BragilMassoud's docking [175 articles] Export

Recent papers added to BragilMassoud's library classified by the tag docking. You can also see everyone's docking.

	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
	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
	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
	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
	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
	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
	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
	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
	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
	Surflex-Dock 2.1: robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search. [My Copy] Journal of computer-aided molecular design, Vol. 21, No. 5. (27 May 2007), pp. 281-306. by A. N. Jain posted to docking surflex by BragilMassoud on 2007-03-29 14:44:56 as along with 3 people and 3 groups vpenelle oteri sangeetha Structural Biology Group TorVergata Bioinformatics insilicodrug
	Docking small ligands in flexible binding sites [My Copy] Journal of Computational Chemistry, Vol. 19, No. 1. (1998), pp. 21-37. by Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch posted to docking flexible_protein mc minimization by BragilMassoud on 2007-03-05 13:48:11 as along with 3 people karinaecomp klexa schlauchi
	A new implicit solvent model for protein-ligand docking. [My Copy] Proteins (28 February 2007) by Antonio Morreale, Rubén Gil-Redondo, Angel R R. Ortiz posted to docking electrostatics energyfunctions by BragilMassoud on 2007-03-04 13:30:32 as along with 1 person flbarroso
	Gaussian docking functions [My Copy] Biopolymers, Vol. 68, No. 1. (2003), pp. 76-90. by Mark R. Mcgann, Harold R. Almond, Anthony Nicholls, Andrew J. Grant, Frank K. Brown posted to docking energyfunctions openeye by BragilMassoud on 2007-02-19 11:10:26 as along with 1 person ima
	Diverse, High-Quality Test Set for the Validation of Protein−Ligand Docking Performance [My Copy] Journal of Medicinal Chemistry, Vol. 50, No. 4. (1 February 2007), pp. 726-741. by Michael J. Hartshorn, Marcel L. Verdonk, Gianni Chessari, et al.Suzanne C. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray posted to benchmark docking by BragilMassoud on 2007-02-18 12:24:11 as along with 9 people flbarroso GermanErlenkamp massivemayhem higueruelo daevans ramensky hmk superpyrin thanatos
	Supervised Consensus Scoring for Docking and Virtual Screening. [My Copy] J Chem Inf Model (13 February 2007) by Reiji Teramoto, Hiroaki Fukunishi posted to docking energyfunctions screening by BragilMassoud on 2007-02-15 16:59:15 as
	TrixX: structure-based molecule indexing for large-scale virtual screening in sublinear time. [My Copy] J Comput Aided Mol Des (9 February 2007) by Ingo Schellhammer, Matthias Rarey posted to docking flexx screening by BragilMassoud on 2007-02-15 15:46:35 as along with 2 people and 2 groups sangeetha peprovy Bioinformatics insilicodrug
	Stochastic roadmap simulation: an efficient representation and algorithm for analyzing molecular motion [My Copy] In RECOMB '02: Proceedings of the sixth annual international conference on Computational biology (2002), pp. 12-21. by Mehmet S. Apaydin, Douglas L. Brutlag, Carlos Guestrin, David Hsu, Jean-Claude Latombe posted to docking by BragilMassoud on 2007-02-12 12:45:53 as
	A semiempirical free energy force field with charge-based desolvation [My Copy] Journal of Computational Chemistry, Vol. 28, No. 6. (1 February 2007), pp. 1145-1152. by Ruth Huey, Garrett M. Morris, Arthur J. Olson, David S. Goodsell posted to solvation screening forcefield energyfunctions docking autodock by BragilMassoud on 2007-02-04 15:03:24 as along with 6 people and 1 group trishul nickolay joule oteri IrinaMoreira carlescorbi Structural Biology Group TorVergata
	Analysis of Ligand-Bound Water Molecules in High-Resolution Crystal Structures of Protein-Ligand Complexes. [My Copy] J Chem Inf Model (1 February 2007) by Yipin Lu, Renxiao Wang, Chao-Yie Y. Yang, Shaomeng Wang posted to structure protein hydration docking by BragilMassoud on 2007-02-04 14:59:12 as along with 2 people npt11tpn LamBras
