REPRESENTATION OF PROTEIN DYNAMICS
    Biophys. J. (16 May 2008), biophysj.107.119115.
    by Agusti Emperador, Oliver Carrillo, Manuel Rueda, Modesto Orozco
    posted to protein_dynamics journal coarse_grained_model by joseph_x_zhou on 2008-10-15 16:34:48 as **** along with 1 person and 1 group paulschlesinger protein_Dyn
  • Gaussian Dynamics of Folded Proteins
    Physical Review Letters, Vol. 79, No. 16. (20 October 1997), 3090.
    by Turkan Haliloglu, Ivet Bahar, Burak Erman
    posted to protein_dynamics journal by joseph_x_zhou on 2008-09-15 20:59:24 as ** along with 1 person and 1 group aqeel protein_Dyn
  • Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.
    J Mol Biol, Vol. 281, No. 5. (4 September 1998), pp. 871-884.
    by I Bahar, RL Jernigan
    posted to soft_mode protein_dynamics by joseph_x_zhou on 2008-09-09 15:54:01 as ** along with 2 people and 1 group aqeel simone protein_Dyn
  • Biochemistry: Fit for an enzyme
    Nature, Vol. 454, No. 7206. (13 August 2008), pp. 832-833.
    by Shiven Kapur, Chaitan Khosla
    posted to protein_dynamics protein_strut_func by joseph_x_zhou on 2008-08-24 20:16:06 as ** along with 1 person and 1 group reyez protein_Dyn
  • Anisotropic fluctuations of amino acids in protein structures: insights from X-ray crystallography and elastic network models
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. i175-184.
    by Eran Eyal, Chakra Chennubhotla, Lee-Wei Yang, Ivet Bahar
    posted to protein_dynamics journal enm aa_specific by joseph_x_zhou on 2008-09-10 16:42:46 as ** along with 3 people and 1 group simone aqeel jlh64 protein_Dyn
  • notes <it>i</it>GNM: a database of protein functional motions based on Gaussian Network Model
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2978-2987.
    by Lee-Wei Yang, Xiong Liu, Christopher J Jursa, Mark Holliman, A Rader, Hassan A Karimi, Ivet Bahar
    posted to protein_dynamics by joseph_x_zhou on 2008-05-18 20:44:49 as ** along with 2 people baaden qwermish
  • Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins.
    Proc Natl Acad Sci U S A, Vol. 100, No. 22. (28 October 2003), pp. 12570-12575.
    by O Miyashita, JN Onuchic, PG Wolynes
    posted to protein_dynamics by joseph_x_zhou on 2008-08-28 21:47:49 as ** along with 1 person and 2 groups aqeel biophysics protein_Dyn
  • Large Amplitude Elastic Motions in Proteins from a Single-Parameter, Atomic Analysis
    Physical Review Letters, Vol. 77, No. 9. (1996), 1905.
    by Monique M Tirion
    posted to protein_dynamics by joseph_x_zhou on 2008-09-09 15:47:30 as ** along with 2 people and 1 group aqeel Diego_Prada protein_Dyn
  • Dynamic thiolation–thioesterase structure of a non-ribosomal peptide synthetase
    Nature, Vol. 454, No. 7206., pp. 903-906.
    by Dominique P Frueh, Haribabu Arthanari, Alexander Koglin, David A Vosburg, Andrew E Bennett, Christopher T Walsh, Gerhard Wagner
    posted to protein_dynamics protein_strut_func by joseph_x_zhou on 2008-08-24 20:18:47 as ** along with 1 group protein_Dyn
  • Discrete breathers in protein structures
    Phys. Biol., Vol. 5, No. 2. (21 June 2008), 026001.
