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sobolevnrm's enhanced_sampling [19 articles]

Recent papers added to sobolevnrm's library classified by the tag enhanced_sampling. You can also see everyone's enhanced_sampling.
  • Investigating protein dynamics in collective coordinate space.
    Curr Opin Struct Biol, Vol. 9, No. 2. (April 1999), pp. 164-169.
    by A Kitao, N Go
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-06-06 11:37:30 as read along with 4 people and 1 group ttjoseph ffranca barry choonpeng baker-group
  • Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3
    Journal of Computational Chemistry, Vol. 22, No. 1. (2000), pp. 21-30.
    by I Kolossváry, GM Keserü
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-05-27 16:08:08 as read along with 1 group baker-group
  • Collective Langevin dynamics of conformational motions in proteins
    The Journal of Chemical Physics, Vol. 124, No. 21. (2006)
    by Oliver F Lange, Helmut Grubmuller
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-05-27 16:06:12 as read along with 1 person and 1 group choonpeng baker-group
  • Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses
    The Journal of Chemical Physics, Vol. 99, No. 11. (1993), pp. 9070-9079.
    by Brian Space, Herschel Rabitz, Attila Askar
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-05-27 16:04:43 as read along with 1 group baker-group
  • Molecular dynamics simulations of peptides and proteins with amplified collective motions.
    Biophys J, Vol. 84, No. 6. (June 2003), pp. 3583-3593.
    by Z Zhang, Y Shi, H Liu
    posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2008-05-27 16:03:06 as read along with 2 people and 1 group baaden aqeel baker-group
  • Improved Sampling for Simulations of Interfacial Membrane Proteins: Application of Generalized Shadow Hybrid Monte Carlo to a Peptide Toxin/Bilayer System
    J. Phys. Chem. B, Vol. 112, No. 18. (8 May 2008), pp. 5710-5717.
    by CL Wee, MSP Sansom, S Reich, E Akhmatskaya
    posted to biomembranes enhanced_sampling molecular_dynamics molecular_simulation protein-membrane_interactions by sobolevnrm on 2008-05-19 11:38:22 as read along with 1 group baker-group
  • How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach
    J. Chem. Theory Comput., Vol. 4, No. 4. (8 April 2008), pp. 626-636.
    by Hugh Nymeyer
    posted to enhanced_sampling molecular_simulation by sobolevnrm on 2008-04-28 11:43:26 as read along with 3 people and 3 groups agrossfield loison barry baker-group structural_bioinformatics McCammon
  • Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Luca Monticelli, Eric J Sorin, Peter D Tieleman, Vijay S Pande, Giorgio Colombo
    posted to enhanced_sampling molecular_simulation by sobolevnrm on 2008-04-03 12:01:58 as read along with 1 group baker-group
  • Finding Transition Pathways Using the String Method with Swarms of Trajectories
    J. Phys. Chem. B (22 February 2008)
    by AC Pan, D Sezer, B Roux
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm on 2008-03-27 11:18:16 as read along with 1 person and 1 group dmobley baker-group
  • Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 77, No. 2. (2008)
    by Matthew A Wyczalkowski, Rohit V Pappu
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm on 2008-03-27 10:49:38 as read along with 1 group baker-group
  • Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 1. (2006), pp. 164-179.
    by Amarda Shehu, Cecilia Clementi, Lydia E Kavraki
    posted to enhanced_sampling molecular_simulation by sobolevnrm on 2008-01-30 12:48:13 as read along with 6 people and 2 groups apaydin nigham aqeel yongzhao elham hmk TSRI_MGL baker-group
  • Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints
    The Journal of Chemical Physics, Vol. 127, No. 12. (2007)
    by Ilja V Khavrutskii, Andrew J Mccammon
    posted to biomembranes enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-19 12:31:32 as read along with 1 group baker-group
  • Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
    The Journal of Chemical Physics, Vol. 127, No. 17. (2007)
    by César, Donald Hamelberg, Andrew J Mccammon
    posted to enhanced_sampling kinetics molecular_dynamics by sobolevnrm on 2007-12-17 12:55:05 as read along with 1 group baker-group
  • Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin
    Proceedings of the National Academy of Sciences, Vol. 104, No. 46. (13 November 2007), pp. 18043-18048.
    by Bin W Zhang, David Jasnow, Daniel M Zuckerman
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm on 2007-12-10 12:33:23 as read along with 1 person and 1 group RamuAnandakrishnan baker-group
  • Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations
    J. Phys. Chem. B, Vol. 110, No. 47. (30 November 2006), pp. 24121-24137.
    by H Lou, RI Cukier
    posted to allostery enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-05 12:35:49 as read along with 1 person and 1 group allmensch baker-group
  • Hamiltonian and Distance Replica Exchange Method Studies of Met-Enkephalin
    J. Phys. Chem. B, Vol. 111, No. 42. (25 October 2007), pp. 12310-12321.
    by L Su, RI Cukier
    posted to allostery enhanced_sampling molecular_simulation by sobolevnrm on 2007-12-05 12:35:23 as ** along with 1 group baker-group
  • Accelerated entropy estimates with accelerated dynamics
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by David DL Minh, Donald Hamelberg, Andrew J Mccammon
    posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm on 2007-11-02 11:13:50 as read along with 3 people and 1 group pgasper afenley dmobley baker-group
  • Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian
    Biophys. J., Vol. 93, No. 10. (15 November 2007), pp. 3460-3469.
    by Kei Moritsugu, Jeremy C Smith
    posted to enhanced_sampling molecular_simulation multiscale quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm on 2007-11-01 11:59:51 as read along with 3 people and 1 group aqeel hmk choonpeng baker-group
  • Sampling of slow diffusive conformational transitions with accelerated molecular dynamics
    The Journal of Chemical Physics, Vol. 127, No. 15. (2007)
    by D Hamelberg, CAF de Oliveira, JA Mccammon
    posted to diffusion enhanced_sampling molecular_simulation by sobolevnrm on 2007-11-01 11:10:19 as read along with 1 person and 1 group pgasper baker-group
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