Group: baker-group - with tag enhanced_sampling [33 articles] Export

Recent papers posted by members of the baker-group group with tag enhanced_sampling

	Elucidating the Inhibition Mechanism of HIV-1 Non-Nucleoside Reverse Transcriptase Inhibitors through Multicopy Molecular Dynamics Simulations [My Copy] Journal of Molecular Biology, Vol. 388, No. 3. (08 May 2009), pp. 644-658. by Anthony Ivetac, J. Andrew Mccammon posted to enhanced_sampling molecular_simulation protein-ligand_interactions by sobolevnrm to the group baker-group on 2009-04-23 12:32:31 as along with 2 people bmduggan paulschlesinger
	Self-guided Langevin dynamics study of regulatory interactions in NtrC. [My Copy] Proteins (26 March 2009) by Ana Damjanović, Bertrand E E. García-Moreno, Bernard R R. Brooks posted to electrostatics enhanced_sampling pka solvation by sobolevnrm to the group baker-group on 2009-04-23 12:30:23 as
	Long-timescale molecular dynamics simulations of protein structure and function. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (08 April 2009), pp. 120-127. by John L. Klepeis, Kresten Lindorff-Larsen, Ron O. Dror, David E. Shaw posted to enhanced_sampling molecular_dynamics review by sobolevnrm to the group baker-group on 2009-04-21 12:30:19 as along with 11 people xdeupi agrossfield allmensch bmduggan r2s2 apaydin kiekyon Borelli idoerg edws paulschlesinger
	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 enhanced_sampling molecular_dynamics by sobolevnrm to the group baker-group on 2009-04-14 12:50:27 as along with 5 people and 2 groups skywalkerus02 dimka operon barry bourby structural_bioinformatics McCammon
	Sampling conformations in high dimensions using low-dimensional distribution functions [My Copy] The Journal of Chemical Physics, Vol. 130, No. 13. (2009), 134102. by Sandeep Somani, Benjamin J. Killian, Michael K. Gilson posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-04-03 12:49:33 as along with 1 person VGreiff
	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 allostery enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2009-03-26 11:32:54 as along with 7 people and 1 group anuragsethi Diego_Prada bmduggan allmensch guhjy barry jmccammon McCammon
	Building alternate protein structures using the elastic network model [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA. by Qingyi Yang, Kim A. Sharp posted to enhanced_sampling quasiharmonic_models structure_prediction by sobolevnrm to the group baker-group on 2009-03-25 11:36:50 as along with 5 people and 1 group pansapiens klexa abovell oteri middledomain Structural Biology Group TorVergata
	Path integral analysis of Jarzynski's equality: Analytical results [My Copy] Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 79, No. 2. (2009), 021122. by David D. L. Minh, Artur B. Adib posted to enhanced_sampling free_energy statistical_mechanics by sobolevnrm to the group baker-group on 2009-03-23 11:56:27 as
	Gaussian-Mixture Umbrella Sampling [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Paul Maragakis, Arjan van der Vaart, Martin Karplus posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-23 11:51:09 as along with 2 people willard agrossfield
	Iterative cluster-NMA: A tool for generating conformational transitions in proteins. [My Copy] Proteins, Vol. 74, No. 3. (15 February 2009), pp. 760-776. by A. D. Schuyler, R. L. Jernigan, P. K. Qasba, B. Ramakrishnan, G. S. Chirikjian posted to enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-22 14:02:45 as along with 1 person aqeel
	StoneHinge: hinge prediction by network analysis of individual protein structures. [My Copy] Protein science : a publication of the Protein Society, Vol. 18, No. 2. (February 2009), pp. 359-371. by K. S. Keating, S. C. Flores, M. B. Gerstein, L. A. Kuhn posted to clustering enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-03-22 14:02:38 as along with 1 person and 1 group barry structural_bioinformatics
	SHARPEN-Systematic Hierarchical Algorithms for Rotamers and Proteins on an Extended Network. [My Copy] Journal of computational chemistry (23 January 2009) by Ilya V V. Loksha, James R R. Maiolo, Cheng W W. Hong, Albert Ng, Christopher D D. Snow posted to enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2009-03-19 12:07:42 as along with 3 people and 2 groups apaydin A_Coletta_Thesis barry Structural Biology Group TorVergata structural_bioinformatics
	Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 51. (23 December 2008), pp. 20227-20232. by Lianqing Zheng, Mengen Chen, Wei Yang posted to enhanced_sampling free_energy molecular_simulation by sobolevnrm to the group baker-group on 2009-03-04 13:07:09 as along with 3 people and 1 group sas iivanov phoenixzxl McCammon
	A method for the analysis of domain movements in large biomolecular complexes [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Guru P. Poornam, Atsushi Matsumoto, Hisashi Ishida, Steven Hayward posted to clustering enhanced_sampling quasiharmonic_models by sobolevnrm to the group baker-group on 2009-02-28 21:52:03 as along with 1 person and 3 groups barry structural_bioinformatics McCammon Bioinformatics
	Investigating protein dynamics in collective coordinate space [My Copy] Current Opinion in Structural Biology, 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 to the group baker-group on 2008-06-06 11:37:30 as along with 6 people bmduggan Scis0000002 ttjoseph ffranca barry choonpeng
	Hessian-free low-mode conformational search for large-scale protein loop optimization: application to c-jun N-terminal kinase JNK3 [My Copy] Journal of Computational Chemistry, Vol. 22, No. 1. (2000), pp. 21-30. by I. Kolossváry, G. M. Keserü posted to enhanced_sampling quasiharmonic-models_elastic-network_gnm_nma_pca_etc by sobolevnrm to the group baker-group on 2008-05-27 16:08:08 as
