jmccammon's molecular_dynamics_simulations [16 articles] Export Sort

Recent papers added to jmccammon's library classified by the tag molecular_dynamics_simulations. You can also see everyone's molecular_dynamics_simulations.

Hide details

	Hamiltonian Replica Exchange Method Study of Escherichia coli and Yersinia pestis HPPK [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 50. (17 December 2009), pp. 16197-16208. by Li Su, Robert I. Cukier posted to simulation_methodology replica_exchange protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation functional_modes drug-discovery conformational_transitions clustering binding by jmccammon on 2009-12-31 19:13:05 as along with 1 group McCammon
	Salt-Specific Stability of Short and Charged Alanine-Based α-Helices [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16689-16694. by Joachim Dzubiella posted to solvation peptides molecular_dynamics_simulations md_simulation ions electrostatics electrolyte by jmccammon on 2009-12-31 19:04:10 as along with 1 group McCammon
	Computational Identification of Slow Conformational Fluctuations in Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16669-16680. by Arvind Ramanathan, Pratul K. Agarwal posted to quasiharmonic proteins protein_dynamics normal_modes molecular_dynamics_simulations md_simulation functional_modes by jmccammon on 2009-12-31 18:59:41 as along with 3 people and 1 group anuragsethi agrossfield qshao McCammon
	Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16603-16611. by David R. Glowacki, Emanuele Paci, Dmitrii V. Shalashilin posted to umbrella peptides molecular_dynamics_simulations md_simulation kinetics free_energy conformational_transitions by jmccammon on 2009-12-31 18:51:11 as along with 5 people and 1 group agrossfield mfajer yangsiyang anuragsethi sobolevnrm McCammon
	Reoptimization of the AMBER Force Field Parameters for Peptide Bond (Omega) Torsions Using Accelerated Molecular Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 52. (31 December 2009), pp. 16590-16595. by Urmi Doshi, Donald Hamelberg posted to peptides molecular_mechanics_calculations molecular_dynamics_simulations md_simulation free_energy conformational_transitions accelerated_md by jmccammon on 2009-12-31 18:44:48 as along with 1 person and 1 group mfajer McCammon
	Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site [My Copy] Journal of Molecular Biology, Vol. 394, No. 4. (11 December 2009), pp. 747-763. by Sarah E. Boyce, David L. Mobley, Gabriel J. Rocklin, Alan P. Graves, Ken A. Dill, Brian K. Shoichet posted to protein-ligand molecular_dynamics_simulations md_simulation free_energy drug-discovery binding by jmccammon on 2009-12-30 23:54:02 as along with 2 people and 1 group anuragsethi ahmetbakan McCammon
	Using the local elevation method to construct optimized umbrella sampling potentials: Calculation of the relative free energies and interconversion barriers of glucopyranose ring conformers in water [My Copy] Journal of Computational Chemistry, Vol. 31, No. 1. (2010), pp. 1-23. by Halvor S. Hansen, Philippe H. Hünenberger posted to umbrella molecular_dynamics_simulations md_simulation free_energy conformational_transitions by jmccammon on 2009-12-30 23:07:46 as along with 2 people and 1 group anuragsethi agrossfield McCammon
	Introducing sampling entropy in repository based adaptive umbrella sampling [My Copy] The Journal of Chemical Physics, Vol. 131, No. 21. (2009), 214105. by Han Zheng, Yingkai Zhang posted to umbrella simulation_methodology protein_dynamics peptides molecular_dynamics_simulations md_simulation free_energy conformational_transitions by jmccammon on 2009-12-30 22:27:15 as along with 1 person and 1 group anuragsethi McCammon
	Automated Event Detection and Activity Monitoring in Long Molecular Dynamics Simulations [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2595-2605. by Willy Wriggers, Kate A. Stafford, Yibing Shan, et al.Stefano Piana, Paul Maragakis, Kresten Lindorff-Larsen, Patrick J. Miller, Justin Gullingsrud, Charles A. Rendleman, Michael P. Eastwood, Ron O. Dror, David E. Shaw posted to simulation_methodology protein_dynamics molecular_dynamics_simulations md_simulation functional_modes conformational_transitions by jmccammon on 2009-12-12 23:15:07 as along with 4 people and 1 group paulymer anuragsethi sobolevnrm pmung McCammon
