Group: McCammon - with tag free_energy [30 articles] Export

Recent papers posted by members of the McCammon group with tag free_energy

	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 to the group McCammon on 2009-12-12 23:13:04 as along with 2 people anuragsethi sobolevnrm
	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 to the group McCammon on 2009-12-12 23:11:08 as along with 3 people loison qshao sobolevnrm
	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 to the group McCammon on 2009-11-12 01:00:02 as along with 7 people and 1 group cchang agrossfield anuragsethi sobolevnrm dr_proton qshao paulschlesinger Chang group
	Prediction of the Water Content in Protein Binding Sites [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 40. (8 October 2009), pp. 13337-13346. by Julien Michel, Julian Tirado-Rives, William L. Jorgensen posted to water_molecules solvation simulation_methodology protein-ligand monte_carlo md_simulation free_energy drug-discovery binding by jmccammon to the group McCammon on 2009-10-10 21:07:02 as along with 2 people snichols15 qshao
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted to free_energy by barry to the group McCammon on 2009-09-04 00:41:41 as along with 3 people pmung sobolevnrm RamuAnandakrishnan
	First Principle Theory for pKa Prediction at Molecular Level: pH Effects Based on Explicit Solvent Model [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10509-10514. by Kentaro Kido, Hirofumi Sato, Shigeyoshi Sakaki posted to electrostatics free_energy titration by jmccammon to the group McCammon on 2009-07-25 21:45:08 as along with 4 people and 1 group scampos qshao franklu310 whitead Jiang Research Group
	Configurational Entropy in Protein–Peptide Binding:Computational Study of Tsg101 Ubiquitin E2 Variant Domain with an HIV-Derived PTAP Nonapeptide [My Copy] Journal of Molecular Biology, Vol. 389, No. 2. (05 June 2009), pp. 315-335. by Benjamin J. Killian, Joslyn Y. Kravitz, Sandeep Somani, Paramita Dasgupta, Yuan-Ping Pang, Michael K. Gilson posted to binding free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-06-11 01:30:05 as
	Free Energies and Entropies of Water Molecules at the Inhibitor−Protein Interface of DNA Gyrase [My Copy] Journal of the American Chemical Society, Vol. 131, No. 18. (13 May 2009), pp. 6608-6613. by Hongtao Yu, Steven W. Rick posted to binding drug-discovery free_energy md_simulation protein-ligand solvation by jmccammon to the group McCammon on 2009-06-06 22:06:15 as
	Force Field Bias in Protein Folding Simulations [My Copy] Biophysical Journal, Vol. 96, No. 9. (06 May 2009), pp. 3772-3780. by Peter L. Freddolino, Sanghyun Park, Benoît Roux, Klaus Schulten posted to free_energy md_simulation proteins by jmccammon to the group McCammon on 2009-05-12 19:00:58 as
	Inclusion of ionization states of ligands in affinity calculations [My Copy] Proteins (2009) by S. Donnini, A. Villa, G. Groenhof, A. E. Mark, R. K. Wierenga, A. H. Juffer posted to binding drug-discovery electrostatics free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-09 20:32:41 as
	Standard Free Energy of Binding from a One-Dimensional Potential of Mean Force [My Copy] Journal of Chemical Theory and Computation In Journal of Chemical Theory and Computation, Vol. 5, No. 4. (14 April 2009), pp. 909-918. by Slimane Doudou, Neil A. Burton, Richard H. Henchman posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-05-05 19:26:05 as along with 5 people and 2 groups dcheong A_Coletta_Thesis carlosjavierna ibuch sobolevnrm Structural Biology Group TorVergata baker-group
	Efficient Drug Lead Discovery and Optimization [My Copy] Accounts of Chemical Research, Vol. 0, No. 0. (0000) by William L. Jorgensen posted to drug-discovery free_energy md_simulation monte_carlo protein-ligand solvation by jmccammon to the group McCammon on 2009-04-25 18:44:19 as along with 6 people and 1 group nanonan tbinbal Thermaneutist superpyrin sschurer sobolevnrm baker-group
	Computational studies of H5N1 influenza virus resistance to oseltamivir [My Copy] Protein Science, Vol. 18, No. 4. (2009), pp. 707-715. by Nick X. Wang, Jie J. Zheng posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-04-23 21:42:59 as
	Protein Side-Chain Dynamics and Residual Conformational Entropy [My Copy] Journal of the American Chemical Society, Vol. 131, No. 2. (21 January 2009), pp. 615-622. by Nikola Trbovic, Jae-Hyun Cho, Robert Abel, Richard A. Friesner, Mark Rance, Arthur G. Palmer posted to free_energy nmr by barry to the group McCammon on 2009-03-08 02:43:57 as along with 2 people and 2 groups bmduggan sobolevnrm structural_bioinformatics baker-group
	Computations of Standard Binding Free Energies with Molecular Dynamics Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 8. (26 February 2009), pp. 2234-2246. by Yuqing Deng, Benoît Roux posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-03-01 01:00:11 as along with 10 people and 1 group loison anuragsethi flbarroso mikaellund sobolevnrm barry willard agrossfield carlosjavierna ibuch baker-group