    by Francesco Piazza, Yves-Henri Sanejouand
    posted to protein_dynamics protein_strut_func by joseph_x_zhou on 2008-07-21 13:08:24 as *****
  • Computing the Amino Acid Specificity of Fluctuations in Biomolecular Systems
    J. Chem. Theory Comput., Vol. 2, No. 3. (9 May 2006), pp. 873-878.
    by K Hamacher, JA Mccammon
    posted to drug_resistance h hiv hiv_pr protein_dynamics by joseph_x_zhou on 2008-08-27 15:35:49 as read along with 1 group protein_Dyn
  • Under DNA stress, gyrase makes the sign of the cross
    Nature Structural & Molecular Biology, Vol. 14, No. 4., pp. 256-258.
    by Patrick N Higgins
    posted to protein_dynamics protein_strut_func single_molecule_experiment by joseph_x_zhou on 2008-06-08 22:46:39 as ****
  • Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations.
    Proc Natl Acad Sci U S A, Vol. 103, No. 32. (8 August 2006), pp. 11844-11849.
    by K Okazaki, N Koga, S Takada, JN Onuchic, PG Wolynes
    posted to large_deformation protein_dynamics protein_strut_func by joseph_x_zhou on 2008-08-27 14:37:03 as ** along with 2 people and 1 group allmensch choonpeng protein_Dyn
  • Effects of surface water on protein dynamics studied by a novel coarse-grained normal mode approach.
    Biophys J (22 January 2008)
    by Lei Zhou, Steven A A Siegelbaum
    posted to coarse_model protein_dynamics surface_water by joseph_x_zhou on 2008-06-08 22:53:01 as ** along with 1 person and 1 group choonpeng protein_Dyn
  • Protein backbone dynamics from N-HN dipolar couplings in partially aligned systems: a comparison of motional models in the presence of structural noise.
    J Magn Reson, Vol. 173, No. 2. (April 2005), pp. 328-338.
    by G Bouvignies, P Bernadó, M Blackledge
    posted to correlated_motions nmr protein_dynamics rdc by Guyhiom on 2005-10-16 23:01:57 as read
  • Systematic analysis of domain motions in proteins from conformational change: new results on citrate synthase and T4 lysozyme.
    Proteins, Vol. 30, No. 2. (1 February 1998), pp. 144-154.
    by S Hayward, HJ Berendsen
    posted to bioinf_methods domain_motions protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-10-09 08:22:02 as read along with 1 group structural_bioinformatics
  • A database of macromolecular motions
    Nucleic Acids Research, Vol. 26, No. 18. (15 September 1998), pp. 4280-4290.
    by M Gerstein, W Krebs
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-09-28 01:13:56 as read along with 1 group structural_bioinformatics
  • Network of dynamically important residues in the open/closed transition in polymerases is strongly conserved.
    Structure, Vol. 13, No. 4. (April 2005), pp. 565-577.
    by W Zheng, BR Brooks, S Doniach, D Thirumalai
    posted to nma protein_dynamics protein_sequence protein_structure by barry to the group Bioinformatics on 2006-08-15 19:16:49 as * along with 1 group structural_bioinformatics
  • Backbone and side chain dynamics of mutant calmodulin-Peptide complexes.
    Biochemistry, Vol. 44, No. 38. (27 September 2005), pp. 12627-12639.
    by TI Igumenova, AL Lee, AJ Wand
    posted to protein_dynamics protein_function protein_structure structure_comparison by ana to the group Bioinformatics on 2005-10-09 04:05:20 as ** along with 1 person and 1 group lna 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
  • Allosteric Regulation of Hsp70 Chaperones by a Proline Switch
    Molecular Cell, Vol. 21, No. 3. (3 February 2006), pp. 359-367.
    by Markus Vogel, Bernd Bukau, Matthias P Mayer
    posted to allosteric hsp70 protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-02-03 02:52:39 as *** along with 1 person and 2 groups pdelosri structural_bioinformatics EPFL_SB_ITP_LBS
  • Dynamics of large proteins through hierarchical levels of coarse-grained structures.
