Tag protein-ligand [125 articles] Export

Recent papers classified by the tag protein-ligand.

	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
	STITCH 2: an interaction network database for small molecules and proteins [My Copy] Nucl. Acids Res. (6 November 2009), gkp937. by Michael Kuhn, Damian Szklarczyk, Andrea Franceschini, et al.Monica Campillos, Christian von Mering, Lars J. Jensen, Andreas Beyer, Peer Bork posted to stitch protein-protein protein-ligand network interaction database by neils on 2009-11-08 22:18:17 as
	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
	Flexible protein-ligand docking by global energy optimization in internal coordinates [My Copy] Proteins: Structure, Function, and Genetics, Vol. 29, No. S1. (1997), pp. 215-220. by Maxim Totrov, Ruben Abagyan posted to protein-ligand flexibility docking 1997 by klexa on 2009-09-29 23:00:44 as along with 1 person schlauchi
	GlamDock: Development and Validation of a New Docking Tool on Several Thousand Protein-Ligand Complexes. [My Copy] J Chem Inf Model, Vol. 47, No. 4. (g 2007), pp. 1657-1672. by S. Tietze, J. Apostolakis posted to protein-ligand flexibility docking 2007 by klexa on 2009-09-29 21:19:16 as along with 3 people BragilMassoud schlauchi sim82
	A Flexible Approach to Induced Fit Docking [My Copy] J. Med. Chem. (22 November 2007) by Sander B. Nabuurs, Markus Wagener, Jacob de Vlieg posted to sbdd protein-ligand induced_fit flexibility docking 2007 by klexa on 2009-09-29 21:17:05 as along with 2 people oteri daevans
	Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 2. (1 January 2006), pp. 534-553. by Woody Sherman, Tyler Day, Matthew P. Jacobson, Richard A. Friesner, Ramy Farid posted to protein_flexibility protein-ligand induced_fit 2006 by klexa on 2009-09-29 21:16:40 as along with 7 people and 1 group sschurer cen4ik LamBras BragilMassoud yongzhao daevans kazemi TSRI_MGL
	Optimal docking area: a new method for predicting protein-protein interaction sites. [My Copy] Proteins, Vol. 58, No. 1. (1 January 2005), pp. 134-143. by J. Fernandez-Recio, M. Totrov, C. Skorodumov, R. Abagyan posted to structural_model solvation protein-protein protein-ligand docking 2005 by klexa on 2009-09-29 20:57:02 as along with 5 people and 2 groups jwm bicko schlauchi cjeans marti Radiation_Damage Stressosome
	Structure-based virtual ligand screening with LigandFit: Pose prediction and enrichment of compound collections. [My Copy] Proteins, Vol. 68, No. 3. (15 August 2007), pp. 712-725. by M. Montes, M. A. Miteva, B. O. Villoutreix posted to screening protein-ligand lead drug_discovery docking 2007 by klexa on 2009-09-29 20:56:33 as along with 1 person schlauchi
	Methods for the prediction of protein-ligand binding sites for structure-based drug design and virtual ligand screening. [My Copy] Current protein & peptide science, Vol. 7, No. 5. (October 2006), pp. 395-406. by Alasdair T. Laurie, Richard M. Jackson posted to virtual structure sites screening protein-ligand prediction of methods ligand for drug design binding based and by jinghu_fandm on 2009-09-15 19:15:27 as along with 2 people and 1 group mkotlyar caporaso biomedical-nlp
	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 5 people 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 1 person 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 structure scoring sbdd protein-ligand pocket binding aug09 by klexa on 2009-08-11 19:38:16 as along with 3 people and 1 group oteri jmccammon RamuAnandakrishnan McCammon
	Blind docking of 260 protein-ligand complexes with EADock 2.0 [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2021-2030. by Aurélien Grosdidier, Vincent Zoete, Olivier Michielin posted to protein-ligand jcc eadock docking aug09 by klexa on 2009-08-11 17:34:20 as
	Use of Amino Acid Composition to Predict Ligand-Binding Sites [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 2. (1 March 2007), pp. 400-406. by Shinji Soga, Hiroki Shirai, Masato Kobori, Noriaki Hirayama posted to amino-acids binding-site-analysis p1 protein protein-ligand structure surface by nickolay on 2009-08-06 19:01:15 as along with 1 person iaolier
	Propensities of polar and aromatic amino acids in noncanonical interactions: nonbonded contacts analysis of protein-ligand complexes in crystal structures. [My Copy] Journal of medicinal chemistry, Vol. 50, No. 6. (22 March 2007), pp. 1189-1196. by Yumi N. Imai, Yoshihisa Inoue, Yoshio Yamamoto posted to amino-acids aromatics p1 props protein protein-ligand structure by nickolay on 2009-08-06 17:15:31 as
	Substrate Binding Mechanism of HIV-1 Protease from Explicit-Solvent Atomistic Simulations [My Copy] Journal of the American Chemical Society, Vol. 131, No. 33. (26 August 2009), pp. 11811-11818. by Fabio Pietrucci, Fabrizio Marinelli, Paolo Carloni, Alessandro Laio posted to 2009 aug09 binding hivp molecular_dynamics protein-ligand by klexa on 2009-08-05 14:26:49 as along with 2 people dicksmit fabiopietrucci
	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
	Thermodynamics of Buried Water Clusters at a Protein−Ligand Binding Interface [My Copy] The Journal of Physical Chemistry B, Vol. 110, No. 3. (1 January 2006), pp. 1464-1475. by Zheng Li, Themis Lazaridis posted to protein-ligand water by krapnik on 2009-07-27 11:45:18 as along with 1 person jteyra
