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barrys protein_dynamics [113 articles]

Neue Publikationen in barrys Bibliothek eingetragen unter dem Bezeichner: protein_dynamics. You can also see everyone's protein_dynamics.
  • Computational techniques for efficient conformational sampling of proteins
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, Harold A Scheraga
    posted to review protein_dynamics coarse_grain by barry on 2008-10-02 19:59:47 as ** along with 2 people aqeel j3xucite
  • notes Understanding mechanisms governing protein-protein interactions from synthetic binding interfaces
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Anthony A Kossiakoff, Shohei Koide
    posted to review protein_protein protein_dynamics by barry on 2008-10-02 19:21:01 as ** along with 1 person and 3 groups paulschlesinger structural_bioinformatics McCammon Bioinformatics
  • Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 105, No. 37. (16 September 2008), pp. 13829-13834.
    by SM Sullivan, T Holyoak
    posted to protein_structure protein_dynamics allosteric by barry on 2008-10-02 18:34:05 as ** along with 1 person and 2 groups TonyIvetac structural_bioinformatics McCammon
  • Essential Dynamics of Helices Provide a Functional Classification of EF-Hand Proteins
    J. Proteome Res., Vol. 6, No. 11. (2 November 2007), pp. 4245-4255.
    by F Capozzi, C Luchinat, C Micheletti, F Pontiggia
    posted to dynamic_similarity nma protein_dynamics by barry on 2008-08-12 18:06:25 as ** along with 1 person aqeel
  • Convergent Dynamics in the Protease Enzymatic Superfamily
    J. Am. Chem. Soc., Vol. 128, No. 30. (2 August 2006), pp. 9766-9772.
    by V Carnevale, S Raugei, C Micheletti, P Carloni
    posted to dynamic_similarity nma protein_dynamics by barry on 2008-08-12 18:05:13 as ** along with 1 person ucbcjbm
  • Proteins with Similar Architecture Exhibit Similar Large-Scale Dynamic Behavior
    Biophys. J., Vol. 78, No. 4. (1 April 2000), pp. 2093-2106.
    by O Keskin, RL Jernigan, I Bahar
    posted to dynamic_similarity nma protein_dynamics by barry on 2008-08-12 18:03:02 as ** along with 5 people ubcg08l aqeel insectopalo saravan edvin
  • BIOCHEMISTRY: Metamorphic Proteins
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1725-1726.
    by Alexey G Murzin
    posted to protein_dynamics protein_structure review by barry on 2008-07-07 23:55:32 as ** along with 1 person and 1 group marck structural_bioinformatics
  • A Simple Model of Backbone Flexibility Improves Modeling of Side-chain Conformational Variability
    Journal of Molecular Biology, Vol. 380, No. 4. (18 July 2008), pp. 757-774.
    by Gregory D Friedland, Anthony J Linares, Colin A Smith, Tanja Kortemme
    posted to protein_dynamics protein_structure by barry on 2008-06-30 17:35:43 as **
  • 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
  • Structural Basis of the Honey Bee PBP Pheromone and pH-induced Conformational Change
    Journal of Molecular Biology, Vol. 380, No. 1. (27 June 2008), pp. 158-169.
    by Marion E Pesenti, Silvia Spinelli, Valérie Bezirard, Loïc Briand, Jean-Claude Pernollet, Mariella Tegoni, Christian Cambillau
    posted to docking protein_dynamics protein_structure by barry on 2008-06-09 17:43:48 as **
  • 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 **
  • Transition networks for modeling the kinetics of conformational change in macromolecules
    Current Opinion in Structural Biology, Vol. 18, No. 2. (April 2008), pp. 154-162.
    by Frank Noé, Stefan Fischer
    posted to protein_dynamics protein_structure review smd by barry on 2008-04-17 19:15:44 as *** along with 4 people and 3 groups aqeel sobolevnrm paulschlesinger toerst structural_bioinformatics baker-group McCammon
  • Allostery: Absence of a Change in Shape Does Not Imply that Allostery Is Not at Play.
