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タグ: coarse-grained [136 articles]

Recent papers classified by the tag coarse-grained.
  • Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis
    Biophys. J. (30 May 2008), biophysj.108.129072.
    by Yeshitila Gebremichael, Jhih-Wei Chu, Gregory A Voth
    posted to tubulin-dimer simulation microtubule md coarse-grained 2008 by tengli on 2008-09-16 15:30:59 as **
  • REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes
    Biophys. J. (9 May 2008), biophysj.108.131714.
    by Kei Moritsugu, Jeremy C Smith
    posted to coarse-grained force_field md simulation by rok on 2008-08-21 19:45:50 as ** along with 5 people and 1 group A_Coletta_Thesis paulschlesinger choonpeng aqeel jmccammon McCammon
  • Comparison of Thermodynamic Properties of Coarse-Grained and Atomic-Level Simulation Models.
    Chemphyschem, Vol. 8, No. 3. (8 February 2007), pp. 452-461.
    by Riccardo Baron, Daniel Trzesniak, Alex H H de Vries, Andreas Elsener, Siewert J J Marrink, Wilfred F F van Gunsteren
    posted to coarse-grained dynamics entropy fluid gibbs helmoltz hydrocarbons method modeling molecular multiscale reorganization solute solvent thermodynamics by rbaron on 2008-08-05 01:55:58 as read along with 1 person choonpeng
  • Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model
    Nanotechnology, Vol. 15, No. 9. (2004), pp. 1289-1295.
    by Goundla Srinivas, Michael L Klein
    posted to simulation membrane coarse-grained by Marine on 2008-09-21 19:56:59 as ** along with 1 group Molecular dynamics in MSU
  • The MARTINI Coarse-Grained Force Field: Extension to Proteins
    J. Chem. Theory Comput. (16 April 2008)
    by Luca Monticelli, Senthil K Kandasamy, Xavier Periole, Ronald G Larson, Peter D Tieleman, Siewert-Jan Marrink
    posted to simulation protein martini force-field coarse-grained by Marine on 2008-09-22 10:01:58 as ** along with 6 people and 2 groups middledomain sobolevnrm Ema aqeel DanielParton softsimu Molecular dynamics in MSU baker-group
  • Coarse Grained Model for Semiquantitative Lipid Simulations
    J. Phys. Chem. B, Vol. 108, No. 2. (15 January 2004), pp. 750-760.
    by SJ Marrink, AH Devries, AE Mark
    posted to coarse-grained by Marine on 2008-09-22 09:58:13 as ** along with 3 people and 1 group choonpeng softsimu sunnytov Molecular dynamics in MSU
  • The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations.
    J Phys Chem B (15 June 2007)
    by Siewert J Marrink, H J Risselada, Serge Yefimov, D P Tieleman, Alex H Vries
    posted to simulation martini coarse-grained by Marine on 2008-09-22 09:59:35 as ** along with 4 people and 1 group choonpeng softsimu dimka sunnytov Molecular dynamics in MSU
  • Structure and Dynamics of Model Pore Insertion into a Membrane
    Biophys. J., Vol. 88, No. 5. (1 May 2005), pp. 3083-3094.
    by Carlos F Lopez, Steve O Nielsen, Bernd Ensing, Preston B Moore, Michael L Klein
    posted to coarse-grained pore simulation theory by loison on 2006-11-28 11:16:51 as **** along with 1 person softsimu
  • Lipid Bilayer Perturbations around a Transmembrane Nanotube: A Coarse Grain Molecular Dynamics Study
    Biophys. J., Vol. 88, No. 6. (1 June 2005), pp. 3822-3828.
    by Steve O Nielsen, Bernd Ensing, Vanessa Ortiz, Preston B Moore, Michael L Klein
    posted to coarse-grained pore simulation theory by loison on 2006-11-28 12:49:31 as ** along with 2 people Marine dimka
  • Probing Membrane Insertion Activity of Antimicrobial Polymers via Coarse-Grain Molecular Dynamics
