BragilMassoud's library 385 articles Export

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	The structures of four macrolide antibiotics bound to the large ribosomal subunit. [My Copy] Mol Cell, Vol. 10, No. 1. (July 2002), pp. 117-128. by J. L. Hansen, J. A. Ippolito, N. Ban, P. Nissen, P. B. Moore, T. A. Steitz posted to antibiotics docking pharmacology protein structure by BragilMassoud on 2005-06-08 15:10:23 as
	Structures of MLSBK antibiotics bound to mutated large ribosomal subunits provide a structural explanation for resistance. [My Copy] Cell, Vol. 121, No. 2. (22 April 2005), pp. 257-270. by D. Tu, G. Blaha, P. B. Moore, T. A. Steitz posted to antibiotics docking pharmacology protein structure by BragilMassoud on 2005-06-08 15:07:38 as
	Structural basis for the interaction of antibiotics with the peptidyl transferase centre in eubacteria. [My Copy] Nature, Vol. 413, No. 6858. (25 October 2001), pp. 814-821. by F. Schlünzen, R. Zarivach, J. Harms, et al.A. Bashan, A. Tocilj, R. Albrecht, A. Yonath, F. Franceschi posted to antibiotics docking pharmacology protein structure by BragilMassoud on 2005-06-08 14:28:12 as along with 2 people softsimu Gehrke
	Structural Bioinformatics-Based Design of Selective, Irreversible Kinase Inhibitors [My Copy] Science, Vol. 308, No. 5726. (27 May 2005), pp. 1318-1321. by Michael S. Cohen, Chao Zhang, Kevan M. Shokat, Jack Taunton posted to alignment design docking kinases pharmacology protein screening by BragilMassoud on 2005-06-08 17:31:31 as along with 3 people kokphinchooi RJDReid MaggieYe
	Strategies to overcome resistance to targeted protein kinase inhibitors. [My Copy] Nat Rev Drug Discov, Vol. 3, No. 12. (December 2004), pp. 1001-1010. by H. Daub, K. Specht, A. Ullrich posted to docking kinases pharmacology screening by BragilMassoud on 2005-06-08 17:27:34 as
	Evaluation of library ranking efficacy in virtual screening. [My Copy] J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 11-22. by M. Kontoyianni, G. S. Sokol, L. M. McClellan posted to docking energyfunctions screening by BragilMassoud on 2005-05-10 16:15:47 as along with 3 people and 2 groups nachtalp marcius schuwi BioinfoCIPF SGU-CIPF
	Emerging role of the FGF system in psychiatric disorders. [My Copy] Trends Pharmacol Sci, Vol. 26, No. 5. (May 2005), pp. 228-231. by M. A. Riva, R. Molteni, F. Bedogni, G. Racagni, F. Fumagalli posted to brain pharmacology by BragilMassoud on 2005-05-07 15:24:28 as along with 1 person cphufstedler
	Stimulants and the developing brain. [My Copy] Trends Pharmacol Sci, Vol. 26, No. 5. (May 2005), pp. 237-243. by S. L. Andersen posted to brain pharmacology by BragilMassoud on 2005-05-07 15:23:37 as
	Structure alignment via Delaunay tetrahedralization. [My Copy] Proteins (26 April 2005) by Jeffrey Roach, Shantanu Sharma, Maryna Kapustina, Charles W W. Carter posted to alignment protein structure by BragilMassoud on 2005-05-07 14:50:28 as along with 3 people and 9 groups ana barry shantanu MuraLab structural_bioinformatics MathBio Biostatistics Bioinformatics microRNA Computational_Systems_Biology EvolutionaryComputation Computational-Neurobiology
	Docking screens: right for the right reasons? [My Copy] Current topics in medicinal chemistry, Vol. 9, No. 9. (2009), pp. 755-770. by Peter Kolb, John J. Irwi posted to docking by BragilMassoud on 2009-09-19 09:37:50 as
