Group: structural_bioinformatics - with tag md_simulation [64 articles] Export

Recent papers posted by members of the structural_bioinformatics group with tag md_simulation

	Nucleotide-dependent conformational states of actin [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 31. (4 August 2009), pp. 12723-12728. by Jim Pfaendtner, Davide Branduardi, Michele Parrinello, Thomas D. Pollard, Gregory A. Voth posted to actin md_simulation metadynamics by barry to the group structural_bioinformatics on 2009-08-07 00:31:56 as along with 3 people and 1 group pmung okapi anuragsethi McCammon
	Improving Structure-Based Function Prediction Using Molecular Dynamics [My Copy] Vol. 17, No. 7. (15 July 2009), pp. 919-929. by Dariya S. Glazer, Randall J. Radmer, Russ B. Altman posted to function_prediction md_simulation by barry to the group structural_bioinformatics on 2009-07-22 19:04:59 as along with 1 person and 1 group apaydin McCammon
	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
	Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (20 March 2009), e1000325. by Barry J. Grant, Alemayehu A. Gorfe, Andrew J. Mccammon posted to accelerated_md md_simulation protein_structure ras by barry to the group structural_bioinformatics on 2009-03-20 17:13:40 as along with 2 people and 2 groups ana allmensch McCammon Bioinformatics
	Solvent dramatically affects protein structure refinement [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20239-20244. by Gaurav Chopra, Christopher M. Summa, Michael Levitt posted to md_simulation structure_refinement by barry to the group structural_bioinformatics on 2009-03-08 02:52:55 as along with 7 people and 3 groups rabio pavanghatty mijam dgront sobolevnrm biehl itmeson McCammon Bioinformatics baker-group
	Similarity Measures for Protein Ensembles [My Copy] PLoS ONE, Vol. 4, No. 1. (15 January 2009), e4203. by Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg posted to clustering md_simulation by barry to the group structural_bioinformatics on 2009-02-16 07:52:52 as along with 8 people and 2 groups anuragsethi klexa apaydin sobolevnrm gane5h jmccammon reyez biehl baker-group McCammon
	Proteins as networks: usefulness of graph theory in protein science. [My Copy] Current protein & peptide science, Vol. 9, No. 1. (February 2008), pp. 28-38. by A. Krishnan, J. P. Zbilut, M. Tomita, A. Giuliani posted to md_simulation networks protein_structure review by barry to the group structural_bioinformatics on 2009-02-09 18:43:51 as
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to gpus md_simulation by barry to the group structural_bioinformatics on 2009-02-06 18:14:37 as along with 11 people and 2 groups oteri anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque sobolevnrm ruvido massivemayhem RamuAnandakrishnan baker-group McCammon
	Small and large scale conformational changes of adenylate kinase: a molecular dynamics study of the subdomain motion and mechanics. [My Copy] Biophysical journal (17 October 2008) by Francesco Pontiggia, Andrea Zen, Cristian Micheletti posted to adk conformational_selection md_simulation by barry to the group structural_bioinformatics on 2008-10-23 12:23:59 as along with 1 group McCammon
	Flexible ligand docking to multiple receptor conformations: a practical alternative. [My Copy] Current opinion in structural biology, Vol. 18, No. 2. (April 2008), pp. 178-184. by M. Totrov, R. Abagyan posted to docking md_simulation review by barry to the group structural_bioinformatics on 2008-10-02 19:48:14 as along with 3 people and 2 groups klexa oteri aqeel McCammon Bioinformatics
	Rate of Loop Formation in Peptides: A Simulation Study [My Copy] Journal of Molecular Biology, Vol. 382, No. 2. (3 October 2008), pp. 556-565. by Matthias J. Feige, Emanuele Paci posted to md_simulation by barry to the group structural_bioinformatics on 2008-08-29 19:03:07 as along with 1 group McCammon
	Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin [My Copy] 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 structural_bioinformatics on 2008-08-18 20:21:10 as along with 1 person and 1 group okapi Bioinformatics
	How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach [My Copy] J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636. by Hugh Nymeyer posted to md_simulation replica_exchange by barry to the group structural_bioinformatics on 2008-07-08 01:17:17 as along with 3 people and 2 groups agrossfield sobolevnrm loison baker-group McCammon
