Group: McCammon - with tag coarse_grain [34 articles] Export

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

	SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and Nanoparticles in Dilute Solution [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2606-2618. by José G. de la Torre, José G. Hernández Cifre, Álvaro Ortega, et al.Ricardo R. Schmidt, Miguel X. Fernandes, Horacio E. Pérez Sánchez, R. Pamies posted to simulation_methodology nucleic_acids diffusion conformational_transitions coarse_grain brownian_dynamics by jmccammon to the group McCammon on 2009-12-12 23:17:21 as along with 2 people and 1 group barry qshao structural_bioinformatics
	Structure and Dynamics of the Actin Filament. [My Copy] Journal of molecular biology (18 November 2009) by Jim Pfaendtner, Edward Lyman, Thomas D. Pollard, Gregory A. Voth posted to coarse_grain actin by barry to the group McCammon on 2009-12-08 02:55:48 as along with 1 group structural_bioinformatics
	Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations [My Copy] Proceedings of the National Academy of Sciences In Proceedings of the National Academy of Sciences, Vol. 106, No. 43. (27 October 2009), pp. 18237-18242. by Nobuyasu Koga, Tomoshi Kameda, Kei-ichi Okazaki, Shoji Takada posted to molecular_motors coarse_grain aaa by barry to the group McCammon on 2009-12-08 02:11:00 as along with 1 person okapi
	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
	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 of the United States of America, 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 2 people apaydin 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 nma force_field coarse_grain by barry to the group McCammon on 2009-09-28 19:29:39 as along with 1 person and 1 group jmccammon structural_bioinformatics
	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
	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-ligand coarse_grain binding by jmccammon to the group McCammon on 2009-08-29 21:34:06 as along with 6 people mittinatten ahmetbakan apaydin anuragsethi okapi boris_aguilar
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted to coarse_grain allostery by jmccammon to the group McCammon on 2009-08-29 21:27:01 as along with 4 people sobolevnrm pmung agrossfield okapi
	General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 31. (6 August 2009), pp. 10891-10904. by Artem B. Mamonov, Divesh Bhatt, Derek J. Cashman, Ying Ding, Daniel M. Zuckerman posted to coarse_grain drug-discovery monte_carlo proteins by jmccammon to the group McCammon on 2009-08-08 19:20:36 as
	Complexes of HIV-1 integrase with HAT proteins: multiscale models, dynamics, and hypotheses on allosteric sites of inhibition. [My Copy] Proteins, Vol. 76, No. 4. (September 2009), pp. 946-958. by Armida Di Fenza, Walter Rocchia, Valentina Tozzini posted to coarse_grain correlated_motions hiv_integrase by barry to the group McCammon on 2009-08-07 00:09:13 as
	Self-assembly of actin monomers into long filaments: Brownian dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 1. (2009), 015102. by Kunkun Guo, Julian Shillcock, Reinhard Lipowsky posted to binding brownian_dynamics coarse_grain diffusion protein-protein by jmccammon to the group McCammon on 2009-07-10 22:23:32 as
	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (17 April 2009), e1000360. by Zheng Yang, Peter Májek, Ivet Bahar posted to allostery coarse_grain protein-protein by jmccammon to the group McCammon on 2009-05-11 20:41:15 as along with 2 people and 1 group barry sobolevnrm baker-group
	Systematic multiscale simulation of membrane protein systems [My Copy] Current Opinion in Structural Biology, Vol. 19, No. 2. (09 April 2009), pp. 138-144. by Gary Ayton,, Gregory Voth, posted to coarse_grain membranes review by barry to the group McCammon on 2009-04-21 08:03:11 as along with 3 people and 1 group loison sobolevnrm paulschlesinger baker-group
	Multiscale characterization of protein conformational ensembles [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 76, No. 4. (2009), pp. 837-851. by Amarda Shehu, Lydia E. Kavraki, Cecilia Clementi posted to clustering coarse_grain by barry to the group McCammon on 2009-03-26 19:48:25 as along with 4 people and 2 groups anuragsethi okapi sobolevnrm apaydin structural_bioinformatics 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
	A Systematic Methodology for Defining Coarse-Grained Sites in Large Biomolecules [My Copy] Biophysical Journal, Vol. 95, No. 11. (01 December 2008), pp. 5073-5083. by Z. Zhang, L. Lu, W. Noid, V. Krishna, J. Pfaendtner, G. Voth posted to coarse_grain pca by barry to the group McCammon on 2009-02-26 02:08:44 as along with 6 people and 1 group loison okapi sobolevnrm choonpeng agrossfield paulschlesinger structural_bioinformatics
	Inherent flexibility determines the transition mechanisms of the EF-hands of calmodulin. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (3 February 2009) by Swarnendu Tripathi, John J J. Portman posted to coarse_grain cracking by barry to the group McCammon on 2009-02-06 18:26:36 as along with 1 group structural_bioinformatics