	Modeling of metal interaction geometries for protein-ligand docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Birte Seebeck, Ingo Reulecke, Andreas Kämper, Matthias Rarey posted to docking energy_functions flexx metal by BragilMassoud on 2009-06-20 12:59:37 as along with 2 people and 2 groups arlam sobolevnrm Chang group baker-group
	An Alternative Method for the Evaluation of Docking Performance: RSR vs RMSD [My Copy] J. Chem. Inf. Model. (4 July 2008) by Dilmurat Yusuf, Andrew M. Davis, Gerard J. Kleywegt, Stefan Schmitt posted to benchmarks density docking xray by BragilMassoud on 2009-06-17 11:31:29 as along with 3 people ahmetbakan reyez mcaruso13
	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 benchmarks docking glamdock by BragilMassoud on 2009-06-17 11:19:03 as along with 3 people klexa schlauchi sim82
	Scoring ligand similarity in structure-based virtual screening [My Copy] Journal of Molecular Recognition, Vol. 9999, No. 9999. (2009), n/a. by Maria I. Zavodszky, Anjali Rohatgi, Jeffrey R. Van Voorst, Honggao Yan, Leslie A. Kuhn posted to docking similarity slide by BragilMassoud on 2009-02-27 13:44:27 as
	eHiTS: A new fast, exhaustive flexible ligand docking system [My Copy] Journal of Molecular Graphics and Modelling, Vol. 26, No. 1. (July 2007), pp. 198-212. by Z. Zsoldos, D. Reid, A. Simon, S. Sadjad, A. Johnson posted to docking ehits by BragilMassoud on 2009-02-27 13:41:53 as
	Protein−Ligand Docking against Non-Native Protein Conformers [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 11. (24 November 2008), pp. 2214-2225. by Marcel L. Verdonk, Paul N. Mortenson, Richard J. Hall, Michael J. Hartshorn, Christopher W. Murray posted to docking flexible_protein gold by BragilMassoud on 2008-11-07 16:17:04 as along with 2 people oteri zimbo1
	On Random Rotations in $R^3$ [My Copy] Biometrika, Vol. 52, No. 3/4. (1965), pp. 636-639. by R. E. Miles posted to geometry math random rotation by BragilMassoud on 2008-10-31 19:03:19 as
	Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method. [My Copy] Journal of chemical information and modeling (25 September 2008) by Jürgen Koska, Velin Z. Spassov, Allister J. Maynard, et al.Lisa Yan, Nic Austin, Paul K. Flook, C M. Venkatachalam posted to docking flexible_protein by BragilMassoud on 2008-10-14 14:05:16 as
	Assessment of programs for ligand binding affinity prediction. [My Copy] Journal of computational chemistry, Vol. 29, No. 8. (June 2008), pp. 1316-1331. by R. Kim, J. Skolnick posted to affinity docking review by BragilMassoud on 2008-07-04 12:58:15 as
	Managing bias in ROC curves. [My Copy] J Comput Aided Mol Des (7 February 2008) by Robert D. Clark, Daniel J. Webster-Clark posted to math roc screening statistics by BragilMassoud on 2008-02-10 12:21:30 as along with 1 person ihaque
	How to do an evaluation: pitfalls and traps. [My Copy] J Comput Aided Mol Des (23 January 2008) by Paul C. Hawkins, Gregory L. Warren, A G. Skillman, Anthony Nicholls posted to benchmarks comparison docking by BragilMassoud on 2008-01-27 13:49:59 as along with 3 people massivemayhem LamBras thanatos
	Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints [My Copy] J. Chem. Inf. Model. (23 January 2008) by S. Renner, S. Derksen, S. Radestock, F. Morchen posted to consensus docking similarity by BragilMassoud on 2008-01-25 21:23:42 as along with 1 person middledomain
	Ligand-Protein Docking with Water Molecules [My Copy] J. Chem. Inf. Model. (23 January 2008) by B. C. Roberts, R. L. Mancera posted to docking water by BragilMassoud on 2008-01-25 21:23:17 as along with 2 people daevans middledomain