    J Mol Biol (29 February 2008)
    by Chung-Jung J Tsai, Antonio Del Sol, Ruth Nussinov
    posted to allosteric protein_dynamics protein_structure review by barry on 2008-03-31 18:11:48 as *** along with 6 people and 3 groups choonpeng cactus sobolevnrm CameronNeylon higueruelo cchang structural_bioinformatics McCammon group
  • notes Structural flexibility in proteins: impact of the crystal environment
    Bioinformatics, Vol. 24, No. 4. (15 February 2008), pp. 521-528.
    by Konrad Hinsen
    posted to nma protein_dynamics protein_structure by barry on 2008-03-20 00:43:49 as ** along with 3 people and 2 groups sobolevnrm jlh64 scienbox baker-group 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 allosteric protein_dynamics protein_structure review by barry on 2007-12-04 22:56:25 as ** along with 8 people and 4 groups aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_bioinformatics Bioinformatics baker-group McCammon
  • 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 4 people and 3 groups raik lna allmensch cursonivel1 structural_bioinformatics Bioinformatics cursonivel1
  • Exploring the range of protein flexibility, from a structural proteomics perspective
    Current Opinion in Chemical Biology, Vol. 8, No. 1. (February 2004), pp. 14-19.
    by Mark Gerstein, Nathaniel Echols
    posted to protein_dynamics protein_structure review by barry on 2007-09-27 19:19:21 as read
  • Signal Propagation in Proteins and Relation to Equilibrium Fluctuations
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e172.
    by Chakra Chennubhotla, Ivet Bahar
    posted to allosteric correlated_motions nma protein_dynamics protein_structure time_series_analysis by barry on 2007-09-22 23:29:36 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Detecting similarities among distant homologous proteins by comparison of domain flexibilities
    Protein Engineering, Design and Selection (30 June 2007), gzm021.
    by Alessandro Pandini, Giancarlo Mauri, Annalisa Bordogna, Laura Bonati
    posted to protein_dynamics protein_structure by barry on 2007-09-05 01:57:38 as * along with 2 people and 2 groups aqeel edvin structural_bioinformatics Bioinformatics
  • Evolutionary Conservation of Protein Backbone Flexibility
    Journal of Molecular Evolution, Vol. 63, No. 4. (14 October 2006), pp. 448-457.
    by Sandra Maguid, Sebastián Fernández-Alberti, Gustavo Parisi, Julián Echave
    posted to nma protein_dynamics protein_structure by barry on 2007-09-05 01:48:20 as ** along with 4 people and 2 groups gisle jlh64 edvin tny structural_bioinformatics Bioinformatics
  • Association of putative concave protein-binding sites with the fluctuation behavior of residues.
    Protein Sci, Vol. 15, No. 10. (October 2006), pp. 2265-2277.
    by A Ertekin, R Nussinov, T Haliloglu
    posted to nma protein_dynamics protein_protein by barry on 2007-09-04 20:13:14 as ***** along with 1 person and 2 groups aqeel structural_bioinformatics Bioinformatics
  • Computational Design of a Single Amino Acid Sequence that Can Switch between Two Distinct Protein Folds.
    J Am Chem Soc, Vol. 128, No. 4. (1 February 2006), pp. 1154-1161.
    by XI Ambroggio, B Kuhlman
    posted to protein_design protein_dynamics protein_sequence protein_structure by barry on 2007-09-04 19:32:05 as ** along with 5 people and 2 groups shuns jwm kevinchannon bethbromley ca3295 structural_bioinformatics Bioinformatics
  • How Well Can We Understand Large-Scale Protein Motions Using Normal Modes of Elastic Network Models?
    Biophys J (4 May 2007)
    by Lei Yang, Guang Song, Robert L L Jernigan
    posted to correlated_motions nma protein_dynamics protein_structure by barry on 2007-08-13 19:53:33 as ** along with 3 people and 2 groups aqeel choonpeng willpitt structural_bioinformatics Bioinformatics
  • Protein Flexibility and Mobility in Structure-Based Drug Design
    pp. 455-476.
    by Aqeel Ahmed
    posted to docking drug_design protein_dynamics protein_ligand protein_structure review by barry on 2007-08-13 19:47:46 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Intrinsic disorder as a mechanism to optimize allosteric coupling in proteins.