    J. Chem. Theory Comput., Vol. 2, No. 3. (9 May 2006), pp. 649-655.
    by CF Lopez, SO Nielsen, G Srinivas, WF Degrado, ML Klein
    posted to antimicrobial coarse-grained simulation theory by loison on 2006-11-28 10:59:20 as **
  • Variable-free exploration of stochastic models: a gene regulatory network example
    (6 Nov 2006)
    by Radek Erban, Thomas A Frewen, Xiao Wang, Timothy C Elston, Ronald Coifman, Boaz Nadler, Ioannis G Kevrekidis
    posted to coarse-grained regulatory_network stochastic by j_vinals on 2008-08-06 02:44:43 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Diffusion maps, spectral clustering and reaction coordinates of dynamical systems
    ArXiv Mathematics e-prints (March 2005)
    by B Nadler, S Lafon, RR Coifman, IG Kevrekidis
    posted to coarse-grained stochastic by j_vinals on 2008-08-06 02:46:16 as ** along with 2 people and 1 group sobolevnrm kb baker-group
  • Coarse-grained models for simulations of multi-protein complexes: Application to ubiquitin binding
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Young C Kim, Gerhard Hummer
    posted to coarse-grained protein_protein ubiqutin by barry to the group Bioinformatics on 2008-01-10 19:41:25 as ** along with 3 people and 2 groups sobolevnrm iantunbridge mikaellund structural_bioinformatics baker-group
  • Crucial stages of protein folding through a solvable model: Predicting target sites for enzyme-inhibiting drugs
    Protein Sci, Vol. 11, No. 8. (1 August 2002), pp. 1878-1887.
    by Cristian Micheletti, Fabio Cecconi, Alessandro Flammini, Amos Maritan
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 17:36:33 as read
  • Design of amino acid sequences to fold into C[sub alpha]-model proteins
    The Journal of Chemical Physics, Vol. 123, No. 5. (2005)
    by A Amatori, G Tiana, L Sutto, Ferkinghoff J Borg, A Trovato, RA Broglia
    posted to coarse-grained by Diego_Prada on 2008-02-18 18:48:21 as ****
  • Annealed importance sampling of dileucine peptide
    (3 Apr 2007)
    by Edward Lyman, Daniel M Zuckerman
    posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:15:40 as **
  • Free energy landscapes of model peptides and proteins
    The Journal of Chemical Physics, Vol. 118, No. 8. (2003), pp. 3891-3897.
    by David A Evans, David J Wales
    posted to coarse-grained free-energy proteins by Diego_Prada on 2008-04-11 20:05:03 as **
  • Folding core predictions from network models of proteins
    Polymer, Vol. 45, No. 2. (January 2004), pp. 659-668.
    by AJ Rader, Ivet Bahar
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:07:31 as read along with 1 person choonpeng
  • Escherichia coli adenylate kinase dynamics: comparison of elastic network model modes with mode-coupling (15)N-NMR relaxation data.
    Proteins, Vol. 57, No. 3. (15 November 2004), pp. 468-480.
    by NA Temiz, E Meirovitch, I Bahar
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:04:46 as read along with 2 people apaydin aqeel
  • The influence of conformational fluctuations on enzymatic activity: modelling the functional motion of $β$-secretase
    Journal of Physics Condensed Matter, Vol. 17 (May 2005), 1581.
    by M Neri, M Cascella, C Micheletti
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 17:41:12 as read
  • Comparison of mode analyses at different resolutions applied to nucleic acid systems.
    Biophys J, Vol. 89, No. 5. (November 2005), pp. 2939-2949.
    by AW Van Wynsberghe, Q Cui
    posted to coarse-grained csn gnm pca by Diego_Prada on 2008-02-18 18:18:29 as **** along with 2 people aqeel eckart_bindewald
  • Important fluctuation dynamics of large protein structures are preserved upon coarse-grained renormalization
    International Journal of Quantum Chemistry, Vol. 90, No. 2. (2002), pp. 822-837.
    by Pemra Doruker, Robert L Jernigan, Isabelle Navizet, Rigoberto Hernandez
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:39:25 as read
  • Elastic Properties of Proteins: Insight on the Folding Process and Evolutionary Selection of Native Structures
    Journal of Molecular Biology, Vol. 321, No. 5. (30 August 2002), pp. 909-921.
    by Cristian Micheletti, Gianluca Lattanzi, Amos Maritan
    posted to coarse-grained gnm go by Diego_Prada on 2008-02-18 17:44:17 as read along with 2 people and 2 groups barry Einat structural_bioinformatics Bioinformatics
  • Energy landscape of a model protein
    The Journal of Chemical Physics, Vol. 111, No. 14. (1999), pp. 6610-6616.