	A Pharmacophore Map of Small Molecule Protein Kinase Inhibitors. [My Copy] J Chem Inf Model (17 October 2007) by Malcolm J. McGregor posted to kinase pharmacophore by BragilMassoud on 2007-10-21 13:29:20 as along with 1 person hchmani
	Accelerating molecular modeling applications with graphics processors [My Copy] Journal of Computational Chemistry, Vol. 28, No. 16. (25 September 2007), pp. 2618-2640. by John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, Klaus Schulten posted to energyfunctions forcefield gpu by BragilMassoud on 2007-09-28 16:56:49 as along with 9 people and 1 group ihaque naoya charris5 timg ruvido sobolevnrm yalexeev mikaellund afenley baker-group
	Novel ATP-Competitive Kinesin Spindle Protein Inhibitors. [My Copy] J Med Chem, Vol. 50, No. 20. (4 October 2007), pp. 4939-4952. by Cynthia A. Parrish, Nicholas D. Adams, Kurt R. Auger, et al.Joelle L. Burgess, Jeffrey D. Carson, Amita M. Chaudhari, Robert A. Copeland, Melody A. Diamond, Carla A. Donatelli, Kevin J. Duffy, Leo F. Faucette, Jeffrey T. Finer, William F. Huffman, Erin D. Hugger, Jeffrey R. Jackson, Steven D. Knight, Lusong Luo, Michael L. Moore, Ken A. Newlander, Lance H. Ridgers, Roman Sakowicz, Antony N. Shaw, Chiu-Mei M. Sung, David Sutton, Kenneth W. Wood, Shu-Yun Y. Zhang, Michael N. Zimmerman, Dashyant Dhanak posted to kinesin by BragilMassoud on 2007-09-28 16:56:24 as
	Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm. [My Copy] J Chem Inf Model (25 September 2007) by Mikko J. Vainio, Mark S. Johnson posted to conformaations ligand by BragilMassoud on 2007-09-27 11:35:46 as along with 1 person middledomain
	Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins [My Copy] J. Chem. Inf. Model. (19 September 2007) by M. H. Hao, O. Haq, I. Muegge posted to conformations ligand structure by BragilMassoud on 2007-09-22 19:28:50 as along with 1 person daevans
	Conformational memories with variable bond angles. [My Copy] J Comput Chem (17 September 2007) by Robert M M. Whitnell, Dow P P. Hurst, Patricia H H. Reggio, Frank Guarnieri posted to conforamtions mc by BragilMassoud on 2007-09-20 13:45:43 as
	Progress in computational protein design [My Copy] Current Opinion in Biotechnology, Vol. 18, No. 4. (17 August 2007), pp. 305-311. by S. Lippow, B. Tidor posted to design protein review structure by BragilMassoud on 2007-09-17 17:58:44 as along with 3 people and 1 group baiaixi Lombardo_7 msuarezdiez Bioinformatics
	Visualization software for molecular assemblies [My Copy] Current Opinion in Structural Biology, Vol. In Press, Corrected Proof by Thomas D. Goddard, Thomas E. Ferrin posted to protein structure visualization by BragilMassoud on 2007-09-10 13:36:11 as along with 4 people and 1 group guhjy sobolevnrm higueruelo dgront baker-group
	DITOP: drug-induced toxicity related protein database. [My Copy] Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1710-1712. by Jing-Xian X. Zhang, Wei-Juan J. Huang, Jing-Hua H. Zeng, et al.Wen-Hui H. Huang, Yi Wang, Rui Zhao, Bu-Cong C. Han, Qing-Feng F. Liu, Yu-Zong Z. Chen, Zhi-Liang L. Ji posted to database pharmacology tox by BragilMassoud on 2007-07-29 11:02:28 as along with 1 person guhjy
	On sampling of fragment space. [My Copy] J Med Chem, Vol. 50, No. 14. (12 July 2007), pp. 3214-3221. by G. M. Makara posted to fragments hts by BragilMassoud on 2007-07-07 15:55:52 as along with 2 people npt11tpn daevans
