jmccammon's free_energy [35 articles] Export Sort

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	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 group 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
	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
	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 on 2009-10-10 21:07:02 as along with 2 people and 1 group snichols15 qshao McCammon
	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 on 2009-07-25 21:45:08 as along with 4 people and 2 groups scampos qshao franklu310 whitead McCammon Jiang Research Group
	Prediction of protein-protein interaction sites using electrostatic desolvation profiles [My Copy] Biophysical Journal (submitted) (2009) by S. Fiorucci, M. Zacharias posted to binding coarse_grain electrostatics free_energy protein-protein solvation by jmccammon on 2009-07-16 20:06:58 as
	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 on 2009-06-11 01:30:05 as along with 1 group McCammon
	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 on 2009-06-06 22:06:15 as along with 1 group McCammon
	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 on 2009-05-12 19:00:58 as along with 1 group McCammon
	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 on 2009-05-09 20:32:41 as along with 1 group McCammon
	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 on 2009-05-05 19:26:05 as along with 5 people and 3 groups dcheong A_Coletta_Thesis carlosjavierna ibuch sobolevnrm McCammon 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 on 2009-04-25 18:44:19 as along with 6 people and 2 groups nanonan tbinbal Thermaneutist superpyrin sschurer sobolevnrm McCammon 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 on 2009-04-23 21:42:59 as along with 1 group McCammon
	Simultaneous Escaping of Explicit and Hidden Free Energy Barriers: Application of the Orthogonal Space Random Walk Strategy in Generalized Ensemble Based Conformational Sampling [My Copy] preprint by L. Zheng, M. Chen, W. Yang posted to free_energy md_simulation by jmccammon on 2009-04-22 20:12:54 as
	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 on 2009-03-01 01:00:10 as along with 10 people and 2 groups loison anuragsethi flbarroso mikaellund sobolevnrm barry willard agrossfield carlosjavierna ibuch baker-group McCammon
	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 on 2009-02-14 21:53:11 as along with 1 person and 2 groups sobolevnrm baker-group McCammon
	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 on 2009-02-07 00:51:36 as along with 2 people and 1 group allmensch ibuch McCammon
	Inverting the Nonequilibrium Path Sampling Problem [My Copy] Preprint (2009) by D. D. L. Minh posted to free_energy md_simulation by jmccammon on 2009-01-22 17:17:28 as along with 1 group McCammon
	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 on 2009-01-10 21:31:09 as along with 1 person and 1 group flbarroso McCammon
	Theory of Free Energy and Entropy in Noncovalent Binding [My Copy] Chemical Reviews (submitted) (2009) by H. X. Zhou, M. K. Gilson posted to binding drug-discovery free_energy md_simulation protein-ligand by jmccammon on 2008-12-30 23:34:35 as
	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 on 2008-11-15 01:18:56 as along with 15 people and 3 groups mijogiffin flbarroso GermanErlenkamp onufriev arlam oteri bmduggan dimka neils hmk ashaytan ras cchang boris_aguilar qaiser_fatmi Chang group Structural Biology Group TorVergata McCammon
	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 on 2008-10-23 20:39:58 as along with 3 people and 2 groups arlam ibuch yzlab Chang group McCammon
	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 on 2008-10-23 20:17:09 as along with 1 group McCammon
	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 on 2008-10-23 20:14:16 as along with 1 group McCammon
	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 on 2008-09-28 00:04:07 as along with 1 person and 1 group dmobley McCammon
	Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations [My Copy] J. Chem. Theory Comput., Vol. 4 (13 August 2008), pp. 1516-1525. by C. A. F. de Oliveira, D. Hamelberg, J. A. Mccammon posted to accelerated_md free_energy md_simulation by jmccammon on 2008-09-27 23:51:04 as along with 3 people and 1 group pmk dmobley cesar McCammon
	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 on 2008-08-08 21:27:43 as along with 1 group McCammon
	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 jmccammon on 2008-07-03 00:57:58 as along with 1 person and 1 group barry McCammon
	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 jmccammon on 2008-05-26 21:33:02 as along with 3 people and 3 groups Lombardo_7 barry sobolevnrm structural_bioinformatics McCammon baker-group
	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 jmccammon on 2008-05-26 21:31:42 as along with 6 people and 3 groups krapnik flbarroso onufriev biehl sobolevnrm barry baker-group structural_bioinformatics McCammon

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coarse_grain	24
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solvation	16
molecular_dynamics_simulations	16
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ions	1
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jmccammon's free_energy [35 articles] Export Sort

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