    Proc Natl Acad Sci U S A (9 May 2007)
    by Vincent J J Hilser, E Brad B Thompson
    posted to allosteric disorder protein_dynamics protein_protein protein_structure by barry on 2007-05-25 01:36:39 as **** along with 5 people and 3 groups apaydin choonpeng cursonivel1 cactus allmensch structural_bioinformatics Bioinformatics cursonivel1
  • Multivariate Analysis of Conserved Sequence-Structure Relationships in Kinesins: Coupling of the Active Site and a Tubulin-binding Sub-domain
    Journal of Molecular Biology, Vol. 368, No. 5. (18 May 2007), pp. 1231-1248.
    by Barry J Grant, Andrew J Mccammon, Leo S Caves, Robert A Cross
    posted to bioinf_methods clustering core_structure correlated_motions domain_motions kinesin mine molecular_motors ntpases p-loop pca protein_dynamics protein_sequence protein_structure r sca structural_bioinformatics swi-swii torsion_angles by barry on 2007-04-27 17:41:06 as read along with 3 people and 2 groups choonpeng cactus insectopalo 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
  • 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 on 2007-01-19 22:06:49 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • PAS domains. Common structure and common flexibility.
    J Biol Chem, Vol. 278, No. 20. (16 May 2003), pp. 18434-18439.
    by J Vreede, MA van der Horst, KJ Hellingwerf, W Crielaard, DM van Aalten
    posted to protein_dynamics allosteric by barry on 2007-01-19 21:58:55 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Exploring the common dynamics of homologous proteins. Application to the globin family.
    Biophys J, Vol. 89, No. 1. (July 2005), pp. 3-13.
    by S Maguid, S Fernandez-Alberti, L Ferrelli, J Echave
    posted to protein_structure protein_dynamics nma by barry on 2007-01-19 21:54:41 as ** along with 4 people and 2 groups gisle Einat jlh64 edvin structural_bioinformatics Bioinformatics
  • notes Conformational diversity and protein evolution--a 60-year-old hypothesis revisited.
    Trends Biochem Sci, Vol. 28, No. 7. (July 2003), pp. 361-368.
    by LC James, DS Tawfik
    posted to review protein_structure protein_sequence protein_evolution protein_dynamics by barry on 2007-01-18 19:39:58 as ***** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • notes Bio3d: an R package for the comparative analysis of protein structures.
    Bioinformatics (29 August 2006)
    by Barry J J Grant, Ana P C P Rodrigues, Karim M M Elsawy, J Andrew A McCammon, Leo S D S Caves
    posted to kinesin mine protein_dynamics protein_sequence protein_structure r structural_bioinformatics structure_comparison by barry on 2007-01-05 01:03:37 as **** along with 7 people and 2 groups gisle ana Einat plofje krishnaJCSG insectopalo cdeane structural_bioinformatics Bioinformatics
  • Evaluation of Energetic and Dynamic Coupling Networks in a PDZ Domain Protein
    Journal of Molecular Biology, Vol. 364, No. 3. (1 December 2006), pp. 337-351.
    by Ernesto J Fuentes, Steven A Gilmore, Randall V Mauldin, Andrew L Lee
    posted to allosteric pdz protein_dynamics protein_structure by barry on 2006-11-15 19:16:56 as ** along with 2 people and 2 groups lna choonpeng structural_bioinformatics Bioinformatics
  • Hydrophobic Core Fluidity of Homologous Protein Domains: Relation of Side-Chain Dynamics to Core Composition and Packing
    Biochemistry, Vol. 43, No. 5. (10 February 2004), pp. 1145-1155.
    by RB Best, TJ Rutherford, SMV Freund, J Clarke
    posted to core_residues core_structure correlated_motions protein_dynamics protein_packing protein_structure by barry on 2006-11-15 19:14:54 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • High-resolution cryo-EM maps show the nucleotide binding pocket of KIF1A in open and closed conformations
    The EMBO Journal, Vol. 25, No. 18. (20 September 2006), pp. 4187-4194.
    by Masahide Kikkawa, Nobutaka Hirokawa
    posted to kinesin molecular_motors motor_model mts protein_dynamics by barry on 2006-10-30 19:26:11 as **** along with 2 groups structural_bioinformatics Bioinformatics
  • Targeted Molecular Dynamics Study of C-Loop Closure and Channel Gating in Nicotinic Receptors.
    PLoS Comput Biol, Vol. 2, No. 9. (29 September 2006)
    by Xiaolin Cheng, Hailong Wang, Barry Grant, Steven M M Sine, J Andrew A McCammon
    posted to mine nachr protein_dynamics protein_structure by barry on 2006-10-24 02:35:48 as ** along with 1 person and 2 groups ruvido structural_bioinformatics Bioinformatics
  • An automated approach for defining core atoms and domains in an ensemble of NMR-derived protein structures.