    by Mark A Miller, David J Wales
    posted to coarse-grained hp_model by Diego_Prada on 2008-08-20 10:44:26 as **
  • Global ribosome motions revealed with elastic network model
    Journal of Structural Biology, Vol. 147, No. 3. (September 2004), pp. 302-314.
    by Yongmei Wang, AJ Rader, Ivet Bahar, Robert L Jernigan
    posted to coarse-grained gnm by Diego_Prada on 2008-02-18 18:10:07 as read along with 3 people aqeel eckart_bindewald ffranca
  • Demonstrated convergence of the equilibrium ensemble for a fast united-residue protein model
    (24 Mar 2007)
    by Marty F Ytreberg, Svetlana, Daniel M Zuckerman
    posted to coarse-grained protein_dynamics struct_decorr by Diego_Prada on 2008-04-21 10:13:08 as **
  • Coarse molecular dynamics of a peptide fragment: Free energy, kinetics, and long-time dynamics computations
    J. Chem. Phys., Vol. 118 (June 2003), pp. 10762-10773.
    by G Hummer, IG Kevrekidis
    posted to coarse-grained dialanine md by Diego_Prada on 2008-08-01 19:40:41 as **
  • Contact pair dynamics during folding of two small proteins: chicken villin head piece and the Alzheimer protein beta-amyloid.
    J Chem Phys, Vol. 120, No. 3. (15 January 2004), pp. 1602-1612.
    by A Mukherjee, B Bagchi
    posted to coarse-grained protein-folding by choonpeng on 2007-06-25 02:30:32 as ** along with 1 person and 2 groups ana structural_bioinformatics Bioinformatics
  • Size, Motion, and Function of the SecY Translocon Revealed by Molecular Dynamics Simulations with Virtual Probes
    Biophys. J., Vol. 90, No. 8. (15 April 2006), pp. 2718-2730.
    by Pu Tian, Ioan Andricioaei
    posted to coarse-grained protein-translocation by choonpeng on 2007-06-24 10:28:57 as read along with 1 person blackbart
  • Coarse-grained models of protein folding: toy models or predictive tools?
    Curr Opin Struct Biol (19 December 2007)
    by Cecilia Clementi
    posted to coarse-grained review by choonpeng on 2008-02-14 11:11:58 as read along with 2 people and 1 group sobolevnrm nh baker-group
  • Membrane remodeling from N-BAR domain interactions: insights from multi-scale simulation.
    Biophys J, Vol. 92, No. 10. (15 May 2007), pp. 3595-3602.
    by GS Ayton, PD Blood, GA Voth
    posted to coarse-grained by choonpeng on 2007-07-15 06:36:59 as ***
  • On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models.
    Biophysical journal (16 May 2008)
    by Christopher B B Wolf, Mohammad R K R Mofrad
    posted to coarse-grained by choonpeng on 2008-06-27 09:13:07 as ***
  • Insights into allosteric control of vinculin function from its large scale conformational dynamics.
    J Biol Chem, Vol. 281, No. 39. (29 September 2006), pp. 29148-29154.
    by Y Chen, NV Dokholyan
    posted to allostery coarse-grained by choonpeng on 2007-03-18 12:20:18 as read
  • Tunable generic model for fluid bilayer membranes.
    Phys Rev E Stat Nonlin Soft Matter Phys, Vol. 72, No. 1 Pt 1. (July 2005)
    by IR Cooke, K Kremer, M Deserno
    posted to coarse-grained by choonpeng on 2007-07-14 05:24:31 as ***
  • Multiscale Modeling of Nucleosome Dynamics
    Biophys. J., Vol. 92, No. 5. (1 March 2007), pp. 1457-1470.
    by Shantanu Sharma, Feng Ding, Nikolay V Dokholyan
    posted to coarse-grained by choonpeng on 2007-06-30 07:53:43 as *** along with 4 people and 9 groups aalibes shantanu skoch3 phisics structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology Koch_Lab
  • Probing Protein Mechanics: Residue-Level Properties and Their Use in Defining Domains
    Biophys. J., Vol. 87, No. 3. (1 September 2004), pp. 1426-1435.
    by Isabelle Navizet, Fabien Cailliez, Richard Lavery
    posted to coarse-grained multi-domain by choonpeng on 2007-03-12 08:31:17 as read along with 1 person aqeel
  • Coarse Grained Protein-Lipid Model with Application to Lipoprotein Particles
    J. Phys. Chem. B, Vol. 110, No. 8. (2 March 2006), pp. 3674-3684.
    by AY Shih, A Arkhipov, PL Freddolino, K Schulten
    posted to coarse-grained by choonpeng on 2007-06-28 15:09:56 as read along with 1 person loison
  • Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.
