BragilMassoud's screening [84 articles] Export

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	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
	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
	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
	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
	Evaluating Virtual Screening Methods: Good and Bad Metrics for the "Early Recognition" Problem. [My Copy] J Chem Inf Model (9 February 2007) by Jean-François F. Truchon, Christopher I. Bayly posted to screening roc by BragilMassoud on 2007-02-11 12:45:37 as along with 3 people kmdaily baldigroup sithmein
	Comparison of Shape-Matching and Docking as Virtual Screening Tools [My Copy] J. Med. Chem., Vol. 50, No. 1. (11 January 2007), pp. 74-82. by P. C. D. Hawkins, A. G. Skillman, A. Nicholls posted to superposition screening dokcing by BragilMassoud on 2007-02-09 14:10:19 as along with 7 people klexa LamBras nachtalp apostola schlauchi daevans thanatos
	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
	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
	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
	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
	Automatic and Efficient Decomposition of Two-Dimensional Structures of Small Molecules for Fragment-Based High-Throughput Docking. [My Copy] J Med Chem, Vol. 49, No. 25. (14 December 2006), pp. 7384-7392. by Peter Kolb, Amedeo Caflisch posted to fragmentation ligands screening by BragilMassoud on 2006-12-09 15:36:42 as along with 2 people nachtalp 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
	Critical evaluation of methods to incorporate entropy loss upon binding in high-throughput docking. [My Copy] Proteins (26 October 2006) by Sumeet Salaniwal, Eric S. S. Manas, Juan C. C. Alvarez, Rayomand J. J. Unwalla posted to affinity energyfunctions entropy screening by BragilMassoud on 2006-10-29 16:42:53 as along with 1 person cat_worth
	Benchmarking Sets for Molecular Docking [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 23. (1 November 2006), pp. 6789-6801. by Niu Huang, Brian K. Shoichet, John J. Irwin posted to benchmark screening by BragilMassoud on 2006-10-27 11:34:59 as along with 4 people and 1 group GermanErlenkamp ihaque yongzhao daevans TSRI_MGL
	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
	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
	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
	Structural interaction fingerprints: a new approach to organizing, mining, analyzing, and designing protein-small molecule complexes. [My Copy] Chem Biol Drug Des, Vol. 67, No. 1. (January 2006), pp. 5-12. by J. Singh, Z. Deng, G. Narale, C. Chuaqui posted to docking fingerprints kinases screening by BragilMassoud on 2006-09-15 15:36:13 as
	Molecular docking and high-throughput screening for novel inhibitors of protein tyrosine phosphatase-1B. [My Copy] J Med Chem, Vol. 45, No. 11. (23 May 2002), pp. 2213-2221. by T. N. Doman, S. L. McGovern, B. J. Witherbee, et al.T. P. Kasten, R. Kurumbail, W. C. Stallings, D. T. Connolly, B. K. Shoichet posted to hts screening by BragilMassoud on 2006-08-04 21:52:10 as along with 1 person peprovy
	Drug research: myths, hype and reality. [My Copy] Nat Rev Drug Discov, Vol. 2, No. 8. (August 2003), pp. 665-668. by H. Kubinyi posted to docking hts pharmacology review screening by BragilMassoud on 2006-08-04 21:36:29 as along with 1 person and 1 group caporaso biomedical-nlp
	Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. [My Copy] J Med Chem, Vol. 48, No. 7. (7 April 2005), pp. 2534-2547. by N. Triballeau, F. Acher, I. Brabet, J. P. Pin, H. O. Bertrand posted to roc screening by BragilMassoud on 2006-07-30 11:38:51 as along with 3 people nachtalp peprovy schlauchi
	Integration of virtual and high-throughput screening. [My Copy] Nat Rev Drug Discov, Vol. 1, No. 11. (November 2002), pp. 882-894. by J. Bajorath posted to hts review screening by BragilMassoud on 2006-07-28 18:01:47 as along with 3 people and 2 groups jerome sangeetha sithmein Bioinformatics insilicodrug