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] 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 barry to the group structural_bioinformatics on 2008-07-08 01:12:03 as along with 5 people and 2 groups flbarroso onufriev jmccammon biehl sobolevnrm baker-group McCammon
	From the Cover: A dry ligand-binding cavity in a solvated protein [My Copy] 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 barry to the group structural_bioinformatics on 2008-07-08 01:11:30 as along with 3 people and 2 groups Lombardo_7 jmccammon sobolevnrm McCammon baker-group
	Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins [My Copy] 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 structural_bioinformatics on 2008-06-10 22:34:01 as along with 1 person and 1 group allmensch Bioinformatics
	Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways [My Copy] Journal of Molecular Biology, Vol. 378, No. 5. (16 May 2008), pp. 1155-1173. by Michael J. Bradley, Peter T. Chivers, Nathan A. Baker posted to allosteric md_simulation by barry to the group structural_bioinformatics on 2008-04-27 22:02:29 as along with 2 people and 1 group sobolevnrm skoddet baker-group
	Wordom: a program for efficient analysis of molecular dynamics simulations [My Copy] Bioinformatics, Vol. 23, No. 19. (1 October 2007), pp. 2625-2627. by Michele Seeber, Marco Cecchini, Francesco Rao, Giovanni Settanni, Amedeo Caflisch posted to bioinf_methods md_simulation by barry to the group structural_bioinformatics on 2007-11-27 23:33:01 as along with 6 people and 1 group guhjy tmmurali choonpeng hmk sobolevnrm LamBras baker-group
	Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 47. (20 November 2007), pp. 18496-18501. by Karunesh Arora, Charles L. Brooks posted to allosteric kinases md_simulation by barry to the group structural_bioinformatics on 2007-11-27 23:23:59 as along with 7 people and 1 group xdeupi jrperillaj allmensch cactus sobolevnrm jlh64 karunesh baker-group
	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 clustering md_simulation protein_structure by barry to the group structural_bioinformatics on 2007-10-26 22:44:54 as along with 10 people and 2 groups karinaecomp anuragsethi Diego_Prada scampos oteri daevans sobolevnrm LamBras allmensch GermanErlenkamp Structural Biology Group TorVergata baker-group
	Complementarity of Structure Ensembles in Protein-Protein Binding [My Copy] 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 structural_bioinformatics on 2007-10-02 03:05:14 as along with 4 people and 2 groups raik lna allmensch cursonivel1 Bioinformatics cursonivel1
	Dihedral angle principal component analysis of molecular dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 126, No. 24. (2007) by Alexandros Altis, Phuong H. Nguyen, Rainer Hegger, Gerhard Stock posted to md_simulation pca torsion_angles by barry to the group structural_bioinformatics on 2007-09-27 20:06:59 as along with 4 people scampos Diego_Prada ruvido nh
	Dihedral angle principal component analysis of molecular dynamics simulations [My Copy] Journal of Chemical Physics, Vol. 126 (2007) by A. Altis, P. H. Nguyen, R. Hegger, G. Stock posted to torsion_angles pca md_simulation by barry to the group structural_bioinformatics on 2007-08-28 02:10:54 as along with 1 person and 2 groups sobolevnrm Bioinformatics baker-group
	Coarse-grained molecular dynamics simulations of membrane proteins and peptides [My Copy] Journal of Structural Biology, Vol. 157, No. 3. (2007), pp. 593-605. by P. J. Bond, J. Holyoake, A. Ivetac, S. Khalid, M. S. P. Sansom posted to md_simulation ion_channels coarse-grained by barry to the group structural_bioinformatics on 2007-08-28 01:58:49 as along with 1 person and 2 groups sobolevnrm Bioinformatics baker-group
	Characterization of Protein Conformational States by Normal-Mode Frequencies [My Copy] J. Am. Chem. Soc. (23 August 2007) by B. A. Hall, S. L. Kaye, A. Pang, R. Perera, P. C. Biggin posted to protein_structure pca nma md_simulation clustering by barry to the group structural_bioinformatics on 2007-08-27 19:15:41 as along with 7 people and 2 groups Diego_Prada Scis0000002 ubcg08l aqeel choonpeng sobolevnrm LamBras Bioinformatics baker-group
	Phylogeny of protein-folding trajectories reveals a unique pathway to native structure. [My Copy] 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 structural_bioinformatics on 2007-08-10 18:38:42 as along with 1 group Bioinformatics
