Group: McCammon - with tag md_simulation [86 articles] Export

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

	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter In Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted to molecular_dynamics_simulations membrane md_simulation diffusion conformational_transitions coarse_grain by jmccammon to the group McCammon on 2009-11-27 23:01:41 as along with 4 people loison flbarroso anuragsethi sobolevnrm
	Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14343-14354. by Zunnan Huang, Chung F. Wong posted to solvation protein_dynamics protein-ligand peptides molecular_dynamics_simulations md_simulation drug-discovery conformational_transitions binding by jmccammon to the group McCammon on 2009-11-21 20:27:49 as along with 1 person anuragsethi
	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
	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
	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
	Prediction of the Water Content in Protein Binding Sites [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13337-13346. by Julien Michel, Julian Tirado-Rives, William L. Jorgensen posted to water_molecules solvation simulation_methodology protein-ligand monte_carlo md_simulation free_energy drug-discovery binding by jmccammon to the group McCammon on 2009-10-10 21:07:02 as along with 2 people snichols15 qshao
	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
	Detection of Functional Modes in Protein Dynamics [My Copy] PLoS Computational Biology (August 2009) by J. S. Hub, B. L. de Groot posted to proteins protein_dynamics md_simulation functional_modes coarse_grain by jmccammon to the group McCammon on 2009-09-03 01:15:01 as
	Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 15. (13 August 2009), pp. 4860-4868. by Dariusz Ekonomiuk, Xun-Cheng Su, Kiyoshi Ozawa, et al.Christophe Bodenreider, Siew P. Lim, Gottfried Otting, Danzhi Huang, Amedeo Caflisch posted to protein-ligand md_simulation drug-discovery binding by jmccammon to the group McCammon on 2009-08-13 20:03:20 as along with 3 people ubcg08l pmung carlosjavierna
	Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin [My Copy] Journal of the American Chemical Society, Vol. 131, No. 32. (19 August 2009), pp. 11338-11340. by Peter M. Kasson, Daniel L. Ensign, Vijay S. Pande posted to protein-ligand md_simulation kinetics drug-discovery binding allostery by jmccammon to the group McCammon on 2009-08-13 19:20:53 as along with 2 people oteri dicksmit
	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 McCammon on 2009-08-07 00:31:56 as along with 3 people and 1 group pmung okapi anuragsethi structural_bioinformatics
	Polarization effects in molecular mechanical force fields [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 33. (2009), 333102. by Piotr Cieplak, Francois-Yves Dupradeau, Yong Duan, Junmei Wang posted to electrostatics md_simulation solvation by jmccammon to the group McCammon on 2009-07-27 18:02:24 as along with 1 person anuragsethi
	Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10059-10062. by M. P. Gaigeot posted to md_simulation by jmccammon to the group McCammon on 2009-07-25 21:21:43 as along with 3 people and 1 group loison whitead carlosjavierna Jiang Research Group
	Cooperativity dominates the genomic organization of p53-response elements: a mechanistic view. [My Copy] PLoS computational biology, Vol. 5, No. 7. (24 July 2009), e1000448. by Yongping Pan, Ruth Nussinov posted to md_simulation transcription_factor by barry to the group McCammon on 2009-07-24 18:55:37 as along with 1 person ubcg08l
	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 McCammon on 2009-07-22 19:04:59 as along with 1 person and 1 group apaydin structural_bioinformatics
	ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639. by M. J. Harvey, G. Giupponi, G. De Fabritiis posted to accelerated_md md_simulation by jmccammon to the group McCammon on 2009-07-11 23:43:25 as along with 4 people qshao r2s2 ibuch mmuecke
	Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1624-1631. by Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg posted to langevin_dynamics md_simulation by jmccammon to the group McCammon on 2009-07-11 23:42:28 as along with 2 people and 1 group edws sobolevnrm baker-group
	Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8800-8812. by Pavel I. Zhuravlev, Christopher K. Materese, Garegin A. Papoian posted to md_simulation proteins by jmccammon to the group McCammon on 2009-07-08 21:22:30 as along with 1 person carlosjavierna
	Configurational Entropy in Protein–Peptide Binding:Computational Study of Tsg101 Ubiquitin E2 Variant Domain with an HIV-Derived PTAP Nonapeptide [My Copy] Journal of Molecular Biology, Vol. 389, No. 2. (05 June 2009), pp. 315-335. by Benjamin J. Killian, Joslyn Y. Kravitz, Sandeep Somani, Paramita Dasgupta, Yuan-Ping Pang, Michael K. Gilson posted to binding free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-06-11 01:30:05 as
	Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase [My Copy] Journal of the American Chemical Society, Vol. 131, No. 18. (13 May 2009), pp. 6608-6613. by Hongtao Yu, Steven W. Rick posted to binding drug-discovery free_energy md_simulation protein-ligand solvation by jmccammon to the group McCammon on 2009-06-06 22:06:15 as
	Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. [My Copy] Biochemistry (20 April 2009) by Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger posted to allostery binding drug-discovery md_simulation protein-ligand by jmccammon to the group McCammon on 2009-06-06 01:02:47 as along with 3 people arnaucordomi agrossfield xdeupi
	Activation of the West Nile virus NS3 protease: molecular dynamics evidence for a conformational selection mechanism. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 5. (May 2009), pp. 1003-1011. by D. Ekonomiuk, A. Caflisch posted to conformational_selection md_simulation by barry to the group McCammon on 2009-05-21 04:10:42 as
	Characterizing Structural Transitions Using Localized Free Energy Landscape Analysis [My Copy] PLoS ONE, Vol. 4, No. 5. (13 May 2009), e5525. by Nilesh K. Banavali, Alexander D. Mackerell posted to md_simulation wham by barry to the group McCammon on 2009-05-21 04:04:55 as along with 1 person and 1 group sobolevnrm baker-group
	Molecular Mechanics of the alpha-Actinin Rod Domain: Bending, Torsional, and Extensional Behavior. [My Copy] PLoS computational biology, Vol. 5, No. 5. (May 2009) by J. Golji, R. Collins, M. R. Mofrad posted to alpha_actinin cytoskeleton md_simulation nma by barry to the group McCammon on 2009-05-18 20:09:50 as
	Force Field Bias in Protein Folding Simulations [My Copy] Biophysical Journal, Vol. 96, No. 9. (06 May 2009), pp. 3772-3780. by Peter L. Freddolino, Sanghyun Park, Benoît Roux, Klaus Schulten posted to free_energy md_simulation proteins by jmccammon to the group McCammon on 2009-05-12 19:00:58 as
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins (2009) by S. Donnini, A. Villa, G. Groenhof, A. E. Mark, R. K. Wierenga, A. H. Juffer posted to binding drug-discovery electrostatics free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-09 20:32:41 as
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted to allostery binding md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-09 19:39:36 as along with 4 people and 1 group anuragsethi jeargle AbnerCYH sobolevnrm baker-group
	Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method [My Copy] Journal of Structural Biology, Vol. 166, No. 3. (June 2009), pp. 288-294. by Srinivasaraghavan Kannan, Martin Zacharias posted to md_simulation replica_exchange by jmccammon to the group McCammon on 2009-05-08 23:03:23 as
	Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 19. (14 May 2009), pp. 6971-6985. by David S. Cerutti, Isolde L. Trong, Ronald E. Stenkamp, Terry P. Lybrand posted to md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-08 20:13:28 as
	Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Slimane Doudou, Neil A. Burton, Richard H. Henchman posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-05 19:26:05 as along with 4 people and 2 groups A_Coletta_Thesis carlosjavierna ibuch sobolevnrm Structural Biology Group TorVergata baker-group
	Computational studies of protein regulation by post-translational phosphorylation. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (April 2009), pp. 156-163. by Arjun Narayanan, Matthew P. Jacobson posted to electrostatics md_simulation proteins by jmccammon to the group McCammon on 2009-04-27 22:59:27 as along with 1 person guhjy
	Efficient Drug Lead Discovery and Optimization [My Copy] Accounts of Chemical Research, Vol. 0, No. 0. (0000) by William L. Jorgensen posted to drug-discovery free_energy md_simulation monte_carlo protein-ligand solvation by jmccammon to the group McCammon on 2009-04-25 18:44:19 as along with 6 people and 1 group nanonan tbinbal Thermaneutist superpyrin sschurer sobolevnrm baker-group
	Computational studies of H5N1 influenza virus resistance to oseltamivir [My Copy] Protein Science, Vol. 18, No. 4. (2009), pp. 707-715. by Nick X. Wang, Jie J. Zheng posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-04-23 21:42:59 as
	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 McCammon on 2009-04-06 17:55:04 as along with 5 people and 2 groups skywalkerus02 dimka operon sobolevnrm bourby baker-group structural_bioinformatics
	Modeling Signal Propagation Mechanisms and Ligand-Based Conformational Dynamics of the Hsp90 Molecular Chaperone Full-Length Dimer [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (20 March 2009), e1000323. by Giulia Morra, Gennady Verkhivker, Giorgio Colombo posted to hsp90 md_simulation by barry to the group McCammon on 2009-03-27 17:18:50 as along with 1 person and 1 group sobolevnrm baker-group
