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	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
	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
	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
	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
	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
	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
	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
	Enhanced protein steering: cooperative electrostatic and van der waals forces in antigen-antibody complexes. [My Copy] The journal of physical chemistry. B, Vol. 113, No. 30. (30 July 2009), pp. 10459-10464. by Björn A. Persson, Bo Jönsson, Mikael Lund posted to binding electrostatics protein-protein by jmccammon on 2009-07-25 21:38:23 as along with 2 people and 1 group mikaellund flbarroso McCammon
	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
	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
	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
	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
	A Novel Small-Molecule Inhibitor of the Avian Influenza H5N1 Virus Determined through Computational Screening against the Neuraminidase [My Copy] Journal of Medicinal Chemistry, Vol. 0, No. 0. (0000) by Jianghong An, Davy C. Lee, Anna H. Law, et al.Cindy L. Yang, Leo L. Poon, Allan S. Lau, Steven J. Jones posted to binding drug-discovery protein-ligand by jmccammon on 2009-06-10 01:30:51 as along with 3 people and 1 group idoerg zwang friendpine 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
	Fruitful and Futile Encounters along the Association Reaction between Proteins [My Copy] Biophysical Journal, Vol. 96, No. 10. (20 May 2009), pp. 4237-4248. by Michal Harel, Alexander Spaar, Gideon Schreiber posted to binding brownian_dynamics diffusion electrostatics protein-protein by jmccammon on 2009-06-06 01:46:56 as along with 1 person and 2 groups barry structural_bioinformatics McCammon
	Observation of Ionic Lock Formation in Molecular Dynamics Simulations of Wild Type 1 and 2 Adrenergic Receptors. [My Copy] Biochemistry (20 April 2009) by Stefano Vanni, Marilisa Neri, Ivano Tavernelli, Ursula Rothlisberger posted to allostery binding drug-discovery md_simulation protein-ligand by jmccammon on 2009-06-06 01:02:46 as along with 3 people and 1 group arnaucordomi agrossfield xdeupi 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
	Dynamical networks in tRNA:protein complexes [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 16. (21 April 2009), pp. 6620-6625. by Anurag Sethi, John Eargle, Alexis A. Black, Zaida Luthey-Schulten posted to allostery binding md_simulation protein-ligand by jmccammon on 2009-05-09 19:39:36 as along with 4 people and 2 groups anuragsethi jeargle AbnerCYH sobolevnrm McCammon baker-group
	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
	Accurate characterization of weak macromolecular interactions by titration of NMR residual dipolar couplings: application to the CD2AP SH3-C:ubiquitin complex [My Copy] Nucl. Acids Res. (9 April 2009), gkp211. by Jose L. Ortega-Roldan, Malene R. Jensen, Bernhard Brutscher, Ana I. Azuaga, Martin Blackledge, Nico A. van Nuland posted to binding protein-protein by jmccammon on 2009-04-25 18:53:22 as along with 1 group McCammon
	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
	Fundamental Aspects of Protein−Protein Association Kinetics [My Copy] Chemical Reviews, Vol. 109, No. 3. (11 March 2009), pp. 839-860. by G. Schreiber, G. Haran, H. X. Zhou posted to binding brownian_dynamics diffusion electrostatics protein-protein by jmccammon on 2009-03-24 23:26:50 as along with 10 people and 2 groups anuragsethi barry sunhwan sobolevnrm willard kafuitay carlosjavierna sschurer hadesnumb paulschlesinger McCammon 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 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
	AutoGrow: A Novel Algorithm for Protein Inhibitor Design [My Copy] Chemical Biology & Drug Design (2009) by J. D. Durrant, R. E. Amaro, J. A. Mccammon posted to binding drug-discovery protein-ligand by jmccammon on 2009-02-14 22:32:04 as along with 1 group McCammon
	CREDO: A Protein–Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design (2009) by A. Schreyer, T. Blundell posted to binding drug-discovery protein-ligand by jmccammon on 2009-02-14 22:28:58 as along with 1 group McCammon
	Finding and Characterizing Tunnels in Macromolecules with Application to Ion Channels and Pores [My Copy] Biophysical Journal (2009) by R. G. Coleman, K. A. Sharp posted to binding ion_channel by jmccammon on 2009-02-14 22:06:11 as along with 1 person and 2 groups oteri LOX-1 Receptor 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
	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
	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
	What induces pocket openings on protein surface patches involved in protein-protein interactions? [My Copy] Journal of computer-aided molecular design, Vol. 23, No. 2. (6 February 2009), pp. 73-86. by Susanne Eyrisch, Volkhard Helms posted to binding drug-discovery md_simulation protein-protein by jmccammon on 2009-01-10 21:35:58 as along with 3 people and 1 group arifor allmensch higueruelo 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
	Fundamental Aspects of Protein-Protein Association Kinetics [My Copy] Chemical Reviews (to appear) (2009) by G. Schreiber, G. Haran, H. X. Zhou posted to binding brownian_dynamics diffusion electrostatics kinetics protein-protein by jmccammon on 2008-12-30 23:41:13 as
	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
	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
	Stochastic Binding of Ca2+ Ions in the Dyadic Cleft; Continuous versus Random Walk Description of Diffusion [My Copy] Biophys. J., Vol. 94, No. 11. (1 June 2008), pp. 4184-4201. by Johan Hake, Glenn T. Lines posted to binding brownian_dynamics ion_channel by jmccammon on 2008-07-07 23:35:58 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
	Recognition Dynamics Up to Microseconds Revealed from an RDC-Derived Ubiquitin Ensemble in Solution [My Copy] Science, Vol. 320, No. 5882. (13 June 2008), pp. 1471-1475. by Oliver F. Lange, Nils-Alexander Lakomek, Christophe Fares, et al.Gunnar F. Schroder, Korvin F. A. Walter, Stefan Becker, Jens Meiler, Helmut Grubmuller, Christian Griesinger, Bert L. de Groot posted to binding protein-protein by jmccammon on 2008-06-27 00:55:23 as along with 6 people and 3 groups anna_yershova edws paulschlesinger higueruelo barry cchang structural_bioinformatics McCammon Chang 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
	Protein-protein binding is often associated with changes in protonation state [My Copy] Proteins, Vol. 71 (2008), pp. 81-91. by A. C. Mason, J. H. Jensen posted to binding protein-protein titration by jmccammon on 2008-03-21 17:00:41 as

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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

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