Tag coarse_grain [53 articles] Export

Recent papers classified by the tag coarse_grain.

	Combining a polarizable force-field and a coarse-grained polarizable solvent model: Application to long dynamics simulations of bovine pancreatic trypsin inhibitor [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (2008), pp. 1707-1724. by Michel Masella, Daniel Borgis, Philippe Cuniasse posted to implicit_solvation coarse_grain by boris_aguilar on 2009-11-05 22:14:29 as along with 2 people middledomain sunhwan
	Coarse Point Charge Models For Proteins From Smoothed Molecular Electrostatic Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Laurence Leherte, Daniel P. Vercauteren posted to coarse_grain by RamuAnandakrishnan on 2009-11-04 21:01:20 as
	Multiscale simulation of soft matter systems - from the atomistic to the coarse-grained level and back [My Copy] Soft Matter, Vol. 5, No. 22. (2009), pp. 4357-4366. by Christine Peter, Kurt Kremer posted to soft_matter multiscale_modeling modeling force-fields coarse_grain by flbarroso on 2009-11-03 18:03:01 as along with 2 people anuragsethi sobolevnrm
	Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 3, No. 3. (1 May 2007), pp. 1100-1105. by Bernd Ensing, Steven O. Nielsen, Preston B. Moore, Michael L. Klein, Michele Parrinello posted to energy_conservation coarse_grain by RamuAnandakrishnan on 2009-11-03 12:16:52 as along with 1 person onufriev
	Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-Grain Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 2, No. 3. (1 May 2006), pp. 649-655. by Carlos F. Lopez, Steven O. Nielsen, Goundla Srinivas, William F. DeGrado, Michael L. Klein posted to coarse_grain antimicrobial_compounds by jjurban on 2009-11-02 21:38:42 as along with 1 person loison
	The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations. [My Copy] Journal of Physical Chemistry B, Vol. 111, No. 27. (1 July 2007), pp. 7812-7824. by Siewert J. Marrink, H. J. Risselada, Serge Yefimov, D. P. Tieleman, Alex H. Vries posted to forcefield coarse_grain by anuragsethi on 2009-10-25 03:00:52 as along with 7 people and 2 groups sunrise A_Coletta_Thesis Marine choonpeng softsimu dimka sunnytov Structural Biology Group TorVergata Molecular dynamics in MSU
	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 groel coarse_grain allostery by barry on 2009-10-23 04:58:26 as along with 2 people and 2 groups jmccammon sobolevnrm McCammon baker-group
	Simulations of theoretically informed coarse grain models of polymeric systems [My Copy] Faraday Discuss., Vol. 144 (2010), pp. 111-125. by Francois A. Detcheverry, Darin Q. Pike, Paul F. Nealey, Marcus Muller, Juan J. Pablo posted to polymer modeling coarse_grain by flbarroso on 2009-10-22 12:06:35 as
	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
	Monte Carlo Simulations of a Coarse Grain Model for Block Copolymers and Nanocomposites [My Copy] Macromolecules, Vol. 41, No. 13. (1 July 2008), pp. 4989-5001. by François A. Detcheverry, Huiman Kang, Kostas C. Daoulas, Marcus Müller, Paul F. Nealey, Juan J. de Pablo posted to coarse_grain block_copolymers by Xusheng on 2009-10-11 23:34:27 as along with 1 person j_vinals
	Systematic coarse graining from structure using internal states: Application to phospholipid/cholesterol bilayer [My Copy] The Journal of Chemical Physics, Vol. 131, No. 5. (2009), 055101. by Teemu Murtola, Mikko Karttunen, Ilpo Vattulainen posted to dynamics coarse_grain by anuragsethi on 2009-10-07 14:27:07 as along with 3 people sobolevnrm cjryan agrossfield
	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
	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 5 people 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
	An <I>N</I> log <I>N</I> approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Ramu Anandakrishnan, Alexey V. Onufriev posted to coarse_grain electrostatics by RamuAnandakrishnan on 2009-07-02 01:04:02 as along with 1 person sobolevnrm
	Systematic multiscale simulation of membrane protein systems [My Copy] Current Opinion in Structural Biology (09 April 2009) by Gary S. Ayton, Gregory A. Voth posted to coarse_grain membranes review by barry to the group McCammon on 2009-04-21 08:03:11 as along with 2 people and 1 group 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 structural_bioinformatics on 2009-03-26 19:48:25 as along with 4 people and 2 groups anuragsethi okapi sobolevnrm apaydin McCammon baker-group
	Effective force coarse-graining [My Copy] 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 3 people and 1 group sobolevnrm mbeeby flbarroso baker-group
	Dynamics of protein-protein encounter: A Langevin equation approach with reaction patches [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Jakob Schluttig, Denitsa Alamanova, Volkhard Helms, Ulrich S. Schwarz posted to bd_simulation coarse_grain by barry on 2009-03-17 19:01:55 as along with 3 people and 2 groups anuragsethi sobolevnrm jmccammon baker-group McCammon
	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 barry on 2009-03-04 04:09:41 as along with 7 people and 2 groups sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon rok baker-group McCammon
	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 structural_bioinformatics on 2009-02-26 02:08:44 as along with 5 people and 1 group okapi sobolevnrm choonpeng agrossfield paulschlesinger McCammon
	An Efficient Program for Many-Body Simulation [My Copy] SIAM Journal on Scientific and Statistical Computing, Vol. 6, No. 1. (1985), pp. 85-103. by Andrew W. Appel posted to coarse_grain by onufriev on 2009-02-18 21:08:06 as along with 1 person OndrejMarsalek
	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 structural_bioinformatics on 2009-02-06 18:26:36 as along with 1 group McCammon
	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