	Collective Langevin dynamics of conformational motions in proteins [My Copy] 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 to the group baker-group on 2008-05-27 16:06:12 as along with 1 person choonpeng
	Long time scale molecular dynamics subspace integration method applied to anharmonic crystals and glasses [My Copy] 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 to the group baker-group on 2008-05-27 16:04:43 as
	Molecular dynamics simulations of peptides and proteins with amplified collective motions. [My Copy] 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 to the group baker-group on 2008-05-27 16:03:07 as along with 2 people baaden aqeel
	Improved Sampling for Simulations of Interfacial Membrane Proteins: Application of Generalized Shadow Hybrid Monte Carlo to a Peptide Toxin/Bilayer System [My Copy] J. Phys. Chem. B, Vol. 112, No. 18. (8 May 2008), pp. 5710-5717. by C. L. Wee, M. S. P. Sansom, S. Reich, E. Akhmatskaya posted to biomembranes enhanced_sampling molecular_dynamics molecular_simulation protein-membrane_interactions by sobolevnrm to the group baker-group on 2008-05-19 11:38:23 as
	How Efficient Is Replica Exchange Molecular Dynamics? An Analytic Approach [My Copy] 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 to the group baker-group on 2008-04-28 11:43:27 as along with 3 people and 2 groups agrossfield loison barry structural_bioinformatics McCammon
	Molecular simulation of multistate peptide dynamics: A comparison between microsecond timescale sampling and multiple shorter trajectories [My Copy] Journal of Computational Chemistry, Vol. 29, No. 11. (August 2008), pp. 1740-1752. by Luca Monticelli, Eric J. Sorin, D. Peter Tieleman, Vijay S. Pande, Giorgio Colombo posted to enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2008-04-03 12:01:59 as along with 2 people bmduggan arnaucordomi
	Finding Transition Pathways Using the String Method with Swarms of Trajectories [My Copy] J. Phys. Chem. B (22 February 2008) by A. C. Pan, D. Sezer, B. Roux posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2008-03-27 11:18:17 as along with 1 person dmobley
	Satisfying the fluctuation theorem in free-energy calculations with Hamiltonian replica exchange [My Copy] 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 to the group baker-group on 2008-03-27 10:49:38 as
	Modeling protein conformational ensembles: From missing loops to equilibrium fluctuations [My Copy] 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 to the group baker-group on 2008-01-30 12:48:13 as along with 6 people and 1 group apaydin nigham aqeel yongzhao elham hmk TSRI_MGL
	Generalized gradient-augmented harmonic Fourier beads method with multiple atomic and/or center-of-mass positional restraints [My Copy] 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 to the group baker-group on 2007-12-19 12:31:32 as
	Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study [My Copy] The Journal of Chemical Physics, Vol. 127, No. 17. (2007), 175105. by César Augusto, Donald Hamelberg, J. Andrew Mccammon posted to enhanced_sampling kinetics molecular_dynamics by sobolevnrm to the group baker-group on 2007-12-17 12:55:05 as along with 1 person bmduggan
	Efficient and verified simulation of a path ensemble for conformational change in a united-residue model of calmodulin [My Copy] 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 to the group baker-group on 2007-12-10 12:33:23 as along with 2 people jrperillaj RamuAnandakrishnan
	Molecular Dynamics of Apo-Adenylate Kinase: A Distance Replica Exchange Method for the Free Energy of Conformational Fluctuations [My Copy] J. Phys. Chem. B, Vol. 110, No. 47. (30 November 2006), pp. 24121-24137. by H. Lou, R. I. Cukier posted to allostery enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2007-12-05 12:35:49 as along with 1 person allmensch
	Hamiltonian and Distance Replica Exchange Method Studies of Met-Enkephalin [My Copy] J. Phys. Chem. B, Vol. 111, No. 42. (25 October 2007), pp. 12310-12321. by L. Su, R. I. Cukier posted to allostery enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2007-12-05 12:35:23 as
	Accelerated entropy estimates with accelerated dynamics [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by David D. L. Minh, Donald Hamelberg, Andrew J. Mccammon posted to enhanced_sampling molecular_dynamics molecular_simulation by sobolevnrm to the group baker-group on 2007-11-02 11:13:51 as along with 3 people pgasper afenley dmobley
	Coarse-Grained Biomolecular Simulation with REACH: Realistic Extension Algorithm via Covariance Hessian [My Copy] 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 to the group baker-group on 2007-11-01 11:59:51 as along with 3 people aqeel hmk choonpeng
	Sampling of slow diffusive conformational transitions with accelerated molecular dynamics [My Copy] The Journal of Chemical Physics, Vol. 127, No. 15. (2007) by Donald Hamelberg, César, Andrew J. Mccammon posted to diffusion enhanced_sampling molecular_simulation by sobolevnrm to the group baker-group on 2007-11-01 11:10:39 as along with 1 person pgasper

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molecular_simulation	38
molecular_dynamics	18
quasiharmonic_models	13
free_energy	8
allostery	6
quasiharmonic-models_elastic-network_gnm_nma_pca_etc	5
biomembranes	4
clustering	4
multiscale	3
review	3
2009	2
diffusion	2
electrostatics	2
kinetics	2
pka	2
protein	2
protein-ligand_interactions	2
protein-membrane_interactions	2
solvation	2
statistical_mechanics	2
structure_prediction	2
conformation	1
dynamics	1
flexibility	1
perturbation	1
protein-structure	1
simulation	1
structure	1
torsion_angles	1

Group: baker-group - with tag enhanced_sampling [33 articles] Export

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