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Group: Bioinformatics - with tag protein_dynamics [93 articles]

Recent papers posted by members of the Bioinformatics group with tag protein_dynamics
  • 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 to the group Bioinformatics on 2008-10-02 19:21:01 as ** along with 1 person and 2 groups paulschlesinger structural_bioinformatics McCammon
  • 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
  • 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 to the group Bioinformatics on 2007-12-04 22:56:25 as ** along with 8 people and 3 groups aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras jmccammon structural_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 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
  • 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 to the group Bioinformatics on 2007-09-22 23:29:36 as ***** along with 1 group structural_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_structure protein_dynamics by barry to the group Bioinformatics on 2007-09-05 01:57:38 as * along with 2 people and 1 group aqeel edvin structural_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 protein_structure protein_dynamics nma by barry to the group Bioinformatics on 2007-09-05 01:48:20 as ** along with 4 people and 1 group gisle jlh64 edvin tny structural_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 protein_protein protein_dynamics nma by barry to the group Bioinformatics on 2007-09-04 20:13:14 as ***** along with 1 person and 1 group aqeel structural_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_structure protein_sequence protein_dynamics protein_design by barry to the group Bioinformatics on 2007-09-04 19:32:05 as ** along with 5 people and 1 group shuns jwm kevinchannon bethbromley ca3295 structural_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 protein_structure protein_dynamics nma correlated_motions by barry to the group Bioinformatics on 2007-08-13 19:53:33 as ** along with 3 people and 1 group aqeel choonpeng willpitt 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
  • 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 protein_structure protein_protein protein_dynamics disorder allosteric by barry to the group Bioinformatics on 2007-05-25 01:36:39 as **** along with 5 people and 2 groups apaydin choonpeng cursonivel1 cactus allmensch structural_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 torsion_angles swi-swii structural_bioinformatics sca r protein_structure protein_sequence protein_dynamics pca p-loop ntpases molecular_motors mine kinesin domain_motions correlated_motions core_structure clustering bioinf_methods by barry to the group Bioinformatics on 2007-04-27 17:41:06 as read along with 3 people and 1 group choonpeng cactus insectopalo 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
  • 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 protein_structure protein_function protein_evolution protein_dynamics by ana to the group Bioinformatics on 2007-01-24 03:21:40 as **** along with 1 person and 1 group barry structural_bioinformatics
  • 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
  • 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 to the group Bioinformatics on 2007-01-19 21:58:55 as ** along with 1 group structural_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 to the group Bioinformatics on 2007-01-19 21:54:41 as ** along with 4 people and 1 group gisle Einat jlh64 edvin structural_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 to the group Bioinformatics on 2006-11-15 19:16:56 as ** along with 2 people and 1 group lna choonpeng structural_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 to the group Bioinformatics on 2006-11-15 19:14:54 as ** along with 1 group structural_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 to the group Bioinformatics on 2006-10-30 19:26:11 as **** along with 1 group structural_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 to the group Bioinformatics on 2006-10-24 02:35:48 as ** along with 1 person and 1 group ruvido structural_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 to the group Bioinformatics on 2006-10-06 03:17:24 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
  • 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 to the group Bioinformatics on 2006-08-17 20:10:25 as ** along with 11 people and 6 groups csrocha BragilMassoud dimka aqeel shuns yongzhao xdeupi choonpeng joergkurtwegner daevans LamBras structural_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 to the group Bioinformatics on 2006-08-17 19:35:30 as ** along with 1 group 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
  • 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 to the group Bioinformatics on 2006-08-15 19:31:25 as ** along with 1 person and 1 group nigham structural_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 to the group Bioinformatics on 2006-08-15 19:19:43 as ** along with 2 people and 1 group lna aqeel 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
  • 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 to the group Bioinformatics on 2006-07-24 19:02:13 as ***** along with 1 group 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
  • 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 to the group Bioinformatics on 2006-06-12 19:44:32 as ** along with 1 group structural_bioinformatics
  • 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
  • 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
  • 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
  • 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
  • Rotamer Libraries in the 21st Century
    Current Opinion in Structural Biology, Vol. 12, No. 4. (01 August 2002), pp. 431-440.