	Structure-based virtual screening of chemical libraries for drug discovery. [My Copy] Curr Opin Chem Biol, Vol. 10, No. 3. (June 2006), pp. 194-202. by S. Ghosh, A. Nie, J. An, Z. Huang posted to docking review screening by BragilMassoud on 2006-07-28 18:00:25 as along with 2 people and 1 group oteri yongzhao TSRI_MGL
	Ligand bias of scoring functions in structure-based virtual screening. [My Copy] J Chem Inf Model, Vol. 46, No. 3. (n 2006), pp. 1334-1343. by M. Jacobsson, A. Karlén posted to affinity energyfunctions screening by BragilMassoud on 2006-07-28 18:00:02 as
	Finding New Tricks For Old Drugs: An Efficient Route For Public-Sector Drug Discovery [My Copy] Nature Reviews Drug Discovery, Vol. 4, No. 12., pp. 1005-1014. by Kerry A. O'Connor, Bryan L. Roth posted to review screening by BragilMassoud on 2006-07-28 17:59:42 as
	Virtual screening using protein-ligand docking: avoiding artificial enrichment. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 3. (n 2004), pp. 793-806. by M. L. Verdonk, V. Berdini, M. J. Hartshorn, et al.W. T. Mooij, C. W. Murray, R. D. Taylor, P. Watson posted to docking gold screening by BragilMassoud on 2006-07-22 21:00:24 as along with 3 people and 2 groups nachtalp sangeetha peprovy Bioinformatics insilicodrug
	Comparison of automated docking programs as virtual screening tools. [My Copy] J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 962-976. by M. D. Cummings, R. L. DesJarlais, A. C. Gibbs, V. Mohan, E. P. Jaeger posted to comparison docking screening by BragilMassoud on 2006-07-22 17:07:11 as along with 3 people and 3 groups yongzhao sangeetha kazemi Bioinformatics TSRI_MGL insilicodrug
	Ligand-protein docking and rational drug design. [My Copy] Curr Opin Struct Biol, Vol. 5, No. 2. (April 1995), pp. 224-228. by T. P. Lybrand posted to docking review screening by BragilMassoud on 2006-07-21 23:45:01 as
	Update on computer-aided drug design. [My Copy] Curr Opin Biotechnol, Vol. 6, No. 6. (December 1995), pp. 646-651. by R. C. Jackson posted to docking review screening by BragilMassoud on 2006-07-21 23:44:37 as
	Recovering the true targets of specific ligands by virtual screening of the protein data bank. [My Copy] Proteins, Vol. 54, No. 4. (1 March 2004), pp. 671-680. by N. Paul, E. Kellenberger, G. Bret, P. Mueller, D. Rognan posted to docking inversescreening screening by BragilMassoud on 2006-07-16 21:19:04 as along with 2 people nickolay insilico
	Virtual screening to enrich a compound collection with CDK2 inhibitors using docking, scoring, and composite scoring models. [My Copy] Proteins, Vol. 60, No. 4. (1 September 2005), pp. 629-643. by S. Cotesta, F. Giordanetto, J. Y. Trosset, et al.P. Crivori, R. T. Kroemer, P. F. Stouten, A. Vulpetti posted to affinity docking energyfunctions kinases screening by BragilMassoud on 2006-07-11 20:30:21 as
	An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes. [My Copy] J Chem Inf Comput Sci, Vol. 44, No. 6. (c 2004), pp. 2114-2125. by R. Wang, Y. Lu, X. Fang, S. Wang posted to affinity docking energyfunctions screening by BragilMassoud on 2006-06-29 14:11:29 as along with 1 person and 1 group yongzhao TSRI_MGL
	The maximal affinity of ligands. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 96, No. 18. (31 August 1999), pp. 9997-10002. by I. D. Kuntz, K. Chen, K. A. Sharp, P. A. Kollman posted to affinity docking screening by BragilMassoud on 2006-06-24 21:55:51 as along with 6 people higueruelo ubcg08l bicko pslee alexg superpyrin
	Validation and use of the MM-PBSA approach for drug discovery. [My Copy] J Med Chem, Vol. 48, No. 12. (16 June 2005), pp. 4040-4048. by B. Kuhn, P. Gerber, T. Schulz-Gasch, M. Stahl posted to affinity docking electrostatics energyfunctions screening by BragilMassoud on 2006-06-24 11:28:43 as along with 4 people and 1 group apostola mleis gcaltabiano LamBras LabCompMed
