Group: McCammon - with tag protein-ligand [41 articles] Export

Recent papers posted by members of the McCammon group with tag protein-ligand

	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 to the group McCammon on 2009-11-21 20:27:49 as along with 1 person anuragsethi
	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
	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 to the group McCammon on 2009-10-31 19:59:28 as along with 3 people anuragsethi pmung acpan
	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
	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 to the group McCammon on 2009-08-29 21:34:06 as along with 6 people mittinatten ahmetbakan apaydin anuragsethi okapi boris_aguilar
	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 to the group McCammon on 2009-08-13 20:03:20 as along with 3 people ubcg08l pmung carlosjavierna
	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 to the group McCammon on 2009-08-13 19:20:53 as along with 2 people oteri dicksmit
	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 to the group McCammon on 2009-08-08 20:25:02 as along with 3 people oteri klexa RamuAnandakrishnan
	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 to the group McCammon on 2009-07-27 19:09:08 as along with 4 people and 1 group sobolevnrm scampos anuragsethi flbarroso baker-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 to the group McCammon on 2009-07-09 18:28:58 as along with 1 person carlosjavierna
	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 to the group McCammon on 2009-06-16 23:48:55 as along with 5 people ubcg08l flbarroso reyez barry dolchan
	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
	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 to the group McCammon on 2009-06-10 01:30:51 as along with 3 people idoerg zwang friendpine
	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
	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 to the group McCammon on 2009-06-06 01:02:47 as along with 3 people arnaucordomi agrossfield xdeupi
	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 to the group McCammon on 2009-05-11 23:37:05 as along with 4 people venancio Scis0000002 Takao alfons
	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
	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 to the group McCammon on 2009-05-09 19:39:36 as along with 4 people and 1 group anuragsethi jeargle AbnerCYH sobolevnrm baker-group
	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 to the group McCammon on 2009-05-08 20:13:28 as
	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 to the group McCammon on 2009-05-05 19:26:05 as along with 4 people and 2 groups 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
	Kinase Domain Mutations in Cancer: Implications for Small Molecule Drug Design Strategies [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 6. (26 March 2009), pp. 1493-1509. by Jack A. Bikker, Natasja Brooijmans, Allan Wissner, Tarek S. Mansour posted to drug-discovery protein-ligand by jmccammon to the group McCammon on 2009-03-28 17:53:51 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 to the group McCammon on 2009-03-01 01:00:11 as along with 9 people and 1 group anuragsethi flbarroso mikaellund sobolevnrm barry willard agrossfield carlosjavierna ibuch baker-group
	Targeting the Formation of the Cell Wall Core of M. tuberculosis [My Copy] Infectious Disorders - Drug Targets, Vol. 7 (2007), 182. by C. E. Barry, D. C. Crick, M. R. Mcneil posted to drug-discovery protein-ligand by jmccammon to the group McCammon on 2009-02-26 02:02:30 as
	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 to the group McCammon on 2009-02-14 22:32:04 as
	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 to the group McCammon on 2009-02-14 22:28:58 as
	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
	QM/MM methods for biomolecular systems. [My Copy] Angewandte Chemie (International ed. in English), Vol. 48, No. 7. (2009), pp. 1198-1229. by H. M. Senn, W. Thiel posted to protein-ligand qm-mm by jmccammon to the group McCammon on 2009-02-13 18:29:21 as along with 1 person skoddet
	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
	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
	Disease-associated carbohydrate-recognising proteins and structure-based inhibitor design [My Copy] Current Opinion in Structural Biology, Vol. 18, No. 5. (October 2008), pp. 558-566. by M. Vonitzstein posted to drug-discovery protein-ligand by jmccammon to the group McCammon on 2008-10-23 02:25:15 as
	Automated clustering of probe molecules from solvent mapping of protein surfaces: new algorithms applied to hot-spot mapping and structure-based drug design. [My Copy] Journal of computer-aided molecular design (5 August 2008) by Michael G. Lerner, Kristin L. Meagher, Heather A. Carlson posted to drug-discovery protein-ligand by jmccammon to the group McCammon on 2008-09-27 20:37:40 as along with 2 people sschurer higueruelo
	An improved relaxed complex scheme for receptor flexibility in computer-aided drug design. [My Copy] J Comput Aided Mol Des (15 January 2008) by Rommie E. Amaro, Riccardo Baron, J A. McCammon posted to drug-discovery md_simulation protein-ligand by jmccammon to the group McCammon on 2008-09-27 20:31:32 as along with 6 people and 1 group karinaecomp oteri rbaron higueruelo kazemi LamBras Structural Biology Group TorVergata
	Molecular modeling on pyruvate phosphate dikinase of Entamoeba histolytica and in silico virtual screening for novel inhibitors [My Copy] Journal of Computer-Aided Molecular Design, Vol. 22, No. 9. (2008), pp. 647-660. by Preyesh Stephen, Ramachandran Vijayan, Audesh Bhat, N. Subbarao, R. Bamezai posted to drug-discovery protein-ligand by jmccammon to the group McCammon on 2008-09-27 20:21:34 as
	Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation [My Copy] Current Opinion in Structural Biology In Catalysis and regulation / Proteins, Vol. 17, No. 6. (December 2007), pp. 633-640. by Ivet Bahar, Chakra Chennubhotla, Dror Tobi posted to coarse_grain md_simulation protein-ligand by jmccammon to the group McCammon on 2008-08-21 19:52:40 as along with 10 people and 3 groups allmensch jrperillaj barry aqeel ruvido cactus sobolevnrm jennifermbui higueruelo LamBras structural_bioinformatics Bioinformatics 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 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	90
drug-discovery	77
md_simulation	77
free_energy	53
docking	31
database	29
solvation	23
allostery	16
electrostatics	13
sbdd	10
molecular_dynamics_simulations	9
protein_dynamics	9
structure	9
flexibility	8
prediction	7
scoring	7
2007	6
aug09	6
coarse_grain	6
interactions	6
monte_carlo	6
screening	6
thermodynamics	6
2009	5
application	5
bs-similarity	5
conformation	5
interaction	5
binding-affinity	4
function	4
moad	4
pdb	4
protein-protein	4
review	4
side-chain	4
sift	4
surface	4
virtual-screening	4
2008	3
conformational_transitions	3
crystallography	3
energy	3
entropy	3
interction	3
kinetics	3
ligand	3
md	3
method	3
molecular_dynamics	3
nucleic_acids	3
peptides	3
pocket	3
protein	3
protein_flexibility	3
proteins	3
qm-mm	3
simulation_methodology	3
structure-function	3
titration	3
water_molecules	3
2005	2
2006	2
alignment	2
amino-acids	2
binding-site	2
binding_affinity	2
clustering	2
correlation-based	2
drug_discovery	2
dynamics	2
eadock	2
fingerprint	2
genomics	2
geometric-hashing	2
hivp	2
induced_fit	2
jcc	2
landscape	2
modeling	2
networks	2
nmr	2
orientation	2
p1	2
scoring-functions	2
structural	2
structural_model	2
structure-searching	2
virtual	2
aa-propensity	1
algorithm	1
cleft	1
hydrogen	1
knowledge-based	1
local	1
mm-pbsa	1
protein-drug	1
protein-lipid	1
qsar	1
sites	1
structure-classification	1

Group: McCammon - with tag protein-ligand [41 articles] Export

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