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	Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 31. (2008), pp. 10659-10664. by Christopher K. Materese, Christa C. Goldmon, Garegin A. Papoian posted to md_simulation by jmccammon on 2008-08-19 23:38:22 as along with 1 person and 1 group kevinemamy McCammon
	Assessing the performance of implicit solvation models at a nucleic acid surface [My Copy] Phys. Chem. Chem. Phys., Vol. 10, No. 32. (2008), pp. 4889-4902. by Feng Dong, Jason A. Wagoner, Nathan A. Baker posted to electrostatics solvation by jmccammon on 2008-08-19 23:13:52 as along with 3 people and 1 group sobolevnrm onufriev simone McCammon
	Avian influenza virus, a very sticky situation [My Copy] Current Opinion in Chemical Biology, Vol. 12, No. 1. (February 2008), pp. 102-108. by Mark von Itzstein posted to drug-discovery protein-ligand by jmccammon on 2008-04-04 01:40:32 as along with 1 person and 1 group barry McCammon
	Constant pH replica exchange molecular dynamics in biomolecules using a discrete protonation model [My Copy] Journal of Chemical Theory and Computation, submitted (2009) by Y. Meng, A. E. Roitberg posted to no-tag by jmccammon on 2009-12-18 20:59:30 as
	How to achieve a record in protein binding rate [My Copy] Proc. Natl. Acad. Sci. USA (submitted) (2009) by S. Qin, H. X. Zhou posted to binding diffusion electrostatics protein-ligand by jmccammon on 2009-02-12 01:30:09 as
	The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations [My Copy] Biophys. J. (9 May 2008), biophysj.107.123190. by Chze-Ling Wee, Kia Balali-Mood, David Gavaghan, Mark S. Sansom posted to coarse_grain md_simulation membrane by jmccammon on 2008-08-20 22:15:41 as along with 1 person and 1 group paulschlesinger McCammon
	REACH Coarse-Grained Biomolecular Simulation: Transferability between Different Protein Structural Classes [My Copy] Biophys. J. (9 May 2008), biophysj.108.131714. by Kei Moritsugu, Jeremy C. Smith posted to coarse_grain md_simulation by jmccammon on 2008-08-20 22:13:17 as along with 8 people and 2 groups loison barry sobolevnrm A_Coletta_Thesis paulschlesinger choonpeng aqeel rok baker-group McCammon
	Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics [My Copy] posted to brownian_dynamics electrostatics by jmccammon on 2008-04-30 22:43:31 as
	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
	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
	SIMUFLEX: Algorithms and Tools for Simulation of the Conformation and Dynamics of Flexible Molecules and Nanoparticles in Dilute Solution [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2606-2618. by José G. de la Torre, José G. Hernández Cifre, Álvaro Ortega, et al.Ricardo R. Schmidt, Miguel X. Fernandes, Horacio E. Pérez Sánchez, R. Pamies posted to simulation_methodology nucleic_acids diffusion conformational_transitions coarse_grain brownian_dynamics by jmccammon on 2009-12-12 23:17:21 as along with 2 people and 2 groups barry qshao structural_bioinformatics 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
	pH-Dependent Association of Proteins. The Test Case of Monoclonal Antibody HyHEL-5 and Its Antigen Hen Egg White Lysozyme [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 47. (26 November 2009), pp. 15662-15669. by Maciej Długosz, Jan M. Antosiewicz, Joanna Trylska posted to titration protein-protein kinetics electrostatics diffusion brownian_dynamics binding by jmccammon on 2009-11-21 20:11:32 as along with 1 group 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
	Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 106, No. 37. (15 September 2009), pp. 15673-15678. by Anil Korkut, Wayne A. Hendrickson posted to protein_dynamics molecular_mechanics_calculations functional_modes conformational_transitions coarse_grain adenylate_kinase by jmccammon on 2009-10-17 20:42:54 as along with 2 people and 1 group apaydin anuragsethi McCammon
	A force field for virtual atom molecular mechanics of proteins [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 37. (15 September 2009), pp. 15667-15672. by Anil Korkut, Wayne A. Hendrickson posted to protein_dynamics molecular_mechanics_calculations functional_modes conformational_transitions coarse_grain by jmccammon on 2009-10-17 20:40:56 as along with 1 person and 2 groups barry structural_bioinformatics McCammon
