Tag protein_dynamics [at least 200 articles] Export

Recent papers classified by the tag protein_dynamics.

	Theory of Free Energy and Entropy in Noncovalent Binding [My Copy] Chemical Reviews, Vol. 109, No. 9. (9 September 2009), pp. 4092-4107. by Huan-Xiang Zhou, Michael K. Gilson posted to protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation free_energy entropy drug-discovery binding by jmccammon to the group McCammon on 2009-11-12 01:00:02 as along with 7 people and 1 group cchang agrossfield anuragsethi sobolevnrm dr_proton qshao paulschlesinger Chang group
	Backbone dynamics of Escherichia coli ribonuclease HI: correlations with structure and function in an active enzyme. [My Copy] Journal of Molecular Biology, Vol. 246, No. 1. (10 February 1995), pp. 144-163. by A. M. Mandel, M. Akke, A. G. Palmer posted to relaxation protein_dynamics nmr model-free-approach by bmduggan on 2009-11-02 17:25:31 as
	Protein dynamics from NMR [My Copy] Nat Struct Mol Biol, Vol. 5 Suppl (01 July 1998), pp. 513-517. by Lewis E. Kay posted to review relaxation protein_dynamics nmr by bmduggan on 2009-11-02 15:23:02 as along with 2 people apaydin ruvido
	Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2486-2502. by Christopher L. McClendon, Gregory Friedland, David L. Mobley, Homeira Amirkhani, Matthew P. Jacobson posted to protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation drug-discovery binding allostery by jmccammon to the group McCammon on 2009-10-31 19:59:28 as along with 3 people anuragsethi pmung acpan
	Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15673-15678. by Anil Korkut, Wayne A. Hendrickson posted to protein_dynamics molecular_mechanics_calculations functional_modes conformational_transitions coarse_grain adenylate_kinase by jmccammon to the group McCammon on 2009-10-17 20:42:54 as along with 1 person anuragsethi
	A force field for virtual atom molecular mechanics of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15667-15672. by Anil Korkut, Wayne A. Hendrickson posted to protein_dynamics molecular_mechanics_calculations functional_modes conformational_transitions coarse_grain by jmccammon on 2009-10-17 20:40:56 as along with 1 person and 2 groups barry structural_bioinformatics McCammon
	Atomistic View of the Conformational Activation of Src Kinase Using the String Method with Swarms-of-Trajectories [My Copy] Biophysical Journal, Vol. 97, No. 4. (19 August 2009), pp. L8-L10. by Wenxun Gan, Sichun Yang, Benoît Roux posted to tyrosine_kinase string_method simulation_methodology protein_dynamics molecular_dynamics_simulations md_simulation functional_modes conformational_transitions c_src by jmccammon to the group McCammon on 2009-10-14 23:04:22 as along with 1 person anuragsethi
	Structural biology: Protein dynamics from disorder [My Copy] Nature, Vol. 459, No. 7250. (24 June 2009), pp. 1063-1064. by Joel R. Tolman posted to protein_dynamics disorder by skywalkerus02 on 2009-10-06 12:59:33 as along with 5 people anna_yershova niallhaslam reyez pablocarb yse
	Conservation of Side-Chain Dynamics Within a Protein Family [My Copy] Journal of the American Chemical Society, Vol. 0, No. 0. (0000) by Anthony B. Law, Ernesto J. Fuentes, Andrew L. Lee posted to protein_family protein_dynamics flexibility by skywalkerus02 on 2009-10-06 05:53:15 as along with 4 people and 3 groups anuragsethi pablocarb barry sobolevnrm structural_bioinformatics McCammon baker-group
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to protein_dynamics ligand_binding by apaydin on 2009-10-04 18:02:10 as along with 5 people and 1 group ahmetbakan anuragsethi jmccammon okapi boris_aguilar McCammon
	Flexibility and packing in proteins [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 99, No. 3. (5 February 2002), pp. 1274-1279. by Bertil Halle posted to protein_flexibility protein_dynamics gnm free-energy by Diego_Prada on 2009-09-19 15:55:12 as along with 7 people and 3 groups edws barry sobolevnrm ana aqeel allmensch hmk baker-group structural_bioinformatics Bioinformatics
	Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 6. (1 November 2007), pp. 2312-2334. by Jianyin Shao, Stephen W. Tanner, Nephi Thompson, Thomas E. Cheatham posted to protein_dynamics md communities clustering beta-hairpin by Diego_Prada on 2009-09-19 15:52:15 as along with 9 people and 3 groups anuragsethi scampos oteri barry daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata structural_bioinformatics baker-group
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] Nature (18 November 2007) by Katherine A. Henzler-Wildman, Ming Lei, Vu Thai, Jordan S. Kerns, Martin Karplus, Dorothee Kern posted to struct_decorr proteins protein_dynamics collective_motions allostery active_site by Diego_Prada on 2009-09-19 15:45:21 as along with 9 people and 1 group ruvido tmmurali allmensch cactus sobolevnrm jlh64 RamuAnandakrishnan dmobley chenway baker-group
	Simultaneous determination of protein structure and dynamics [My Copy] 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 proteins protein_folding protein_dynamics by Diego_Prada on 2009-09-19 15:42:18 as along with 15 people and 3 groups xdeupi A_Coletta_Thesis karbak apaydin barry lillekatt baaden lna dgront allmensch daevans rsantana jlh64 biehl rph Structural Biology Group TorVergata structural_bioinformatics Bioinformatics
	Dynamic personalities of proteins [My Copy] Nature, Vol. 450, No. 7172. (12 December 2007), pp. 964-972. by Katherine Henzler-Wildman, Dorothee Kern posted to proteins protein_folding protein_dynamics md free-energy by Diego_Prada on 2009-09-19 15:39:20 as along with 17 people and 1 group xdeupi viktor21614 ruvido barry pavanghatty chad_davis allmensch choonpeng rsantana cjeans sobolevnrm wilbur mijam kjell phoenixzxl higueruelo GeeSharpMinor baker-group
	RedMD - Reduced molecular dynamics package [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2364-2373. by Adam Górecki, Marcin Szypowski, Maciej D&lstrok;ugosz, Joanna Trylska posted to protein_dynamics md_simulation coarse_grain brownian_dynamics by jmccammon to the group McCammon on 2009-09-12 21:46:20 as along with 4 people anuragsethi oteri flbarroso shwu
	Illuminating the mechanistic roles of enzyme conformational dynamics [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18055-18060. by Jeffrey A. Hanson, Karl Duderstadt, Lucas P. Watkins, et al.Sucharita Bhattacharyya, Jason Brokaw, Jhih-Wei Chu, Haw Yang posted to protein_strut_func protein_dynamics journal by joseph_x_zhou to the group protein_Dyn on 2009-08-18 16:00:12 as along with 6 people and 1 group kjell quanwang toerst barry sobolevnrm biehl baker-group
	Navigating the ribosome's metastable energy landscape. [My Copy] Trends in biochemical sciences (30 July 2009) by James B. Munro, Kevin Y. Sanbonmatsu, Christian M. Spahn, Scott C. Blanchard posted to protein_dynamics review ribosome by barry to the group structural_bioinformatics on 2009-08-06 23:38:31 as along with 2 people and 1 group anuragsethi reyez McCammon
	Random Matrix approach to collective behaviour and universality in protein dynamics [My Copy] (29 Jul 2009) by Raffaello Potestio, Fabio Caccioli, Pierpaolo Vivo posted to protein_dynamics rmt_applications by RMT on 2009-07-31 13:37:11 as
	A Natural Coarse Graining for Simulating Large Biomolecular Motion [My Copy] Vol. 91, No. 6. (15 September 2006), pp. 2115-2120. by Holger Gohlke, M. F. Thorpe posted to enm first froda nma protein_dynamics protein_flexibility by fl on 2009-07-13 09:47:21 as
	Prediction of protein conformational freedom from distance constraints. [My Copy] Proteins, Vol. 29, No. 2. (October 1997), pp. 240-251. by B. L. de Groot, D. M. van Aalten, R. M. Scheek, A. Amadei, G. Vriend, H. J. Berendsen posted to concoord essential_dynamics protein_dynamics protein_flexibility by fl on 2009-07-08 13:32:23 as along with 2 people aqeel simone