	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
	A review of protein-small molecule docking methods. [My Copy] J Comput Aided Mol Des, Vol. 16, No. 3. (March 2002), pp. 151-166. by R. D. Taylor, P. J. Jewsbury, J. W. Essex posted to 2002 docking protein-ligand review by klexa on 2009-06-29 15:53:47 as along with 6 people and 5 groups csrocha oteri marcius sangeetha schlauchi massivemayhem Structural Biology Group TorVergata Bioinformatics insilicodrug BioinfoCIPF SGU-CIPF
	Steps towards flexible docking: modeling of three-dimensional structures of the nuclear receptors bound with peptide ligands mimicking co-activators' sequences. [My Copy] J Steroid Biochem Mol Biol, Vol. 103, No. 3-5. (March 2007), pp. 357-360. by M. Kurcinski, A. Kolinski posted to 2007 docking flexibility protein-ligand structural_model by klexa on 2009-06-29 15:32:35 as along with 2 people and 1 group oteri mkurc Structural Biology Group TorVergata
	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
	Structural interaction fingerprint (SIFt): a novel method for analyzing three-dimensional protein-ligand binding interactions. [My Copy] J Med Chem, Vol. 47, No. 2. (15 January 2004), pp. 337-344. by Z. Deng, C. Chuaqui, J. Singh posted to clustering fingerprint interactions protein-ligand sift by bio_dataminer on 2009-05-25 16:51:39 as along with 4 people and 2 groups ubcg08l apostola sangeetha massivemayhem Bioinformatics insilicodrug
	Position Specific Interaction Dependent Scoring Technique for Virtual Screening Based on Weighted Protein−Ligand Interaction Fingerprint Profiles [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 5. (22 May 2009), pp. 1185-1192. by Ravi K. Nandigam, Sangtae Kim, Juswinder Singh, Claudio Chuaqui posted to dimensionality-reduction fingerprint interaction nmf protein-ligand sift by bio_dataminer on 2009-05-24 22:00:45 as along with 3 people ucbcjbm massivemayhem sschurer
	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
	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
	Kinase inhibitors and the case for CH..O hydrogen bonds in protein-ligand binding [My Copy] Proteins: Structure, Function, and Genetics, Vol. 49, No. 4. (2002), pp. 567-576. by Albert C. Pierce, Kathryn L. Sandretto, Guy W. Bemis posted to hydrogen-bonding protein-ligand weak-hbonds by massivemayhem on 2009-04-30 16:09:44 as
	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
	Scoring confidence index: statistical evaluation of ligand binding mode predictions [My Copy] Journal of Computer-Aided Molecular Design by Maria Zavodszky, Andrew Stumpff-Kane, David Lee, Michael Feig posted to binding correlation-based docking energy function landscape orientation protein-ligand score scoring by zimbo1 on 2009-04-15 16:13:56 as
	Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions [My Copy] Journal of Chemical Information and Modeling, Vol. 49, No. 4. (27 April 2009), pp. 944-955. by Robert S. Paton, Jonathan M. Goodman posted to force-field protein-ligand by massivemayhem on 2009-04-01 15:10:24 as along with 2 people middledomain carlosjavierna
	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
	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
	CREDO: A Protein-Ligand Interaction Database for Drug Discovery [My Copy] Chemical Biology & Drug Design, Vol. 73, No. 2. (February 2009), pp. 157-167. by Adrian Schreyer, Tom Blundell posted to protein-ligand by massivemayhem on 2009-01-28 11:02:20 as along with 6 people mijam richardbickerton pansapiens bicko nanonan higueruelo
	Geometrical Preferences of the Hydrogen Bonds on Protein−Ligand Binding Interface Derived from Statistical Surveys and Quantum Mechanics Calculations [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 11. (11 November 2008), pp. 1959-1973. by Zhiguo Liu, Guitao Wang, Zhanting Li, Renxiao Wang posted to bond hydrogen protein-ligand by Zhiguo on 2009-01-28 02:46:33 as along with 1 person Lombardo_7
	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
	Detection of 3D atomic similarities and their use in the discrimination of small molecule protein-binding sites [My Copy] Bioinformatics, Vol. 24, No. 16. (15 August 2008), pp. i105-111. by Rafael Najmanovich, Natalja Kurbatova, Janet Thornton posted to analysis cleft modeling pocket protein-ligand by krapnik on 2008-12-03 17:07:55 as along with 7 people iaolier ramensky apaydin tjimenez neils reyez nickolay
	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

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binding	87
drug-discovery	74
md_simulation	74
free_energy	53
docking	31
database	29
solvation	20
allostery	16
electrostatics	13
sbdd	10
structure	9
flexibility	8
prediction	7
scoring	7
2007	6
aug09	6
coarse_grain	6
interactions	6
molecular_dynamics_simulations	6
monte_carlo	6
protein_dynamics	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
crystallography	3
energy	3
entropy	3
interction	3
kinetics	3
ligand	3
md	3
method	3
molecular_dynamics	3
nucleic_acids	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
based	1
cleft	1
gometry-based	1
hydrogen	1
inhibitor	1
knowledge-based	1
lead	1
local	1
mm-pbsa	1
protein-lipid	1
structural-conservation	1
structure-classification	1

Tag protein-ligand [125 articles] Export

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