jmccammon's library 136 articles Export

	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 3 people and 1 group 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, 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 1 person and 1 group 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
	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
	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
	Dielectric Boundary Forces in Numerical Poisson-Boltzmann Methods: Theory and Numerical Strategies [My Copy] Preprint (2009) by X. Ye, J. Wang, R. Luo posted to solvation proteins electrostatics by jmccammon on 2009-10-03 00:13:51 as
	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 5 people and 1 group 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 1 person and 1 group 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
	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
	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
	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
	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
	A Kernel for Open Source Drug Discovery in Tropical Diseases [My Copy] PLoS Negl Trop Dis, Vol. 3, No. 4. (21 April 2009), e418. by Leticia Ortí, Rodrigo J. Carbajo, Ursula Pieper, et al.Narayanan Eswar, Stephen M. Maurer, Arti K. Rai, Ginger Taylor, Matthew H. Todd, Antonio Pineda-Lucena, Andrej Sali, Marc A. Marti-Renom posted to drug-discovery protein-ligand proteins by jmccammon on 2009-05-11 23:37:05 as along with 4 people and 1 group venancio Scis0000002 Takao alfons McCammon
	Allosteric Transitions of Supramolecular Systems Explored by Network Models: Application to Chaperonin GroEL [My Copy] PLoS Comput Biol, Vol. 5, No. 4. (17 April 2009), e1000360. by Zheng Yang, Peter Májek, Ivet Bahar posted to allostery coarse_grain protein-protein by jmccammon on 2009-05-11 20:41:15 as along with 2 people and 2 groups barry sobolevnrm McCammon baker-group
	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
	Simulated annealing coupled replica exchange molecular dynamics—An efficient conformational sampling method [My Copy] Journal of Structural Biology, Vol. 166, No. 3. (June 2009), pp. 288-294. by Srinivasaraghavan Kannan, Martin Zacharias posted to md_simulation replica_exchange by jmccammon on 2009-05-08 23:03:23 as along with 1 group McCammon
	Dynamics of the Streptavidin−Biotin Complex in Solution and in Its Crystal Lattice: Distinct Behavior Revealed by Molecular Simulations [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 19. (14 May 2009), pp. 6971-6985. by David S. Cerutti, Isolde L. Trong, Ronald E. Stenkamp, Terry P. Lybrand posted to md_simulation protein-ligand by jmccammon on 2009-05-08 20:13:28 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, Vol. 0, No. 0. (0000) 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 4 people and 3 groups A_Coletta_Thesis carlosjavierna ibuch sobolevnrm McCammon Structural Biology Group TorVergata baker-group
	On removal of charge singularity in Poisson--Boltzmann equation [My Copy] Journal of Chemical Physics (2009) by Q. Cai, J. Wang, H. K. Zhao, R. Luo posted to electrostatics by jmccammon on 2009-04-30 00:58:44 as along with 1 group McCammon
	Computational studies of protein regulation by post-translational phosphorylation. [My Copy] Current opinion in structural biology, Vol. 19, No. 2. (April 2009), pp. 156-163. by Arjun Narayanan, Matthew P. Jacobson posted to electrostatics md_simulation proteins by jmccammon on 2009-04-27 22:59:27 as along with 1 person and 1 group guhjy McCammon
	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
	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
	ProteinShader: illustrative rendering of macromolecules [My Copy] BMC Structural Biology, Vol. 9 (30 March 2009), 19. by Joseph R. Weber posted to proteins by jmccammon on 2009-04-23 19:28:54 as along with 1 person and 1 group idoerg McCammon

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md_simulation	72
protein-ligand	46
binding	43
drug-discovery	39
electrostatics	30
free_energy	28
coarse_grain	22
protein-protein	17
brownian_dynamics	13
solvation	13
diffusion	10
allostery	8
proteins	8
ion_channel	7
protein_dynamics	7
kinetics	5
langevin_dynamics	5
accelerated_md	4
functional_modes	4
membrane	4
monte_carlo	4
qm-mm	4
replica_exchange	4
titration	4
conformational_transitions	3
molecular_dynamics_simulations	3
nucleic_acids	3
achr	2
clustering	2
molecular_mechanics_calculations	2
simulation_methodology	2
adenylate_kinase	1
c_src	1
entropy	1
string_method	1
time_correlation_function	1
tyrosine_kinase	1
water_molecules	1

jmccammon's library 136 articles Export

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