	Sampling protein conformations and pathways [My Copy] Journal of Computational Chemistry, Vol. 25, No. 9. (5 April 2004), pp. 1133-1148. by Ming Lei, Maria I. Zavodszky, Leslie A. Kuhn, M. F. Thorpe posted to protein_dynamics protein_flexibility rock by fl on 2009-07-08 10:38:37 as along with 9 people Scis0000002 jrperillaj aqeel blackbart smenor ruvido nh higueruelo apaydin
	Protein flexibility predictions using graph theory [My Copy] Proteins: Structure, Function, and Genetics, Vol. 44, No. 2. (29 May 2001), pp. 150-165. by Donald J. Jacobs, A. J. Rader, Leslie A. Kuhn, M. F. Thorpe posted to first graph_theory protein_dynamics protein_flexibility by fl on 2009-07-07 16:36:04 as along with 6 people and 2 groups Scis0000002 ana aqeel peprovy smenor LamBras structural_bioinformatics Bioinformatics
	Elucidating Protein Thermodynamics from the Three-Dimensional Structure of the Native State Using Network Rigidity [My Copy] Vol. 88, No. 2. (1 February 2005), pp. 903-915. by Donald J. Jacobs, Sargis Dallakyan posted to dcm first flexibility protein_dynamics by fl on 2009-07-07 16:32:35 as
	Protein Flexibility and Mobility in Structure-Based Drug Design [My Copy] Frontiers in Drug Design & Discovery: Structure-Based Drug Design in the 21st Century (March 2007), pp. 455-476. by Aqeel Ahmed, Sina Kazemi, Holger Gohlke posted to docking protein_dynamics protein_flexibility by fl on 2009-07-07 14:24:54 as along with 2 people and 2 groups aqeel barry structural_bioinformatics Bioinformatics
	Pathways for Conformational Change in Nitrogen Regulatory Protein C from Discrete Path Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 112, No. 8. (1 February 2008), pp. 2456-2465. by Mey Khalili, David J. Wales posted to first_passage free-energy protein_dynamics qha reaction_paths transition_path transition_states by Diego_Prada on 2009-07-02 12:02:29 as
	Refined kinetic transition networks for the GB1 hairpin peptide [My Copy] Phys. Chem. Chem. Phys., Vol. 11, No. 18. (2009), pp. 3341-3354. by Joanne M. Carr, David J. Wales posted to beta-hairpin first_passage free-energy hexapeptide protein_dynamics protein_folding qha reaction_paths short-peptides transition_path transition_states by Diego_Prada on 2009-07-02 11:55:15 as
	Protein folding on rugged energy landscapes: Conformational diffusion on fractal networks [My Copy] (24 Jun 2009) by Gregg Lois, J. Blawzdziewicz, Corey S. O'Hern posted to cmn coarse-grained complex_systems first_passage free-energy hp_model networks protein_dynamics protein_folding proteins reaction_paths transition_path by Diego_Prada on 2009-06-25 16:27:33 as
	How Adequate are One- and Two-Dimensional Free Energy Landscapes for Protein Folding Dynamics? [My Copy] Physical Review Letters, Vol. 102, No. 23. (2009), 238102. by Gia G. Maisuradze, Adam Liwo, Harold A. Scheraga posted to protein_dynamics pca funnels free-energy energy_landscape dpca by Diego_Prada on 2009-06-15 09:51:22 as along with 1 person agrossfield
	Relating protein conformational changes to packing efficiency and disorder. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 6. (June 2009), pp. 1230-1240. by N. Bhardwaj, M. Gerstein posted to protein_dynamics by barry to the group structural_bioinformatics on 2009-06-08 04:44:37 as along with 3 people and 1 group skywalkerus02 klexa sobolevnrm McCammon
	Two-state protein folding kinetics through all-atom molecular dynamics based sampling. [My Copy] Frontiers in bioscience : a journal and virtual library, Vol. 14 (2009), pp. 2801-2828. by P. G. Bolhuis posted to free-energy md protein_dynamics by Diego_Prada on 2009-05-30 19:31:01 as
	Prediction of chain flexibility in proteins [My Copy] Naturwissenschaften, Vol. 72, No. 4. (1 April 1985), pp. 212-213. by P. A. Karplus, G. E. Schulz posted to gnm protein_dynamics protein_folding proteins by Diego_Prada on 2009-04-30 11:55:17 as
	Computational Methods for Predicting Sites of Functionally Important Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Adam D. Schuyler, Heather A. Carlson, Eva L. Feldman posted to allosteric nma protein_dynamics by barry on 2009-04-23 03:03:19 as along with 5 people and 1 group skywalkerus02 agrossfield ubcg08l higueruelo sobolevnrm baker-group