	Poisson–Boltzmann model analysis of binding mRNA cap analogues to the translation initiation factor eIF4E [My Copy] Biophysical Chemistry, Vol. 140, No. 1-3. (March 2009), pp. 16-23. by O. Szklarczyk, J. Zuberek, J. Antosiewicz posted to binding electrostatics free_energy nucleic_acids protein-ligand by jmccammon to the group McCammon on 2009-02-14 21:53:11 as along with 1 person and 1 group sobolevnrm baker-group
	Binding specificity of SH2 domains: insight from free energy simulations. [My Copy] Proteins, Vol. 74, No. 4. (2 March 2009), pp. 996-1007. by Wenxun Gan, Benoît Roux posted to binding free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-02-07 00:51:37 as along with 2 people allmensch ibuch
	Inverting the Nonequilibrium Path Sampling Problem [My Copy] Preprint (2009) by D. D. L. Minh posted to free_energy md_simulation by jmccammon to the group McCammon on 2009-01-22 17:17:28 as
	An improved method to predict the entropy term with the MM/PBSA approach [My Copy] Journal of Computer-Aided Molecular Design by Jacob Kongsted, Ulf Ryde posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2009-01-10 21:31:10 as along with 1 person flbarroso
	Calculation of protein-ligand binding affinities. [My Copy] Annual review of biophysics and biomolecular structure, Vol. 36 (2007), pp. 21-42. by Michael K. Gilson, Huan-Xiang X. Zhou posted to drug-discovery free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2008-11-15 01:18:56 as along with 15 people and 2 groups mijogiffin flbarroso GermanErlenkamp onufriev arlam oteri bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata
	Calculation of absolute protein-ligand binding free energy using distributed replica sampling [My Copy] The Journal of Chemical Physics, Vol. 129, No. 15. (2008) by Tomas Rodinger, Lynne P. Howell, Régis Pomès posted to free_energy md_simulation protein-ligand by jmccammon to the group McCammon on 2008-10-23 20:39:58 as along with 3 people and 1 group arlam ibuch yzlab Chang group
	On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals [My Copy] Journal of Chemical Physics (2008) by W. Yang, L. Zheng posted to free_energy md_simulation by jmccammon to the group McCammon on 2008-10-23 20:17:09 as
	Statistically optimal analysis of samples from multiple equilibrium states [My Copy] Journal of Chemical Physics (2008) by M. R. Shirts, J. D. Chodera posted to free_energy md_simulation by jmccammon to the group McCammon on 2008-10-23 20:14:17 as
	Intrinsic Free Energy of the Conformational Transition of the KcsA Signature Peptide from Conducting to Nonconducting State [My Copy] J. Chem. Theory Comput., Vol. 4 (13 August 2008), pp. 1541-1554. by Ilja V. Khavrutskii, Mikolai Fajer, J. A. Mccammon posted to free_energy ion_channel md_simulation by jmccammon to the group McCammon on 2008-09-28 00:04:07 as along with 1 person dmobley
	Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations [My Copy] J. Chem. Theory Comput., Vol. 4 (13 August 2008), 1516-1525. by C. A. F. de Oliveira, D. Hamelberg, J. A. Mccammon posted to accelerated_md free_energy md_simulation by jmccammon to the group McCammon on 2008-09-27 23:51:04 as along with 3 people pmk dmobley cesar
	Synergistic approach to improve "alchemical" free energy calculation in rugged energy surface. [My Copy] The Journal of chemical physics, Vol. 126, No. 14. (14 April 2007) by D. Min, H. Li, G. Li, R. Bitetti-Putzer, W. Yang posted to discussion_free_energy free_energy by barry to the group McCammon on 2008-08-20 22:16:00 as along with 1 group structural_bioinformatics
	Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations [My Copy] Journal of Chemical Physics (2008) by Y. Deng, B. Roux posted to binding free_energy md_simulation by jmccammon to the group McCammon on 2008-08-08 21:27:43 as
	Calculation of protein-ligand binding free energy by using a polarizable potential [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6290-6295. by Dian Jiao, Pavel A. Golubkov, Thomas A. Darden, Pengyu Ren posted to binding free_energy md_simulation protein-ligand by barry to the group McCammon on 2008-07-08 01:12:03 as along with 6 people and 2 groups krapnik flbarroso onufriev jmccammon biehl sobolevnrm baker-group structural_bioinformatics
	From the Cover: A dry ligand-binding cavity in a solvated protein [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 17. (29 April 2008), pp. 6296-6301. by Johan Qvist, Monika Davidovic, Donald Hamelberg, Bertil Halle posted to free_energy md_simulation protein-ligand solvation by barry to the group McCammon on 2008-07-08 01:11:30 as along with 3 people and 2 groups Lombardo_7 jmccammon sobolevnrm structural_bioinformatics baker-group
	Pathway and Endpoint Free Energy Calculations for Cyclic Nucleotide Binding to HCN Channels [My Copy] Biophys. J., Vol. 94, No. 12. (15 June 2008), pp. L90-92. by Lei Zhou, Steven A. Siegelbaum posted to binding electrostatics free_energy md_simulation protein-ligand by barry to the group McCammon on 2008-07-08 00:49:17 as along with 1 person jmccammon