	Scoring noncovalent protein-ligand interactions: a continuous differentiable function tuned to compute binding affinities. [My Copy] J Comput Aided Mol Des, Vol. 10, No. 5. (October 1996), pp. 427-440. by A. N. Jain posted to docking energyfunctions screening surflex by BragilMassoud on 2006-06-20 16:38:54 as
	Incomplete protein packing as a selectivity filter in drug design. [My Copy] Structure, Vol. 13, No. 12. (December 2005), pp. 1829-1836. by A. Fernández posted to affinity dehydron ligands protein screening structure by BragilMassoud on 2006-06-01 14:30:24 as along with 1 person kuhn
	Minimizing false positives in kinase virtual screens. [My Copy] Proteins (17 May 2006) by Emanuele Perola posted to docking kinases screening by BragilMassoud on 2006-05-22 20:01:44 as along with 1 person schlauchi
	Automated docking of substrates to proteins by simulated annealing. [My Copy] Proteins, Vol. 8, No. 3. (1990), pp. 195-202. by D. S. Goodsell, A. J. Olson posted to docking screening by BragilMassoud on 2006-05-21 12:40:22 as along with 4 people joule apostola robert schlauchi
	Hammerhead: fast, fully automated docking of flexible ligands to protein binding sites. [My Copy] Chem Biol, Vol. 3, No. 6. (June 1996), pp. 449-462. by W. Welch, J. Ruppert, A. N. Jain posted to docking hammerhead screening by BragilMassoud on 2006-05-17 13:51:14 as
	Morphological similarity: a 3D molecular similarity method correlated with protein-ligand recognition. [My Copy] J Comput Aided Mol Des, Vol. 14, No. 2. (February 2000), pp. 199-213. by A. N. Jain posted to ligands screening superposition by BragilMassoud on 2006-05-17 13:37:52 as along with 1 person apostola
	Robust Ligand-Based Modeling of the Biological Targets of Known Drugs [My Copy] Journal of Medicinal Chemistry, Vol. 49, No. 10. (1 May 2006), pp. 2921-2938. by Ann E. Cleves, Ajay N. Jain posted to docking pharmacology screening by BragilMassoud on 2006-05-13 14:43:50 as along with 3 people mnishimu nachtalp jarasch
	sc-PDB: an annotated database of druggable binding sites from the Protein Data Bank. [My Copy] J Chem Inf Model, Vol. 46, No. 2. (r 2006), pp. 717-727. by E. Kellenberger, P. Muller, C. Schalon, G. Bret, N. Foata, D. Rognan posted to cavities db docking screening by BragilMassoud on 2006-05-11 21:22:22 as along with 6 people and 1 group caporaso schlauchi daevans ramensky sim82 nickolay biomedical-nlp
	A fast surface-matching procedure for protein-ligand docking. [My Copy] J Mol Model (Online) (4 May 2006) by Michel E. Yamagishi, Natália F. Martins, Goran Neshich, et al.Wensheng Cai, Xueguang Shao, Alexandre Beautrait, Bernard Maigret posted to docking screening by BragilMassoud on 2006-05-06 13:54:17 as
	Development and biological evaluation of potent and specific inhibitors of mitotic Kinesin Eg5. [My Copy] Chembiochem, Vol. 6, No. 7. (July 2005), pp. 1173-1177. by M. Gartner, N. Sunder-Plassmann, J. Seiler, et al.M. Utz, I. Vernos, T. Surrey, A. Giannis posted to docking kinesin pharmacology screening by BragilMassoud on 2006-04-26 13:30:59 as
	Virtual and biomolecular screening converge on a selective agonist for GPR30. [My Copy] Nature chemical biology, Vol. 2, No. 4. (April 2006), pp. 207-212. by C. G. Bologa, C. M. Revankar, S. M. Young, et al.B. S. Edwards, J. B. Arterburn, A. S. Kiselyov, M. A. Parker, S. E. Tkachenko, N. P. Savchuck, L. A. Sklar, T. I. Oprea, E. R. Prossnitz posted to affinity docking hts screening by BragilMassoud on 2006-03-24 16:18:26 as along with 1 person ajaymalik
	On evaluating molecular-docking methods for pose prediction and enrichment factors. [My Copy] J Chem Inf Model, Vol. 46, No. 1. (b 2006), pp. 401-415. by H. Chen, P. D. Lyne, F. Giordanetto, T. Lovell, J. Li posted to docking screening by BragilMassoud on 2006-03-15 17:35:21 as along with 1 person ramensky
	Parameter Estimation for Scoring Protein-Ligand Interactions Using Negative Training Data [My Copy] Journal of medicinal chemistry (2005) by T. A. Pham, A. N. Jain posted to docking energyfunctions screening surflex by BragilMassoud on 2006-02-11 15:42:52 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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