	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 structural_bioinformatics 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 McCammon Bioinformatics
	Computational techniques for efficient conformational sampling of proteins [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Adam Liwo, Cezary Czaplewski, Stanislaw Oldziej, Harold A. Scheraga posted to coarse_grain protein_dynamics review by barry on 2008-10-02 19:59:47 as along with 3 people apaydin aqeel j3xucite
	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 structural_bioinformatics on 2008-09-26 18:14:38 as along with 2 people and 2 groups aqeel mijam McCammon Bioinformatics
	Mesoscopic models of biological membranes [My Copy] Physics Reports, Vol. 437, No. 1-2. (December 2006), pp. 1-54. by Maddalena Venturoli, Maddalena, Marieke Kranenburg, Berend Smit posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 05:02:14 as along with 2 people sunnytov choonpeng
	Biological and synthetic membranes: What can be learned from a coarse-grained description? [My Copy] Physics Reports, Vol. 434, No. 5-6. (November 2006), pp. 113-176. by M. Muller, K. Katsov, M. Schick posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:52:02 as along with 2 people edws loison
	Multiscale modeling of biomolecular systems: in serial and in parallel. [My Copy] Current opinion in structural biology, Vol. 17, No. 2. (April 2007), pp. 192-198. by Gary S. Ayton, Will G. Noid, Gregory A. Voth posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:41:43 as along with 5 people bertelsen jonathancooper Elena_Zubova aqeel choonpeng
	Coarse-grained models for proteins [My Copy] Current Opinion in Structural Biology, Vol. 15, No. 2. (April 2005), pp. 144-150. by V. Tozzini posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:39:25 as along with 9 people flbarroso krapnik baaden aqeel ltrabuco simone cottrell choonpeng iantunbridge
	Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field [My Copy] J. Chem. Theory Comput., Vol. 4, No. 8. (12 August 2008), pp. 1386-1400. by Hujun Shen, Cezary Czaplewski, Adam Liwo, Harold A. Scheraga posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:35:01 as along with 1 person Sylvain_Prigent
	Dynamics of entangled linear polymer melts: A molecular-dynamics simulation [My Copy] The Journal of Chemical Physics, Vol. 92, No. 8. (1990), pp. 5057-5086. by Kurt Kremer, Gary S. Grest posted to coarse_grain md nucleosome by RamuAnandakrishnan on 2008-08-23 14:46:45 as along with 4 people gsub kaz229 jheco 6rheology
	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 md_simulation membrane membrane_proteins by rok on 2008-08-21 21:06:02 as along with 5 people and 1 group oteri choonpeng vahmurk cat_worth jmccammon McCammon
	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
	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
	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
	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
	Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution [My Copy] Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 545-571. by Matej Praprotnik, Luigi Delle Site, Kurt Kremer posted to coarse_grain electrostatics md by RamuAnandakrishnan on 2008-05-21 13:42:03 as along with 4 people and 1 group whitead flbarroso rok softsimu Jiang Research Group
	Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme [My Copy] (17 Sep 2007) by L. Delle Site posted to coarse_grain electrostatics md by RamuAnandakrishnan on 2008-04-16 20:41:19 as
	Coarse-grained force field for the nucleosome from self-consistent multiscaling [My Copy] Journal of Computational Chemistry, Vol. 29, No. 9. (2008), pp. 1429-1439. by Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy Smith posted to coarse_grain md nucleosome by RamuAnandakrishnan on 2008-02-13 14:39:41 as along with 3 people barmak7282 Elena_Zubova onufriev
	Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides [My Copy] The Journal of Chemical Physics, Vol. 97, No. 12. (1992), pp. 9412-9426. by Andrzej Kolinski, Jeffrey Skolnick posted to coarse_grain md by RamuAnandakrishnan on 2007-12-03 19:49:55 as
	Multiscale modeling and simulation methods with applications to dendritic polymers [My Copy] Computational and Theoretical Polymer Science, Vol. 11, No. 5. (October 2001), pp. 345-356. by Tahir Cagin, Guofeng Wang, Ryan Martin, et al.Georgios Zamanakos, Nagarajan Vaidehi, Daniel T. Mainz, William A. Goddard posted to coarse_grain implicit_solvent md by RamuAnandakrishnan on 2007-12-02 15:00:44 as
	Mapping of Explicit Atom onto United Atom Potentials [My Copy] Macromolecules, Vol. 31, No. 26. (29 December 1998), pp. 9362-9368. by J. D. Mccoy, J. G. Curro posted to coarse_grain md by RamuAnandakrishnan on 2007-11-30 20:58:08 as

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md_simulation	23
md	11
membrane	10
brownian_dynamics	9
protein_dynamics	9
allostery	7
electrostatics	7
nma	7
binding	6
diffusion	6
protein-ligand	6
protein-protein	6
conformational_transitions	5
functional_modes	5
molecular_mechanics_calculations	5
replica_exchange	5
review	5
ion_channel	4
membranes	4
molecular_dynamics	4
protein_structure	4
adenylate_kinase	3
clustering	3
cracking	3
drug-discovery	3
force_field	3
monte_carlo	3
nucleosome	3
pca	3
proteins	3
qm-mm	3
correlated_motions	2
cytoskeleton	2
dna	2
dynamics	2
folding	2
forcefield	2
hiv_integrase	2
implicit_solvation	2
modeling	2
potential	2
rafts	2
tubulin	2
alkanes	1
antimicrobial_compounds	1
bd_simulation	1
block_copolymers	1
dna_ions	1
effective_interaction	1
effective_potential	1
ellipsoidal_potential	1
energy_conservation	1
force-fields	1
groel	1
implicit_solvent	1
membrane_proteins	1
multiscale_modeling	1
polymer	1
qm_mm	1
soft_matter	1
surface_tension	1

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