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binding	78
md_simulation	68
protein-ligand	56
solvation	44
electrostatics	32
molecular_simulation	32
drug-discovery	30
protein_structure	28
alchemical	27
entropy	27
md	23
cmn	22
protein_dynamics	22
protein_folding	22
data	21
hexapeptide	21
molecular_dynamics	21
review	18
aux	17
protein-ligand_interactions	17
relative	17
graphical_models	15
proteins	15
protein_protein_interactions	14
chapt_cmn	12
simulation	12
molecular_dynamics_simulations	11
physics	11
water	11
alternatives	10
docking	10
monte_carlo	10
pb	10
short-peptides	10
statistical_mechanics	10
stochastic_processes	10
markov	9
methodology	9
plos	9
transition_states	9
continnum	8
enhanced_sampling	8
glass_transition	8
hydration	8
pes_based	8
thermodynamic_integration	8
complex_systems	7
conformation	7
ligand	7
methods	7
networks	7
pca	7
thermodynamics	7
beta-hairpin	6
dialanine	6
drug_design	6
dynamics	6
first_passage	6
folding	6
nmr	6
simulation_methodology	6
transition_path	6
articulo	5
coarse-grained	5
discussion_free_energy	5
energy_landscape	5
hard_sphere	5
inference	5
nucleic_acids	5
potential_of_mean_force	5
protein	5
protein-protein	5
three_circ_confinement	5
umbrella_sampling	5
2009	4
accelerated_md	4
dna	4
flexibility	4
hiv	4
hp_model	4
hydrophobicity	4
jarzynski	4
markov_state_models	4
mmpbsa	4
nonequilibrium	4
pka	4
qha	4
quasiharmonic_models	4
reaction_paths	4
sampling	4
statistics	4
wham	4
adaptive_biasing_force	3
dielectric	3
grand_canonical	3
kinetic_models	3
md_history	3
milestones	3
string_method	3
water_molecules	3

Group: McCammon - with tag free_energy [30 articles] Export

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