	The molecular face of lipid rafts in model membranes [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 45. (11 November 2008), pp. 17367-17372. by H. Jelger Risselada, Siewert J. Marrink posted to coarse_grain membranes rafts by barry to the group McCammon on 2008-11-10 19:46:06 as along with 8 people and 1 group richardfranzese ARobson wsjames reister paulschlesinger chiufanlee dimka kshundyak Oxford Virology
	Coarse-Grained Molecular Dynamics Simulations of the Energetics of Helix Insertion into a Lipid Bilayer<SUP><A HREF="#fn1">†</A></SUP> [My Copy] Biochemistry (2008) by P. J. Bond, C. L. Wee, M. S. P. Sansom posted to coarse_grain md_simulation membrane by jmccammon to the group McCammon on 2008-11-08 21:37:42 as
	Multiscale methods for macromolecular simulations [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 5. (October 2008), pp. 630-640. by P. Sherwood, B. Brooks, M. Sansom posted to coarse_grain md_simulation membrane qm-mm by jmccammon to the group McCammon on 2008-10-23 02:29:22 as along with 6 people jonathancooper xavierprat flbarroso carlk aqeel choonpeng
	Probing the origin of tubulin rigidity with molecular simulations. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (7 October 2008) by Ruxandra I I. Dima, Harshad Joshi posted to coarse_grain cytoskeleton tubulin by barry to the group McCammon on 2008-10-12 08:16:51 as along with 2 people choonpeng kshundyak
	A minimalist network model for coarse-grained normal mode analysis and its application to biomolecular x-ray crystallography. [My Copy] Proceedings of the National Academy of Sciences of the United States of America (1 October 2008) by Mingyang Lu, Jianpeng Ma posted to coarse_grain nma by barry to the group McCammon on 2008-10-05 19:05:40 as along with 6 people and 4 groups sobolevnrm aqeel apaydin ruvido agrossfield skoddet baker-group Nielsen group structural_bioinformatics Bioinformatics
	Reconstructing atomistic detail for coarse-grained models with resolution exchange [My Copy] Journal of Chemical Physics (2008) by P. Liu, Q. Shi, E. Lyman, G. A. Voth posted to coarse_grain monte_carlo replica_exchange by jmccammon to the group McCammon on 2008-09-27 20:01:44 as
	From coarse-grain to all-atom: Toward multiscale analysis of protein landscapes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (2007), pp. 646-661. by Allison P. Heath, Lydia E. Kavraki, Cecilia Clementi posted to coarse_grain protein_structure by barry to the group McCammon on 2008-09-26 18:14:38 as along with 2 people and 2 groups aqeel mijam structural_bioinformatics Bioinformatics
	Membrane proteins: molecular dynamics simulations [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Erik Lindahl, Mark S. P. Sansom posted to coarse_grain ion_channel md_simulation membrane by jmccammon to the group McCammon on 2008-08-21 19:59:02 as along with 5 people oteri choonpeng vahmurk cat_worth rok
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted to coarse_grain md_simulation protein-ligand by jmccammon to the group McCammon on 2008-08-21 19:52:40 as along with 10 people and 3 groups allmensch jrperillaj barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras structural_bioinformatics Bioinformatics baker-group
	Atomistic Insights into Rhodopsin Activation from a Dynamic Model [My Copy] Journal of the American Chemical Society, Vol. 130 (2008), 10141. by I. G. Tikhonova, R. B. Best, S. Engel, M. C. Gershengorn, G. Hummer, S. Costanzi posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-21 19:28:38 as
	The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations [My Copy] Biophys. J. (9 May 2008), biophysj.107.123190. by Chze-Ling Wee, Kia Balali-Mood, David Gavaghan, Mark S. Sansom posted to coarse_grain md_simulation membrane by jmccammon to the group McCammon on 2008-08-20 22:15:41 as along with 1 person paulschlesinger
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-20 22:13:18 as along with 8 people and 1 group loison barry sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel rok baker-group
	Computational methods for diffusion-influenced biochemical reactions. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 15. (1 August 2007), pp. 1969-1977. by Maciej Dobrzynski, Jordi Vidal V. Rodríguez, Jaap A. Kaandorp, Joke G. Blom posted to brownian_dynamics coarse_grain diffusion by jmccammon to the group McCammon on 2008-08-08 21:33:57 as along with 6 people gabe_rosser jjray ocs m_j balabu dagmar
	Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations [My Copy] Journal of Chemical Theory and Computation (2008) by A. Heyden, D. G. Truhlar posted to coarse_grain md_simulation by jmccammon to the group McCammon on 2008-08-08 21:30:54 as
	Protein model refinement using an optimized physics-based all-atom force field [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273. by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick posted to coarse_grain replica_exchange by barry to the group McCammon on 2008-07-08 00:49:57 as along with 4 people and 1 group krapnik RamuAnandakrishnan jmccammon zwang structural_bioinformatics