	Protein Dynamism and Evolvability [My Copy] Science, Vol. 324, No. 5924. (10 April 2009), pp. 203-207. by Nobuhiko Tokuriki, Dan S. Tawfik posted to protein_dynamics protein_evolution protein_sequence review by barry to the group structural_bioinformatics on 2009-04-23 02:50:03 as along with 19 people and 2 groups tomhebbron anuragsethi ahmetbakan kevinchannon klexa lauresultan dbikard ibuch ramiro2k pablocarb ramanuja sobolevnrm biomcgary hsekiguc VGreiff phoenixzxl zwang jdoconnell paulschlesinger McCammon baker-group
	Probing the Flexibility of Large Conformational Changes in Protein Structures through Local Perturbations [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (3 April 2009), e1000343. by Bosco K. Ho, David A. Agard posted to md_simulation protein_dynamics torsion_angles by barry to the group structural_bioinformatics on 2009-04-06 17:55:04 as along with 5 people and 2 groups skywalkerus02 dimka operon sobolevnrm bourby baker-group McCammon
	Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins [My Copy] PLoS Comput Biol, Vol. 5, No. 2. (20 February 2009), e1000293. by Michael D. Daily, Jeffrey J. Gray posted to allosteric networks protein_dynamics by barry to the group structural_bioinformatics on 2009-02-20 19:17:41 as along with 9 people and 2 groups anuragsethi skywalkerus02 sobolevnrm pablocarb AngelB eallain allmensch gane5h apaydin baker-group McCammon
	Describing Protein Folding Kinetics by Molecular Dynamics Simulations. 1. Theory [My Copy] J. Phys. Chem. B, Vol. 108, No. 21. (27 May 2004), pp. 6571-6581. by W. C. Swope, J. W. Pitera, F. Suits posted to chapt_cmn free-energy markov md plos protein_dynamics stochastic_processes by Diego_Prada on 2009-02-16 11:14:57 as along with 2 people mtw apaydin
	Peptide Folding: When Simulation Meets Experiment [My Copy] Angewandte Chemie International Edition, Vol. 38, No. 1-2. (1999), pp. 236-240. by Xavier Daura, Karl Gademann, Bernhard Jaun, Dieter Seebach, Wilfred F. van Gunsteren, Alan E. Mark posted to beta-hairpin md protein_dynamics short-peptides by Diego_Prada on 2008-12-15 12:06:57 as along with 2 people dsmueller jteyra
	Deviations from the simple two-parameter model-free approach to the interpretation of nitrogen-15 nuclear magnetic relaxation of proteins [My Copy] Journal of the American Chemical Society, Vol. 112, No. 12. (1 June 1990), pp. 4989-4991. by Marius G. Clore, Attila Szabo, Ad Bax, Lewis E. Kay, Paul C. Driscoll, Angela M. Gronenborn posted to relaxation protein_dynamics nmr model-free-approach by bmduggan on 2008-11-26 21:46:56 as
	Toward quantitative simulations of carbon monoxide escape pathways in myoglobin. [My Copy] The journal of physical chemistry. B, Vol. 112, No. 19. (15 May 2008), pp. 6147-6154. by R. Elber, Q. H. Gibson posted to molecular_dynamics myoglobin protein_dynamics by onufriev on 2008-11-18 02:01:48 as
	Similarities between principal components of protein dynamics and random diffusion [My Copy] Physical Review E, Vol. 62, No. 6. (1 December 2000), 8438. by Berk Hess posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:56:06 as along with 1 person tovrstra
	Convergence of sampling in protein simulations [My Copy] Physical Review E, Vol. 65, No. 3. (1 March 2002), 031910. by Berk Hess posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:53:50 as along with 5 people and 1 group anuragsethi klexa tovrstra oteri softsimu Structural Biology Group TorVergata
	Free energy landscape of a biomolecule in dihedral principal component space: sampling convergence and correspondence between structures and minima. [My Copy] Proteins, Vol. 67, No. 3. (15 May 2007), pp. 569-578. by G. G. Maisuradze, D. M. Leitner posted to molecular_dynamics protein_dynamics by onufriev on 2008-11-17 01:39:36 as along with 2 people scampos Diego_Prada