	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
	RedMD - Reduced molecular dynamics package [My Copy] Journal of Computational Chemistry, Vol. 30, No. 14. (2009), pp. 2364-2373. by Adam Górecki, Marcin Szypowski, Maciej D&lstrok;ugosz, Joanna Trylska posted to protein_dynamics md_simulation coarse_grain brownian_dynamics by jmccammon on 2009-09-12 21:46:20 as along with 4 people and 1 group anuragsethi oteri flbarroso shwu McCammon
	Detection of Functional Modes in Protein Dynamics [My Copy] PLoS Computational Biology (August 2009) by J. S. Hub, B. L. de Groot posted to proteins protein_dynamics md_simulation functional_modes coarse_grain by jmccammon on 2009-09-03 01:15:01 as along with 1 group McCammon
	The intrinsic dynamics of enzymes plays a dominant role in determining the structural changes induced upon inhibitor binding [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14349-14354. by Ahmet Bakan, Ivet Bahar posted to protein-ligand coarse_grain binding by jmccammon on 2009-08-29 21:34:06 as along with 6 people and 1 group mittinatten ahmetbakan apaydin anuragsethi okapi boris_aguilar McCammon
	Coarse-grained modeling of allosteric regulation in protein receptors [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 34. (25 August 2009), pp. 14253-14258. by Ilya A. Balabin, Weitao Yang, David N. Beratan posted to coarse_grain allostery by jmccammon on 2009-08-29 21:27:01 as along with 4 people and 1 group sobolevnrm pmung agrossfield okapi McCammon
	Flaviviral Protease Inhibitors Identified by Fragment-Based Library Docking into a Structure Generated by Molecular Dynamics [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 15. (13 August 2009), pp. 4860-4868. by Dariusz Ekonomiuk, Xun-Cheng Su, Kiyoshi Ozawa, et al.Christophe Bodenreider, Siew P. Lim, Gottfried Otting, Danzhi Huang, Amedeo Caflisch posted to protein-ligand md_simulation drug-discovery binding by jmccammon on 2009-08-13 20:03:20 as along with 3 people and 1 group ubcg08l pmung carlosjavierna McCammon
	Combining Molecular Dynamics with Bayesian Analysis To Predict and Evaluate Ligand-Binding Mutations in Influenza Hemagglutinin [My Copy] Journal of the American Chemical Society, Vol. 131, No. 32. (19 August 2009), pp. 11338-11340. by Peter M. Kasson, Daniel L. Ensign, Vijay S. Pande posted to protein-ligand md_simulation kinetics drug-discovery binding allostery by jmccammon on 2009-08-13 19:20:53 as along with 2 people and 1 group oteri dicksmit McCammon
	Automated site preparation in physics-based rescoring of receptor ligand complexes. [My Copy] Proteins, Vol. 77, No. 1. (October 2009), pp. 52-61. by Chaya S. Rapp, Cheryl Schonbrun, Matthew P. Jacobson, Chakrapani Kalyanaraman, Niu Huang posted to binding drug-discovery electrostatics protein-ligand titration by jmccammon on 2009-08-08 20:25:02 as along with 3 people and 1 group oteri klexa RamuAnandakrishnan McCammon
	General Library-Based Monte Carlo Technique Enables Equilibrium Sampling of Semi-atomistic Protein Models [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 31. (6 August 2009), pp. 10891-10904. by Artem B. Mamonov, Divesh Bhatt, Derek J. Cashman, Ying Ding, Daniel M. Zuckerman posted to coarse_grain drug-discovery monte_carlo proteins by jmccammon on 2009-08-08 19:20:36 as along with 1 group McCammon
	Drug discovery chemistry: a primer for the non-specialist. [My Copy] Drug discovery today, Vol. 14, No. 15-16. (2 August 2009), pp. 731-744. by Allan M. Jordan, Stephen D. Roughley posted to drug-discovery by jmccammon on 2009-08-01 21:45:17 as along with 4 people and 1 group richardbickerton pmung zimbo1 jerome McCammon
	Chapter 9 Analyzing Enzymatic pH Activity Profiles and Protein Titration Curves Using Structure-Based pKa Calculations and Titration Curve Fitting [My Copy] Methods in enzymology In Computer Methods, Part A, Vol. 454 (2009), pp. 233-258. by Jens E. Nielsen posted to drug-discovery electrostatics protein-ligand solvation by jmccammon on 2009-07-27 19:09:07 as along with 4 people and 2 groups sobolevnrm scampos anuragsethi flbarroso McCammon baker-group