    Protein Eng, Vol. 10, No. 6. (June 1997), pp. 737-741.
    by LA Kelley, SP Gardner, MJ Sutcliffe
    posted to core_residues core_structure protein_dynamics protein_structure by barry on 2006-10-06 03:17:24 as ** along with 2 groups structural_bioinformatics Bioinformatics
  • Mechanisms of domain closure in proteins.
    J Mol Biol, Vol. 174, No. 1. (25 March 1984), pp. 175-191.
    by AM Lesk, C Chothia
    posted to citrate_synthase ctbp hinge_motion protein_dynamics protein_structure sheer_motion structure_comparison torsion_angles by barry on 2006-09-29 19:31:06 as **** along with 1 person and 2 groups ana 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
  • Can Conformational Change Be Described by Only a Few Normal Modes?
    Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593.
    by Paula Petrone, Vijay S Pande
    posted to nma protein_dynamics by barry on 2006-08-17 20:10:25 as ** along with 10 people and 7 groups BragilMassoud dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
  • The Contribution of Vibrational Entropy to Molecular Association : The Dimerization of Insulin
    Journal of Molecular Biology, Vol. 238, No. 3. (5 May 1994), pp. 405-414.
    by Bruce Tidor, Martin Karplus
    posted to nma protein_dynamics by barry on 2006-08-17 19:35:30 as ** along with 2 groups structural_bioinformatics 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 on 2006-08-16 21:45:51 as ***** along with 2 groups structural_bioinformatics Bioinformatics
  • Normal modes for predicting protein motions: a comprehensive database assessment and associated Web tool.
    Protein Sci, Vol. 14, No. 3. (March 2005), pp. 633-643.
    by V Alexandrov, U Lehnert, N Echols, D Milburn, D Engelman, M Gerstein
    posted to domain_motions nma protein_dynamics by barry on 2006-08-15 19:48:27 as read along with 2 people and 2 groups ana aqeel structural_bioinformatics Bioinformatics
  • Systematic analysis of domain motions in proteins from conformational change: New results on citrate synthase and T4 lysozyme
    Proteins: Structure, Function, and Genetics, Vol. 30, No. 2. (1998), pp. 144-154.
    by Steven Hayward, Herman JC Berendsen
    posted to domain_motions protein_dynamics protein_sequence by barry on 2006-08-15 19:31:25 as ** along with 1 person and 2 groups nigham structural_bioinformatics Bioinformatics
  • Identification of dynamical correlations within the myosin motor domain by the normal mode analysis of an elastic network model.
    J Mol Biol, Vol. 346, No. 3. (25 February 2005), pp. 745-759.
    by W Zheng, B Brooks
    posted to domain_motions kinesin molecular_motors myosin protein_dynamics by barry on 2006-08-15 19:19:43 as ** along with 2 people and 2 groups lna aqeel structural_bioinformatics 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 on 2006-08-15 19:16:49 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Molecular dissection of the inhibitor binding pocket of mitotic kinesin Eg5 reveals mutants that confer resistance to antimitotic agents
    Journal Of Molecular Biology, Vol. 360, No. 2. (7 July 2006), pp. 360-376.
    by Sebastien Brier, David Lemaire, Salvatore Debonis, Eric Forest, Frank Kozielski
    posted to drug_design eg5 inhibitor_design kinesin molecular_motors monastrol protein_dynamics protein_sequence protein_structure by barry on 2006-07-24 19:02:13 as ***** along with 2 groups structural_bioinformatics 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 on 2006-07-22 18:38:37 as * along with 2 groups structural_bioinformatics Bioinformatics
  • Conformational change of the loop L5 in rice Kinesin motor domain induced by nucleotide binding
    Journal Of Biochemistry, Vol. 139, No. 5. (May 2006), pp. 857-864.
    by Nobuhisa Umeki, Toshiaki Mitsui, Kazunori Kondo, Shinsaku Maruta
    posted to kin_loop5 kinesin molecular_motors protein_dynamics protein_structure by barry on 2006-06-12 19:44:32 as ** along with 2 groups structural_bioinformatics Bioinformatics
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