    J Am Chem Soc, Vol. 128, No. 6. (15 February 2006), pp. 1890-1901.
    by HD Nguyen, CK Hall
    posted to coarse-grained protein-folding by choonpeng on 2007-06-25 02:52:57 as ***
  • Folding-based molecular simulations reveal mechanisms of the rotary motor F1-ATPase.
    Proc Natl Acad Sci U S A, Vol. 103, No. 14. (4 April 2006), pp. 5367-5372.
    by N Koga, S Takada
    posted to coarse-grained go-model by choonpeng on 2007-07-08 13:03:57 as read along with 1 person bilab
  • A coarse grained model for the dynamics of flap opening in HIV-1 protease
    Chemical Physics Letters, Vol. 413, No. 1-3. (15 September 2005), pp. 123-128.
    by Valentina Tozzini, Andrew J Mccammon
    posted to coarse-grained by choonpeng on 2007-05-28 13:12:41 as read
  • Coupling between allosteric transitions in GroEL and assisted folding of a substrate protein
    PNAS, Vol. 104, No. 21. (22 May 2007), pp. 8803-8808.
    by George Stan, George H Lorimer, D Thirumalai, Bernard R Brooks
    posted to chaperonin coarse-grained by choonpeng on 2007-06-24 08:34:55 as read along with 2 people cactus rph
  • Dynamics of essential collective motions in proteins: Theory
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 5. (2007)
    by Maria Stepanova
    posted to coarse-grained conformational-change pca by choonpeng on 2008-01-29 08:35:59 as read along with 2 people and 1 group sobolevnrm Diego_Prada baker-group
  • Deriving effective mesoscale potentials from atomistic simulations
    Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1624-1636.
    by Dirk Reith, Mathias Pütz, Florian Müller-Plathe
    posted to coarse-grained methodology by choonpeng on 2007-05-29 14:26:01 as ***
  • Atomistic and coarse-grained analysis of double spectrin repeat units: the molecular origins of flexibility.
    J Mol Biol, Vol. 365, No. 2. (12 January 2007), pp. 523-534.
    by DT Mirijanian, JW Chu, GS Ayton, GA Voth
    posted to coarse-grained by choonpeng on 2007-06-25 04:57:30 as ***
  • Large Amplitude Conformational Change in Proteins Explored with a Plastic Network Model: Adenylate Kinase
    Journal of Molecular Biology, Vol. 352, No. 4. (30 September 2005), pp. 807-822.
    by Paul Maragakis, Martin Karplus
    posted to coarse-grained by choonpeng on 2007-06-24 13:04:34 as *** along with 2 people apaydin aqeel
  • Folding on the Chaperone: Yield Enhancement Through Loose Binding
    Journal of Molecular Biology, Vol. 363, No. 5. (10 November 2006), pp. 945-957.
    by AI Jewett, JE Shea
    posted to chaperone coarse-grained langevin-dynamics protein-folding by choonpeng on 2006-10-23 14:52:40 as read
  • How protein thermodynamics and folding mechanisms are altered by the chaperonin cage: molecular simulations.
    Proc Natl Acad Sci U S A, Vol. 100, No. 20. (30 September 2003), pp. 11367-11372.
    by F Takagi, N Koga, S Takada
    posted to chaperonin coarse-grained by choonpeng on 2007-03-30 12:22:05 as read
  • Coarse-grained protein molecular dynamics simulations.
    J Chem Phys, Vol. 126, No. 2. (14 January 2007), 025101.
    by P Derreumaux, N Mousseau
    posted to coarse-grained by choonpeng on 2007-06-25 03:27:56 as read
  • Allostery of actin filaments: molecular dynamics simulations and coarse-grained analysis.
    Proc Natl Acad Sci U S A, Vol. 102, No. 37. (13 September 2005), pp. 13111-13116.
    by JW Chu, GA Voth
    posted to coarse-grained by choonpeng on 2008-06-29 03:31:28 as *** along with 1 person BragilMassoud
  • A coarse-grained protein force field for folding and structure prediction.
    Proteins (28 June 2007)
    by Julien Maupetit, P Tuffery, Philippe Derreumaux
    posted to coarse-grained protein-folding by choonpeng on 2007-07-14 04:05:48 as ** along with 1 person wouterboomsma
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