	Comparison of Topological, Shape, and Docking Methods in Virtual Screening. [My Copy] J Chem Inf Model (26 June 2007) by Georgia B. McGaughey, Robert P. Sheridan, Christopher I. Bayly, et al.J C. Culberson, Constantine Kreatsoulas, Stacey Lindsley, Vladimir Maiorov, Jean-Francois F. Truchon, Wendy D. Cornell posted to comparison docking fingerprints screening superposition by BragilMassoud on 2007-06-29 11:26:05 as along with 6 people and 1 group LamBras daevans steff83 middledomain ucbcjbm thanatos Computer Aided Drug Design
	Drug repositioning: identifying and developing new uses for existing drugs [My Copy] Nature Reviews Drug Discovery, Vol. 3, No. 8. (01 August 2004), pp. 673-683. by Ted T. Ashburn, Karl B. Thor posted to pharmacology review by BragilMassoud on 2007-06-27 10:21:10 as along with 3 people sjcockell sameersoi apostola
	A large-scale computational approach to drug repositioning. [My Copy] Genome Inform, Vol. 17, No. 2. (2006), pp. 239-247. by Y. Y. Li, J. An, S. J. Jones posted to docking inverse_screening by BragilMassoud on 2007-06-27 10:19:14 as along with 1 person aheilbut
	On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review [My Copy] Journal of Computational Chemistry, Vol. 29, No. 2. (14 June 2008), pp. 157-166. by Markus Christen, Wilfred F. van Gunsteren posted to md review by BragilMassoud on 2007-06-17 12:01:46 as along with 5 people tovrstra dgront rabio somak dmobley
	Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography. [My Copy] Proteins (7 June 2007) by Pablo Englebienne, Hélène Fiaux, Douglas A A. Kuntz, et al.Christopher R R. Corbeil, Sandrine Gerber-Lemaire, David R R. Rose, Nicolas Moitessier posted to benchmark docking flexx glide gold by BragilMassoud on 2007-06-10 14:39:26 as along with 1 person flbarroso
	Unbiasing Scoring Functions: A New Normalization and Rescoring Strategy. [My Copy] J Chem Inf Model (7 June 2007) by Giorgio Carta, Andrew J. Knox, David G. Lloyd posted to energy_functions screening by BragilMassoud on 2007-06-10 14:14:54 as
	FLIPDock: Docking flexible ligands into flexible receptors [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 68, No. 3. (23 May 2007), pp. 726-737. by Yong Zhao, Michel F. Sanner posted to docking flexible_protein by BragilMassoud on 2007-05-28 14:43:46 as along with 7 people and 1 group npt11tpn fl karinaecomp yongzhao kazemi somak LamBras TSRI_MGL
	Multiple targeted tyrosine kinase inhibition in the clinic: all for one or one for all? [My Copy] Eur J Cancer, Vol. 42, No. 10. (July 2006), pp. 1351-1356. by M. J. de Jonge, J. Verweij posted to kinases pharmacology specificity by BragilMassoud on 2007-05-14 15:04:18 as
	Alternative to Consensus Scoring-A New Approach Toward the Qualitative Combination of Docking Algorithms. [My Copy] J Chem Inf Model (11 May 2007) by Antje Wolf, Marc Zimmermann, Martin Hofmann-Apitius posted to autodock consensus docking flexx by BragilMassoud on 2007-05-13 16:47:26 as
	Improved sampling methods for molecular simulation. [My Copy] Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 187-191. by H. Lei, Y. Duan posted to math minimization protein review structure by BragilMassoud on 2007-05-08 13:33:48 as along with 3 people viktor21614 aqeel allmensch