	Free Energy and Kinetics of Conformational Transitions from Voronoi Tessellated Milestoning with Restraining Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2589-2594. by Luca Maragliano, Eric Vanden-Eijnden, Benoît Roux posted to string_method simulation_methodology protein_dynamics molecular_dynamics_simulations milestones md_simulation functional_modes free_energy conformational_transitions by jmccammon on 2009-12-12 23:13:04 as along with 2 people and 1 group anuragsethi sobolevnrm McCammon
	Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2583-2588. by Wei Jiang, Milan Hodoscek, Benoît Roux posted to solvation replica_exchange protein-ligand molecular_dynamics_simulations md_simulation free_energy drug-discovery binding by jmccammon on 2009-12-12 23:11:08 as along with 3 people and 1 group loison qshao sobolevnrm McCammon
	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 on 2009-11-27 23:01:41 as along with 4 people and 1 group loison flbarroso anuragsethi sobolevnrm McCammon
	Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14343-14354. by Zunnan Huang, Chung F. Wong posted to solvation protein_dynamics protein-ligand peptides molecular_dynamics_simulations md_simulation drug-discovery conformational_transitions binding by jmccammon on 2009-11-21 20:27:49 as along with 1 person and 1 group anuragsethi McCammon
	Theory of Free Energy and Entropy in Noncovalent Binding [My Copy] Chemical Reviews, Vol. 109, No. 9. (9 September 2009), pp. 4092-4107. by Huan-Xiang Zhou, Michael K. Gilson posted to protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation free_energy entropy drug-discovery binding by jmccammon on 2009-11-12 01:00:02 as along with 7 people and 2 groups cchang agrossfield anuragsethi sobolevnrm dr_proton qshao paulschlesinger McCammon Chang group
	Quantifying Correlations Between Allosteric Sites in Thermodynamic Ensembles [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2486-2502. by Christopher L. McClendon, Gregory Friedland, David L. Mobley, Homeira Amirkhani, Matthew P. Jacobson posted to protein_dynamics protein-ligand molecular_dynamics_simulations md_simulation drug-discovery binding allostery by jmccammon on 2009-10-31 19:59:28 as along with 4 people and 1 group barry anuragsethi pmung acpan McCammon
	Atomistic View of the Conformational Activation of Src Kinase Using the String Method with Swarms-of-Trajectories [My Copy] Biophysical Journal, Vol. 97, No. 4. (19 August 2009), pp. L8-L10. by Wenxun Gan, Sichun Yang, Benoît Roux posted to tyrosine_kinase string_method simulation_methodology protein_dynamics molecular_dynamics_simulations md_simulation functional_modes conformational_transitions c_src by jmccammon on 2009-10-14 23:04:22 as along with 1 person and 1 group anuragsethi McCammon

Note: You may cite this page as: http://www.citeulike.org/user/jmccammon/tag/molecular_dynamics_simulations

Sort by:
Order:	Default Ascending Descending
Empty fields:	Default First Last

md_simulation	85
protein-ligand	50
binding	48
drug-discovery	43
free_energy	35
electrostatics	32
coarse_grain	24
protein-protein	18
solvation	16
molecular_dynamics_simulations	16
brownian_dynamics	15
protein_dynamics	13
conformational_transitions	13
diffusion	13
proteins	9
functional_modes	8
allostery	8
simulation_methodology	7
kinetics	7
ion_channel	7
replica_exchange	6
membrane	5
accelerated_md	5
peptides	5
langevin_dynamics	5
titration	5
qm-mm	4
nucleic_acids	4
monte_carlo	4
molecular_mechanics_calculations	3
umbrella	3
clustering	3
string_method	2
achr	2
time_correlation_function	1
entropy	1
tyrosine_kinase	1
c_src	1
electrolyte	1
quasiharmonic	1
milestones	1
adenylate_kinase	1
normal_modes	1
ions	1
water_molecules	1

jmccammon's molecular_dynamics_simulations [16 articles] Export Sort

jmccammon's tags