	Statistical Prediction and Molecular Dynamics Simulation [My Copy] Biophys. J. (1 August 2008), biophysj.108.131623. by Ben Cooke, Scott Schmidler posted to journal protein_dynamics statistical_prediction by joseph_x_zhou on 2008-11-16 21:08:25 as along with 3 people Diego_Prada agrossfield paulschlesinger
	Coupling Between Folding and Ionization Equilibria: Effects of pH on the Conformational Preferences of Polypeptides [My Copy] Journal of Molecular Biology (December 1996), pp. 770-783. by D. R. Ripoll, Y. N. Vorobjev, A. Liwo, J. A. Vila, H. A. Scheraga posted to ph protein_dynamics protein_folding by onufriev on 2008-11-08 22:48:34 as
	Visualizing myosin–actin interaction with a genetically-encoded fluorescent strain sensor [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 44. (4 November 2008), pp. 16882-16887. by Sosuke Iwai, Taro Q. Uyeda posted to gfp myosin protein_dynamics by barry to the group McCammon on 2008-11-07 01:41:23 as along with 3 people okapi cactus melting
	Conformational induction versus conformational selection: evidence from allosteric enhancers Allosteric enhancers show that receptor activation proceeds mainly by conformational induction [My Copy] Trends in Pharmacological Sciences, Vol. 17, No. 5. (May 1996), 189. by R. Bruns posted to conformational_selection protein_dynamics review by barry on 2008-11-05 19:06:38 as
	Linking folding with aggregation in Alzheimer's beta-amyloid peptides [My Copy] 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 pka protein_dynamics protein_folding by onufriev on 2008-11-01 02:33:42 as along with 3 people and 1 group scampos Diego_Prada sobolevnrm baker-group
	Intrinsic dynamics of an enzyme underlies catalysis [My Copy] Nature, Vol. 438, No. 7064. (3 November 2005), pp. 117-121. by Elan Z. Eisenmesser, Oscar Millet, Wladimir Labeikovsky, et al.Dmitry M. Korzhnev, Magnus Wolf-Watz, Daryl A. Bosco, Jack J. Skalicky, Lewis E. Kay, Dorothee Kern posted to adk protein_dynamics by barry on 2008-10-27 22:44:16 as along with 8 people mkrishna BragilMassoud karbak lna dlr tny jlh64 rph
	Conservation of μs-ms Enzyme Motions in the Apo- and Substrate-Mimicked State [My Copy] J. Am. Chem. Soc., Vol. 127, No. 25. (29 June 2005), pp. 9167-9176. by H. Beach, R. Cole, M. L. Gill, J. P. Loria posted to allosteric nmr protein_dynamics by barry on 2008-10-27 22:42:57 as along with 1 person and 1 group sobolevnrm baker-group

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protein_structure	198
md_simulation	65
nma	58
review	57
allosteric	47
molecular_motors	43
bioinf_methods	39
nmr	39
kinesin	38
protein_design	35
protein_sequence	33
protein_protein	29
pca	25
domain_motions	23
protein_folding	22
myosin	21
structure_comparison	20
protein_evolution	19
protein_ligand_binding	18
correlated_motions	17
molecular_dynamics	15
free-energy	13
structural_bioinformatics	13
core_residues	12
core_structure	12
binding	11
protein_strut_func	11
mine	10
proteins	10
coarse_grain	9
drug_design	9
eg5	9
journal	9
molecular_dynamics_simulations	9
monastrol	9
nachr	9
ntpases	9
p-loop	9
structure_flexible	9
allostery	8
conformational_transitions	8
docking	8
functional_modes	8
md	8
contacts	7
disorder	7
networks	7
normal_mode_analysis	7
torsion_angles	7
conformational_dynamics	6
drug-discovery	6
enm	6
free_energy	6
gnm	6
inhibitor_design	6
kinases	6
markov	6
motor_model	6
protein-ligand	6
protein_flexibility	6
protein_function	6
replica_exchange	6
smd	6
molecular_mechanics_calculations	5
relaxation	5
transition_path	5
chapt_cmn	4
clustering	4
energy_entropy	4
flexibility	4
myoglobin	4
plos	4
protein_conformations	4
protein_packing	4
protein_structure_determination	4
r	4
struct_decorr	4
tutorial	4
adenylate_kinase	3
adk	3
beta-hairpin	3
brownian_dynamics	3
c_src	3
coarse-grained	3
coarse_model	3
conformation	3
dynamic_similarity	3
entropy	3
f1atpase	3
first_passage	3
g_proteins	3
mts	3
myov	3
ncd	3
nucleotide_analogues	3
protein_ligand	3
ribosome	3
swi-swii	3
time_series_analysis	3
umbrella	3

Tag protein_dynamics [at least 200 articles] Export

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