	Potential energy functions for protein design. [My Copy] Curr Opin Struct Biol (24 March 2007) by F Edward E. Boas, Pehr B B. Harbury posted to design energyfunctions protein review structure by BragilMassoud on 2007-05-08 13:32:47 as along with 5 people kgutwin krapnik msuarezdiez aalibes onufriev
	Accuracy of binding mode prediction with a cascadic stochastic tunneling method. [My Copy] Proteins (11 April 2007) by Bernhard Fischer, Serena Basili, Holger Merlitz, Wolfgang Wenzel posted to docking mc stun by BragilMassoud on 2007-04-22 16:52:42 as
	A simple way to compute protein dynamics without a mechanical model. [My Copy] Proteins (13 April 2007) by Chien-Hua H. Shih, Shao-Wei W. Huang, Shih-Chung C. Yen, Yan-Long L. Lai, Sung-Huan H. Yu, Jenn-Kang K. Hwang posted to nma protein structure by BragilMassoud on 2007-04-20 14:19:53 as along with 3 people bicko cactus jlh64
	From Molecular to Biological Structure and Back. [My Copy] J Chem Inf Model (4 April 2007) by Danail Bonchev, Gregory A. Buck posted to graph graphs networks by BragilMassoud on 2007-04-07 12:37:51 as along with 1 person Scis0000002
	Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions. [My Copy] J Comput Chem (2 April 2007) by Stephan Raub, Christel M M. Marian posted to electrostatics energyfunctions qc by BragilMassoud on 2007-04-07 12:37:03 as
	Joint neighbors approximation of macromolecular solvent accessible surface area. [My Copy] J Comput Chem (3 April 2007) by Georgy Rychkov, Michael Petukhov posted to protein solvation structure by BragilMassoud on 2007-04-07 12:36:36 as along with 3 people dgront mijam hryk
	On Information and Sufficiency [My Copy] The Annals of Mathematical Statistics, Vol. 22, No. 1. (March 1951), pp. 79-86. by S. Kullback, R. Leibler posted to math statistics by BragilMassoud on 2007-03-31 17:10:24 as

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docking	175
structure	91
protein	89
screening	84
pharmacology	43
energyfunctions	42
review	38
math	35
nma	25
affinity	22
forcefield	21
kinases	21
ligands	20
flexible_protein	18
minimization	18
robert	17
db	13
hts	13
md	13
visualization	13
internal_coordinates	12
alignment	11
superposition	11
actin	10
electrostatics	9
gold	9
evolution	8
kinesin	7
ligand	7
dehydron	6
design	6
solvation	6
cavities	5
flexx	5
machinelearning	5
mc	5
specificity	5
statistics	5
stun	5
surflex	5
conformations	4
evotrace	4
glide	4
metabolomics	4
pts	4
qc	4
slide	4
antibiotics	3
autodock	3
benchmark	3
benchmarks	3
brain	3
comment	3
comparison	3
est	3
fingerprints	3
graphs	3
inversescreening	3
physics	3
ribbons	3
roc	3
sasa	3
textmining	3
abinitio	2
born	2
cancer	2
chemogenomics	2
consensus	2
database	2
energy_functions	2
enzyme	2
enzymes	2
ga	2
geneexpression	2
graph	2
ludi	2
pharmacogenetics	2
pharmacophore	2
quaternion	2
ring_flipping	2
similarity	2
tox	2
1acj	1
adme	1
affinitiy	1
algorithm	1
antidepressants	1
antoptimization	1
bench_errors	1
bias	1
clustering	1
conforamtions	1
conformaations	1
conformation	1
denovo	1
density	1
dock	1
dokcing	1
ehits	1
entropy	1
fragmentation	1
fragments	1
framgents	1
geometry	1
ghb	1
glamdock	1
gpu	1
hammerhead	1
hbond	1
hom_model	1
hond	1
hydration	1
inverse_screening	1
kinase	1
language	1
ligandfit	1
loop_quantum	1
mechanics	1
metal	1
networks	1
neuro	1
open_access	1
openeye	1
optimization	1
pain	1
pdk1	1
pharmacolgy	1
pharmacologyy	1
psychedelics	1
psychology	1
qsar	1
qxp	1
random	1
rotation	1
rss	1
salvinorin	1
science	1
sequence	1
spline	1
therapy	1
water	1
xray	1

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