	Polarization effects in molecular mechanical force fields [My Copy] Journal of Physics: Condensed Matter, Vol. 21, No. 33. (2009), 333102. by Piotr Cieplak, Francois-Yves Dupradeau, Yong Duan, Junmei Wang posted to electrostatics md_simulation solvation by jmccammon on 2009-07-27 18:02:24 as along with 1 person and 1 group anuragsethi 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
	Unravelling the Conformational Dynamics of the Aqueous Alanine Dipeptide with First-Principle Molecular Dynamics [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 30. (30 July 2009), pp. 10059-10062. by M. P. Gaigeot posted to md_simulation by jmccammon on 2009-07-25 21:21:42 as along with 3 people and 2 groups loison whitead carlosjavierna 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
	ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639. by M. J. Harvey, G. Giupponi, G. De Fabritiis posted to accelerated_md md_simulation by jmccammon on 2009-07-11 23:43:25 as along with 4 people and 1 group qshao r2s2 ibuch mmuecke McCammon
	Bad Seeds Sprout Perilous Dynamics: Stochastic Thermostat Induced Trajectory Synchronization in Biomolecules [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1624-1631. by Daniel J. Sindhikara, Seonah Kim, Arthur F. Voter, Adrian E. Roitberg posted to langevin_dynamics md_simulation by jmccammon on 2009-07-11 23:42:28 as along with 2 people and 2 groups edws sobolevnrm McCammon baker-group
	Self-assembly of actin monomers into long filaments: Brownian dynamics simulations [My Copy] The Journal of Chemical Physics, Vol. 131, No. 1. (2009), 015102. by Kunkun Guo, Julian Shillcock, Reinhard Lipowsky posted to binding brownian_dynamics coarse_grain diffusion protein-protein by jmccammon on 2009-07-10 22:23:32 as along with 1 group McCammon
	On the Contributions of Diffusion and Thermal Activation to Electron Transfer between Phormidium laminosum Plastocyanin and Cytochrome f: Brownian Dynamics Simulations with Explicit Modeling of Nonpolar Desolvation Interactions and Electron Transfer Events [My Copy] Journal of the American Chemical Society, Vol. 131, No. 26. (8 July 2009), pp. 9230-9238. by Razif R. Gabdoulline, Rebecca C. Wade posted to binding brownian_dynamics diffusion electrostatics protein-protein solvation by jmccammon on 2009-07-10 22:08:28 as along with 2 people and 2 groups choonpeng whitead McCammon Jiang Research Group
	Structure-Based Design of a Periplasmic Binding Protein Antagonist that Prevents Domain Closure [My Copy] ACS Chemical Biology, Vol. 4, No. 6. (19 June 2009), pp. 447-456. by M. Jack Borrok, Yimin Zhu, Katrina T. Forest, Laura L. Kiessling posted to allostery binding drug-discovery protein-ligand by jmccammon on 2009-07-09 18:28:58 as along with 1 person and 1 group carlosjavierna McCammon
	Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 26. (2 July 2009), pp. 8800-8812. by Pavel I. Zhuravlev, Christopher K. Materese, Garegin A. Papoian posted to md_simulation proteins by jmccammon on 2009-07-08 21:22:29 as along with 1 person and 1 group carlosjavierna McCammon
	The rise of fragment-based drug discovery [My Copy] Nature Chemistry (2009) by C. W. Murray, D. C. Rees posted to binding drug-discovery protein-ligand by jmccammon on 2009-06-27 00:55:52 as
	Drug discovery using chemical systems biology: identification of the protein-ligand binding network to explain the side effects of CETP inhibitors. [My Copy] PLoS computational biology, Vol. 5, No. 5. (15 May 2009), e1000387. by Li Xie, Jerry Li, Lei Xie, Philip E. Bourne posted to binding drug-discovery protein-ligand by jmccammon on 2009-06-16 23:48:55 as along with 5 people and 1 group ubcg08l flbarroso reyez barry dolchan McCammon
	Aminoglycoside Association Pathways with the 30S Ribosomal Subunit [My Copy] The Journal of Physical Chemistry B, Vol. 0, No. 0. (0000) by Maciej Długosz, Joanna Trylska posted to binding brownian_dynamics diffusion drug-discovery electrostatics by jmccammon on 2009-06-11 01:54:17 as along with 1 person and 2 groups sobolevnrm McCammon baker-group

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