	Optimizing Fragment and Scaffold Docking by Use of Molecular Interaction Fingerprints [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 1. (1 January 2007), pp. 195-207. by Gilles Marcou, Didier Rognan posted to screening pharmacophore framgents fingerprints docking by BragilMassoud on 2007-02-04 14:14:34 as along with 8 people RebeccaHamer klexa richardbickerton nanonan peprovy schlauchi massivemayhem sithmein
	Ultrafast de novo docking combining pharmacophores and combinatorics. [My Copy] J Comput Aided Mol Des (30 January 2007) by Marcus Gastreich, Markus Lilienthal, Hans Briem, Holger Claussen posted to screening flexx docking denovo by BragilMassoud on 2007-02-02 11:40:49 as along with 1 person peprovy
	Comments on the Article "On Evaluating Molecular-Docking Methods for Pose Prediction and Enrichment Factors" [My Copy] J Chem Inf Model (30 January 2007) by Emanuele Perola, W P. Walters, Paul Charifson posted to docking comment by BragilMassoud on 2007-02-01 16:43:03 as
	Comparison of stochastic optimization methods for receptor-ligand docking [My Copy] Chemical Physics Letters, Vol. 362, No. 3-4. (19 August 2002), pp. 271-277. by H. Merlitz, W. Wenzel posted to stun minimization docking by BragilMassoud on 2007-02-01 15:39:06 as
	Application of the stochastic tunneling method to high throughput database screening [My Copy] Chemical Physics Letters, Vol. 370, No. 1-2. (7 March 2003), pp. 68-73. by H. Merlitz, B. Burghardt, W. Wenzel posted to stun screening minimization docking by BragilMassoud on 2007-02-01 15:38:43 as
	Strong and weak hydrogen bonds in the protein-ligand interface. [My Copy] Proteins (5 January 2007) by Sunil K K. Panigrahi, Gautam R R. Desiraju posted to docking energyfunctions hond by BragilMassoud on 2007-01-10 14:30:44 as along with 3 people and 1 group Lombardo_7 cat_worth friendpine structural_bioinformatics
	SODOCK: Swarm optimization for highly flexible protein-ligand docking. [My Copy] J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623. by H. M. Chen, B. F. Liu, H. L. Huang, S. F. Hwang, S. Y. Ho posted to docking by BragilMassoud on 2007-01-08 20:20:49 as along with 4 people and 1 group npt11tpn oteri dgruiz yongzhao TSRI_MGL
	Development and validation of a modular, extensible docking program: DOCK 5. [My Copy] J Comput Aided Mol Des (6 December 2006) by Demetri T. Moustakas, P T. Lang, Scott Pegg, et al.Eric Pettersen, Irwin D. Kuntz, Natasja Brooijmans, Robert C. Rizzo posted to dock docking screening by BragilMassoud on 2006-12-09 15:50:07 as along with 2 people and 1 group yongzhao schlauchi TSRI_MGL
	Protein-Ligand Binding Affinity Predictions by Implicit Solvent Simulations: A Tool for Lead Optimization? [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 25. (1 December 2006), pp. 7427-7439. by Julien Michel, Marcel L. Verdonk, Jonathan W. Essex posted to affinity docking energyfunctions screening solvation by BragilMassoud on 2006-12-09 15:39:15 as along with 1 person daevans
	Progressive Docking: A Hybrid QSAR/Docking Approach for Accelerating In Silico High Throughput Screening. [My Copy] J Med Chem, Vol. 49, No. 25. (14 December 2006), pp. 7466-7478. by Artem Cherkasov, Fuqiang Ban, Yvonne Li, Magid Fallahi, Geoffrey L. Hammond posted to docking qsar screening by BragilMassoud on 2006-12-09 15:36:10 as along with 1 person and 1 group yongzhao TSRI_MGL
	How Different are Structurally Flexible and Rigid Binding Sites? Sequence and Structural Features Discriminating Proteins that Do and Do not Undergo Conformational Change upon Ligand Binding. [My Copy] J Mol Biol (29 September 2006) by Kannan Gunasekaran, Ruth Nussinov posted to docking flexible_protein by BragilMassoud on 2006-11-28 16:57:23 as along with 10 people and 1 group aqeel reyez dgruiz radestock lna yongzhao choonpeng weisblum higueruelo nickolay TSRI_MGL
	Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 66, No. 2. (9 November 2007), pp. 399-421. by Sheng-You Huang, Xiaoqin Zou posted to docking flexible_protein by BragilMassoud on 2006-11-12 15:10:30 as along with 8 people and 2 groups nickolay oteri AliceWang bicko yongzhao kazemi hmk LamBras Structural Biology Group TorVergata TSRI_MGL