	Unfolding Pathways of Goat [alpha]-Lactalbumin as Revealed in Multiple Alignment of Molecular Dynamics Trajectories [My Copy] 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 structural_bioinformatics on 2007-08-10 18:36:13 as along with 1 person and 1 group choonpeng Bioinformatics
	Molecular dynamics study of time-correlated protein domain motions and molecular flexibility: cytochrome P450BM-3. [My Copy] Biophys. J., Vol. 73, No. 3. (1 September 1997), pp. 1147-1159. by G. E. Arnold, R. L. Ornstein posted to protein_sequence md_simulation distance_matrices correlated_motions by barry to the group structural_bioinformatics on 2007-07-26 02:46:16 as along with 1 group Bioinformatics
	Ensemble-Based Convergence Analysis of Biomolecular Trajectories [My Copy] 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 structural_bioinformatics on 2007-04-27 17:36:16 as along with 1 person and 1 group loison Bioinformatics
	Equilibration of experimentally determined protein structures for molecular dynamics simulation [My Copy] 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 structural_bioinformatics on 2007-04-27 17:32:57 as along with 1 group Bioinformatics
	Analyzing large-scale structural change in proteins: comparison of principal component projection and Sammon mapping. [My Copy] Proteins, Vol. 64, No. 1. (1 July 2006), pp. 210-218. by S. Mesentean, S. Fischer, J. C. Smith posted to pca md_simulation clustering by barry to the group structural_bioinformatics on 2007-03-27 00:20:10 as along with 1 group Bioinformatics
	Mechanochemical Coupling in the Myosin Motor Domain. I. Insights from Equilibrium Active-Site Simulations [My Copy] PLoS Comput Biol, Vol. 3, No. 2. (9 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 structural_bioinformatics on 2007-02-12 23:41:33 as along with 1 person and 1 group Diego_Prada Bioinformatics
	Pump-probe molecular dynamics as a tool for studying protein motion and long range coupling [My Copy] 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 structural_bioinformatics on 2007-01-30 20:09:59 as along with 3 people and 2 groups lna choonpeng sobolevnrm Bioinformatics baker-group
	Exploration of the conformational space of myosin recovery stroke via molecular dynamics [My Copy] 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 structural_bioinformatics on 2006-12-08 18:58:04 as along with 1 group Bioinformatics
	Can MM-PBSA calculations predict the specificities of protein kinase inhibitors? [My Copy] 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 structural_bioinformatics on 2006-12-08 18:52:33 as along with 1 group Bioinformatics
	Ion selectivity in potassium channels [My Copy] Biophysical Chemistry In Ion Hydration Special Issue, 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 structural_bioinformatics on 2006-12-08 18:50:17 as along with 1 group Bioinformatics
	Molecular dynamics -- potential of mean force calculations as a tool for understanding ion permeation and selectivity in narrow channels [My Copy] Biophysical Chemistry In Ion Hydration Special Issue, Vol. 124, No. 3. (1 December 2006), pp. 251-267. by Toby W. Allen, Olaf S. Andersen, Benoit Roux posted to ion_channels md_simulation pmf by barry to the group structural_bioinformatics on 2006-12-08 18:46:14 as along with 2 people and 2 groups ibuch sobolevnrm Bioinformatics baker-group
	Can principal components yield a dimension reduced description of protein dynamics on long time scales? [My Copy] The Journal Of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces & Biophysical, Vol. 110, No. 45. (16 November 2006), pp. 22842-22852. by Oliver F. Lange, Helmut Grubmuller posted to md_simulation pca by barry to the group structural_bioinformatics on 2006-12-08 18:42:44 as along with 1 group Bioinformatics
	The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme. [My Copy] Biopolymers, Vol. 68, No. 1. (January 2003), pp. 47-62. by J. H. Lin, A. L. Perryman, J. R. Schames, J. A. McCammon posted to bioinf_methods docking drug_design md_simulation protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-09-07 20:06:11 as along with 5 people and 2 groups karinaecomp blackbart kazemi sobolevnrm LamBras Bioinformatics baker-group
	Dynamical properties of fasciculin-2 [My Copy] 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 structural_bioinformatics on 2006-07-22 18:38:37 as along with 1 group Bioinformatics
	Flexibility and conformational entropy in protein-protein binding. [My Copy] 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 structural_bioinformatics on 2006-05-22 19:20:49 as along with 6 people and 1 group hmk raik pansapiens lna aqeel allmensch Bioinformatics