    J Comput Chem, Vol. 23, No. 1. (15 January 2002), pp. 119-127.
    by P Doruker, RL Jernigan, I Bahar
    posted to interaction_hierarchy protein_dynamics protein_structure structure_comparison by ana to the group Bioinformatics on 2005-09-02 18:10:40 as ** along with 2 people and 1 group baaden aqeel structural_bioinformatics
  • Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1.5-nm Localization
    Science, Vol. 300, No. 5628. (27 June 2003), pp. 2061-2065.
    by Ahmet Yildiz, Joseph N Forkey, Sean A Mckinney, Taekjip Ha, Yale E Goldman, Paul R Selvin
    posted to fret-fiona molecular_motors motor_model myosin myov protein_dynamics by barry to the group Bioinformatics on 2006-05-11 19:05:06 as *** along with 2 people and 2 groups baniel rodney structural_bioinformatics Kopelman_Group
  • The Limit of Accuracy of Protein Modeling: Influence of Crystal Packing on Protein Structure
    Journal of Molecular Biology, Vol. 351, No. 2. (12 August 2005), pp. 431-442.
    by Eran Eyal, Sergey Gerzon, Vladimir Potapov, Marvin Edelman, Vladimir Sobolev
    posted to crystal_packing protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-05-30 21:44:09 as ** along with 1 person and 1 group pansapiens structural_bioinformatics
  • Protein flexibility acclimatizes photosynthetic energy conversion to the ambient temperature
    Nature, Vol. 442, No. 7104. (23 July 2006), pp. 827-830.
    by Oksana Shlyk-Kerner, Ilan Samish, David Kaftan, Neta Holland, Maruthi PS Sai, Hadar Kless, Avigdor Scherz
    posted to domain_motions protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-08-16 21:45:51 as ***** along with 1 group structural_bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to review protein_structure protein_ligand protein_dynamics drug_design docking by barry to the group Bioinformatics on 2007-08-13 19:47:46 as * along with 1 group structural_bioinformatics
  • Automatic Analysis of Protein Conformational Changes by Multiple Linkage Clustering
    Journal of Molecular Biology, Vol. 253, No. 4. (3 November 1995), pp. 633-647.
    by Nathalie S Boutonnet, Marianne J Rooman, Shoshana J Wodak
    posted to bioinf_methods protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2005-09-28 01:16:22 as ***** along with 1 group structural_bioinformatics
  • Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 187-194.
    by O Schueler-Furman, C Wang, D Baker
    posted to bioinf_methods protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-17 18:52:59 as ** along with 3 people and 1 group jwm bicko bluvsh1 structural_bioinformatics
  • 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 4 people and 2 groups raik lna allmensch cursonivel1 structural_bioinformatics cursonivel1
  • Identification of the protein binding region of S-trityl-L-cysteine, a new potent inhibitor of the mitotic kinesin Eg5.
    Biochemistry, Vol. 43, No. 41. (19 October 2004), pp. 13072-13082.
    by S Brier, D Lemaire, S Debonis, E Forest, F Kozielski
    posted to eg5 kinesin molecular_motors monastrol protein_dynamics by barry to the group Bioinformatics on 2005-06-24 23:11:42 as *** along with 1 group structural_bioinformatics
  • Improved side-chain modeling for protein-protein docking.
    Protein Sci, Vol. 14, No. 5. (May 2005), pp. 1328-1339.
    by C Wang, O Schueler-Furman, D Baker
    posted to protein_dynamics protein_protein by barry to the group Bioinformatics on 2005-10-17 18:53:58 as ** along with 10 people and 2 groups csrocha aqeel jwm bicko yongzhao blackbart bluvsh1 hmk selrac Evangelia structural_bioinformatics TSRI_MGL
  • Conservation and specialization in PAS domain dynamics.
    Protein Eng Des Sel, Vol. 18, No. 3. (March 2005), pp. 127-137.
    by A Pandini, L Bonati
    posted to protein_dynamics pca allosteric by barry to the group Bioinformatics on 2007-01-19 22:06:49 as ** along with 1 group structural_bioinformatics
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