	Conformational Diversity of Ligands Bound to Proteins [My Copy] Journal of Molecular Biology, Vol. 356, No. 4. (3 March 2006), pp. 928-944. by Gareth R. Stockwell, Janet M. Thornton posted to conformation docking ligands protein structure by BragilMassoud on 2006-10-16 13:42:05 as along with 7 people JALumley ubcg08l apaydin kuhn bilab grottenolm thanatos
	A distance geometry heuristic for expanding the range of geometries sampled during conformational search. [My Copy] J Comput Chem (10 October 2006) by Sergei Izrailev, Fangqiang Zhu, Dimitris K K. Agrafiotis posted to conformations docking ligand by BragilMassoud on 2006-10-14 13:43:34 as along with 2 people superpyrin mijam
	Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes [My Copy] J. Med. Chem. (23 September 2006) by R. A. Friesner, R. B. Murphy, M. P. Repasky, et al.L. L. Frye, J. R. Greenwood, T. A. Halgren, P. C. Sanschagrin, D. T. Mainz posted to docking flexible_protein glide by BragilMassoud on 2006-10-11 12:00:28 as along with 6 people snichols15 flbarroso dgruiz daevans LamBras middledomain
	LigandFit: a novel method for the shape-directed rapid docking of ligands to protein active sites. [My Copy] J Mol Graph Model, Vol. 21, No. 4. (January 2003), pp. 289-307. by C. M. Venkatachalam, X. Jiang, T. Oldfield, M. Waldman posted to docking ligandfit screening by BragilMassoud on 2006-10-04 14:31:38 as
	Molecular recognition using a binary genetic search algorithm. [My Copy] J Mol Graph, Vol. 11, No. 2. (June 1993) by A. W. Payne, R. C. Glen posted to docking ring_flipping by BragilMassoud on 2006-10-03 15:44:53 as
	Prediction of Protein-Ligand Interactions. Docking and Scoring: Successes and Gaps. [My Copy] J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5851-5855. by Andrew R. Leach, Brian K. Shoichet, Catherine E. Peishoff posted to docking review by BragilMassoud on 2006-09-30 14:25:03 as along with 4 people ucbcjbm dgruiz kazemi massivemayhem
	PMF Scoring Revisited [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 20. (1 October 2006), pp. 5895-5902. by Ingo Muegge posted to affinitiy docking electrostatics energyfunctions screening by BragilMassoud on 2006-09-30 14:24:46 as along with 3 people nickolay ucbcjbm peprovy
	A Critical Assessment of Docking Programs and Scoring Functions [My Copy] J. Med. Chem., Vol. 49, No. 20. (5 October 2006), pp. 5912-5931. by G. L. Warren, C. W. Andrews, A. M. Capelli, et al.B. Clarke, J. Lalonde, M. H. Lambert, M. Lindvall, N. Nevins, S. F. Semus, S. Senger, G. Tedesco, I. D. Wall, J. M. Woolven, C. E. Peishoff, M. S. Head posted to docking energyfunctions review by BragilMassoud on 2006-09-30 14:24:23 as along with 6 people skoddet ucbcjbm aalibes schlauchi daevans superpyrin
	Critical assessment of the automated AutoDock as a new docking tool for virtual screening. [My Copy] Proteins (20 September 2006) by Hwangseo Park, Jinuk Lee, Sangyoub Lee posted to autodock docking screening by BragilMassoud on 2006-09-23 15:48:25 as along with 3 people and 1 group dgruiz yongzhao insilico TSRI_MGL
	ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (13 September 2006), pp. 538-548. by Jens Meiler, David Baker posted to docking flexible_protein by BragilMassoud on 2006-09-17 14:25:02 as along with 4 people and 1 group mijam kuhn jwm yongzhao TSRI_MGL

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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
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roc	3
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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
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denovo	1
density	1
dock	1
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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
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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

BragilMassoud's docking [175 articles] Export

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