    by Jr Dunbrack
    posted to protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-04-10 19:39:07 as ** along with 3 people and 4 groups apaydin joergkurtwegner LamBras structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • The penultimate rotamer library
    Proteins, Vol. 40, No. 3. (15 August 2000), pp. 389-408.
    by SC Lovell, JM Word, JS Richardson, DC Richardson
    posted to protein_design protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-04-10 19:37:07 as ***** along with 3 people and 4 groups csrocha joergkurtwegner LamBras structural_bioinformatics Molecular-Modelling Drug-Design Cheminformatics
  • Recent advances in Cys-loop receptor structure and function
    Nature, Vol. 440, No. 7083. (23 March 2006), pp. 448-455.
    by Steven M Sine, Andrew G Engel
    posted to nachr protein_dynamics protein_structure review by barry to the group Bioinformatics on 2006-03-22 22:38:22 as ** along with 2 people and 7 groups shantanu frooonk structural_bioinformatics MathBio Biostatistics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
  • Clustering of low-energy conformations near the native structures of small proteins.
    Proc Natl Acad Sci U S A, Vol. 95, No. 19. (15 September 1998), pp. 11158-11162.
    by D Shortle, KT Simons, D Baker
    posted to protein_design protein_dynamics protein_folding protein_sequence protein_structure by barry to the group Bioinformatics on 2006-03-22 20:15:18 as *** along with 3 people and 4 groups thaliana dgront 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
  • Flexibility and packing in proteins
    PNAS, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279.
    by Bertil Halle
    posted to packing_density protein_dynamics protein_structure structure_flexible by ana to the group Bioinformatics on 2006-03-10 07:02:22 as **** along with 3 people and 1 group aqeel allmensch hmk structural_bioinformatics
  • iGNM: a database of protein functional motions based on Gaussian Network Model.
    Bioinformatics, Vol. 21, No. 13. (1 July 2005), pp. 2978-2987.
    by LW Yang, X Liu, CJ Jursa, M Holliman, AJ Rader, HA Karimi, I Bahar
    posted to nma protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-03-06 22:07:42 as ** along with 3 people and 2 groups baaden yongzhao choonpeng structural_bioinformatics TSRI_MGL
  • 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
  • Topological Determinants of Protein Domain Swapping
    Structure, Vol. 14, No. 1. (January 2006), pp. 5-14.
    by Feng Ding, Kirk C Prutzman, Sharon L Campbell, Nikolay V Dokholyan
    posted to contacts core_structure domain_motions domain_swapping networks protein_dynamics protein_folding protein_structure by barry to the group Bioinformatics on 2006-01-16 20:12:22 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
  • Constrained geometric simulation of diffusive motion in proteins
    Physical Biology, Vol. 2, No. 4. (December 2005), S127.
    by Stephen Wells, Scott Menor, Brandon Hespenheide, MF Thorpe
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-01-09 18:36:48 as ** along with 2 people and 1 group apaydin higueruelo structural_bioinformatics
  • Protein flexibility using constraints from molecular dynamics simulations
    Physical Biology, Vol. 2, No. 4. (December 2005), S137.
    by Tatyana Mamonova, Brandon Hespenheide, Rachel Straub, MF Thorpe, Maria Kurnikova
    posted to bioinf_methods protein_dynamics protein_structure by barry to the group Bioinformatics on 2006-01-09 18:30:27 as ** along with 1 person and 2 groups Poincare structural_bioinformatics Algorithms
  • Ran's C-terminal, basic patch, and nucleotide exchange mechanisms in light of a canonical structure for Rab, Rho, Ras, and Ran GTPases.
    Genome Res, Vol. 13, No. 4. (April 2003), pp. 673-692.
    by AF Neuwald, N Kannan, A Poleksic, N Hata, JS Liu
    posted to allosteric bioinf_methods contacts core_residues g_proteins ntpases p-loop protein_design protein_dynamics protein_evolution protein_sequence protein_structure by barry to the group Bioinformatics on 2006-01-07 03:57:13 as ***** along with 1 group structural_bioinformatics
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