	Flexibility and conformational entropy in protein-protein binding [My Copy] 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 structural_bioinformatics on 2006-05-08 20:05:12 as along with 1 person and 4 groups joergkurtwegner 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. [My Copy] Proteins, Vol. 22, No. 1. (May 1995), pp. 45-54. by D. M. van Aalten, A. Amadei, A. B. Linssen, V. G. Eijsink, G. Vriend, H. J. Berendsen posted to md_simulation pca protein_dynamics protein_structure by barry to the group structural_bioinformatics on 2006-03-17 20:07:25 as along with 1 group Bioinformatics
	Molecular Dynamics Simulations of the Complete Satellite Tobacco Mosaic Virus [My Copy] 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 structural_bioinformatics on 2006-03-15 07:47:21 as along with 2 people and 1 group r2s2 RamuAnandakrishnan Bioinformatics
	Intramolecular Signaling Pathways Revealed by Modeling Anisotropic Thermal Diffusion [My Copy] Journal of Molecular Biology, Vol. 351, No. 2. (12 August 2005), pp. 345-354. by Nobuyuki Ota, David A. Agard posted to allosteric contacts correlated_motions correlated_mutations md_simulation by barry to the group structural_bioinformatics on 2006-01-24 18:24:55 as along with 3 people and 1 group pansapiens lna choonpeng Bioinformatics
	The Allosteric Mechanism of Yeast Chorismate Mutase: A Dynamic Analysis [My Copy] 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 structural_bioinformatics on 2006-01-16 20:34:23 as along with 2 people and 1 group ruvido higueruelo Bioinformatics
	Molecular dynamics studies of proteins [My Copy] 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 structural_bioinformatics on 2006-01-09 21:03:10 as along with 1 group Bioinformatics
	Hierarchical structure of the energy landscape of proteins revisited by time series analysis. I. Mimicking protein dynamics in different time scales [My Copy] The Journal Of Chemical Physics, Vol. 123, No. 14. (8 October 2005), pp. 144910-144910. by Burak Alakent, Mehmet C. Camurdan, Pemra Doruker posted to md_simulation pca time_series_analysis by barry to the group structural_bioinformatics on 2005-12-05 19:15:31 as along with 1 group Bioinformatics
	Comparative molecular dynamics--similar folds and similar motions? [My Copy] 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 structural_bioinformatics on 2005-11-29 23:22:16 as along with 1 group Bioinformatics
	Ligand binding affinities from MD simulations. [My Copy] Acc Chem Res, Vol. 35, No. 6. (June 2002), pp. 358-365. by J. Aqvist, V. B. Luzhkov, B. O. Brandsdal posted to free_energy md_simulation by barry to the group structural_bioinformatics on 2005-10-26 00:14:13 as along with 4 people and 1 group flbarroso baaden dimka superpyrin Bioinformatics

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protein-ligand	77
protein_dynamics	68
free_energy	62
binding	57
protein_structure	52
drug-discovery	51
pca	27
coarse_grain	26
solvation	26
clustering	19
review	18
allosteric	17
electrostatics	16
allostery	15
molecular_dynamics_simulations	15
nma	14
bioinf_methods	13
membrane	13
accelerated_md	12
myosin	12
protein_protein	12
contacts	10
structural_bioinformatics	10
conformational_transitions	9
molecular_motors	9
nmr	9
protein_folding	9
proteins	9
replica_exchange	9
correlated_motions	8
torsion_angles	8
docking	7
ion_channel	7
kinases	7
ras	7
drug_design	6
ion_channels	6
monte_carlo	6
pmf	6
qm-mm	6
simulation_methodology	6
smd	6
actin	5
conformational_selection	5
entropy	5
structure_refinement	5
mine	4
protein_sequence	4
adk	3
bd_simulation	3
brownian_dynamics	3
c_src	3
correlated_mutations	3
diffusion	3
distance_matrices	3
function_prediction	3
functional_modes	3
gpus	3
inhibitor_design	3
ion_pairs	3
kinetics	3
ksca	3
langevin_dynamics	3
metadynamics	3
mm-pbsa	3
motor_model	3
ntpases	3
nucleic_acids	3
peptides	3
protein-protein	3
protein_design	3
qm	3
string_method	3
structure_comparison	3
time_series_analysis	3
tyrosine_kinase	3
water_molecules	3
allosteric_regulation	2
alpha_actinin	2
amber	2
coarse-grained	2
conformational_change	2
cooperativity	2
cytoskeleton	2
domain_motions	2
dynamics	2
hsp90	2
interaction_energy	2
ligand_induced_conformational_changes	2
membranes	2
networks	2
pka	2
ribosome	2
synergistic_regulation	2
transcription_factor	2
trps	2
tryptophan_synthase	2
wham	2
arp3	1
indirect_readout	1

Group: structural_bioinformatics - with tag md_simulation [64 articles] Export

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