	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, J. A. Mccammon posted to accelerated_md md_simulation protein_structure ras by barry to the group McCammon on 2009-03-20 17:13:40 as along with 2 people and 2 groups ana allmensch structural_bioinformatics Bioinformatics
	Mapping the conformational transition in Src activation by cumulating the information from multiple molecular dynamics trajectories [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 10. (10 March 2009), pp. 3776-3781. by Sichun Yang, Nilesh K. Banavali, BenoÃ®t Roux posted to md_simulation by jmccammon to the group McCammon on 2009-03-19 22:28:37 as along with 7 people and 1 group anuragsethi Diego_Prada bmduggan allmensch guhjy sobolevnrm barry baker-group
	Effective force coarse-graining [My Copy] Phys. Chem. Chem. Phys. In Phys. Chem. Chem. Phys., Vol. 11, No. 12. (2009), pp. 2002-2015. by Yanting Wang, W. G. Noid, Pu Liu, Gregory A. Voth posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2009-03-19 22:06:00 as along with 4 people and 1 group loison sobolevnrm mbeeby flbarroso baker-group
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry (2009) by M. S. Friedrichs, P. Eastman, Vaidyanathan, et al.M. Houston, S. Legrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande posted to md_simulation by jmccammon to the group McCammon on 2009-03-19 00:06:27 as
	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 McCammon on 2009-03-08 02:52:55 as along with 7 people and 3 groups rabio pavanghatty mijam dgront sobolevnrm biehl itmeson structural_bioinformatics Bioinformatics baker-group
	Kinetics, Statistics, and Energetics of Lipid Membrane Electroporation Studied by Molecular Dynamics Simulations [My Copy] Biophys. J. (9 May 2008), biophysj.108.129437. by Rainer A. Bockmann, Bert L. de Groot, Sergej Kakorin, Eberhard Neumann, Helmut Grubmuller posted to md_simulation membranes by barry to the group McCammon on 2009-03-04 04:07:30 as along with 2 people and 1 group sobolevnrm paulschlesinger baker-group
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-03-01 01:00:11 as along with 9 people and 1 group anuragsethi flbarroso mikaellund sobolevnrm barry willard agrossfield carlosjavierna ibuch 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 jmccammon to the group McCammon on 2009-02-12 18:42:27 as along with 9 people and 2 groups skywalkerus02 anuragsethi klexa apaydin sobolevnrm gane5h barry reyez biehl baker-group structural_bioinformatics
	Binding specificity of SH2 domains: insight from free energy simulations. [My Copy] Proteins, Vol. 74, No. 4. (2 March 2009), pp. 996-1007. by Wenxun Gan, Benoît Roux posted to binding free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-02-07 00:51:37 as along with 2 people allmensch ibuch
	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 McCammon 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 structural_bioinformatics
	Inverting the Nonequilibrium Path Sampling Problem [My Copy] Preprint (2009) by D. D. L. Minh posted to free_energy md_simulation by jmccammon to the group McCammon on 2009-01-22 17:17:28 as
	Achieving energy conservation in Poisson–Boltzmann molecular dynamics: Accuracy and precision with finite-difference algorithms [My Copy] Chemical Physics Letters, Vol. 468, No. 4-6. (22 January 2009), pp. 112-118. by J. Wang, Q. Cai, Z. Li, H. Zhao, R. Luo posted to electrostatics md_simulation solvation by jmccammon to the group McCammon on 2009-01-19 21:39:59 as along with 1 person and 1 group sobolevnrm baker-group
	Efficient evaluation of sampling quality of molecular dynamics simulations by clustering of dihedral torsion angles and Sammon mapping [My Copy] Journal of Computational Chemistry (2009) by S. Frickenhaus, S. Kannan, M. Zacharias posted to clustering md_simulation by jmccammon to the group McCammon on 2009-01-10 21:49:46 as
	What induces pocket openings on protein surface patches involved in protein-protein interactions? [My Copy] Journal of computer-aided molecular design, Vol. 23, No. 2. (6 February 2009), pp. 73-86. by Susanne Eyrisch, Volkhard Helms posted to binding drug-discovery md_simulation protein-protein by jmccammon to the group McCammon on 2009-01-10 21:35:58 as along with 3 people arifor allmensch higueruelo
	An improved method to predict the entropy term with the MM/PBSA approach [My Copy] Journal of Computer-Aided Molecular Design by Jacob Kongsted, Ulf Ryde posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-01-10 21:31:10 as along with 1 person flbarroso

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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
membrane_proteins	1
motor_proteins	1

Group: McCammon - with tag md_simulation [86 articles] Export

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