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md_simulation	26
membrane	14
diffusion	13
brownian_dynamics	12
conformational_transitions	11
md	11
protein_dynamics	9
allostery	7
electrostatics	7
nma	7
binding	6
protein-ligand	6
protein-protein	6
functional_modes	5
molecular_mechanics_calculations	5
replica_exchange	5
review	5
ion_channel	4
membranes	4
molecular_dynamics	4
nucleic_acids	4
protein_structure	4
actin	3
adenylate_kinase	3
clustering	3
cracking	3
drug-discovery	3
dynamics	3
force_field	3
modeling	3
molecular_dynamics_simulations	3
monte_carlo	3
nucleosome	3
pca	3
proteins	3
qm-mm	3
simulation_methodology	3
aaa	2
correlated_motions	2
cytoskeleton	2
dna	2
folding	2
forcefield	2
hiv_integrase	2
implicit_solvation	2
molecular_motors	2
potential	2
rafts	2
tubulin	2
3d	1
algorithm	1
alkanes	1
antimicrobial_compounds	1
bacteria	1
bd_simulation	1
biophysics	1
block_copolymers	1
cell-division	1
crowding	1
cytokinesis	1
development	1
division	1
dna_ions	1
e-cell	1
e-ring	1
effective_interaction	1
ellipsoidal_potential	1
energy_conservation	1
escherichia_coli	1
force-fields	1
ftsz	1
groel	1
imaging	1
lattice	1
method	1
methodology	1
min	1
minde	1
mine	1
model	1
modelling	1
models	1
molecular_crowding	1
multicompartment	1
multiscale	1
multiscale_modeling	1
noise	1
oscillation	1
polymer	1
prediction	1
qm_mm	1
reaction-diffusion	1
simulation	1
simulations	1
software	1
stochastic	1
surface	1
theory	1
three-dimensional	1
visualization	1

Group: McCammon - with tag coarse_grain [34 articles] Export

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