LamBras's docking [53 articles] Export

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

	Docking and scoring in virtual screening for drug discovery: methods and applications. [My Copy] Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949. by D. B. Kitchen, H. Decornez, J. R. Furr, J. Bajorath posted to docking scoring virtual_screening by LamBras on 2008-12-21 13:02:09 as along with 8 people and 9 groups robert85 BragilMassoud dgruiz beapen anita yongzhao marcius sangeetha Bioinformatics structure-bii TSRI_MGL Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
	Muscarinic Receptors: A Comparative Analysis of Structural Features and Binding Modes through Homology Modelling and Molecular Docking [My Copy] Chemistry & Biodiversity, Vol. 3, No. 5. (2006), pp. 481-501. by Alessandro Pedretti, Giulio Vistoli, Cristina Marconi, Bernard Testa posted to docking homology_modeling muscarinic by LamBras on 2008-12-16 09:45:15 as
	Guided Docking Approaches to Structure-Based Design and Screening [My Copy] Current Topics in Medicinal Chemistry, Vol. 4, No. 7. (March 2004), pp. 687-700. by X. Fradera, J. Mestres posted to docking scoring virtual_screening by LamBras on 2008-11-22 16:54:32 as along with 3 people and 3 groups oteri dgruiz sangeetha Structural Biology Group TorVergata Bioinformatics insilicodrug
	Binding site characteristics in structure-based virtual screening: evaluation of current docking tools [My Copy] Journal of Molecular Modeling, Vol. 9, No. 1. (February 2003), pp. 47-57. by Tanja Schulz-Gasch, Martin Stahl posted to docking scoring virtual_screening by LamBras on 2008-11-22 16:53:16 as along with 1 person dgruiz
	Furan-2-ylmethylene Thiazolidinediones as Novel, Potent, and Selective Inhibitors of Phosphoinositide 3-Kinase γ [My Copy] J. Med. Chem., Vol. 49, No. 13. (29 June 2006), pp. 3857-3871. by V. Pomel, J. Klicic, D. Covini, et al.D. D. Church, J. P. Shaw, K. Roulin, F. Burgat-Charvillon, D. Valognes, M. Camps, C. Chabert, C. Gillieron, B. Francon, D. Perrin, D. Leroy, D. Gretener, A. Nichols, P. A. Vitte, S. Carboni, C. Rommel, M. K. Schwarz, T. Ruckle posted to docking flexibility induced_fit scoring virtual_screening by LamBras on 2008-10-14 16:44:33 as
	Motifs for molecular recognition exploiting hydrophobic enclosure in protein-ligand binding. [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 3. (16 January 2007), pp. 808-813. by Tom Young, Robert Abel, Byungchan Kim, Bruce J. Berne, Richard A. Friesner posted to docking free_energy lipophilicity sar scoring water_replacement by LamBras on 2008-10-14 16:36:25 as along with 5 people ubcg08l Diego_Prada daevans jwagoner zwang
	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 docking flexibility scoring sidechain virtual_screening by LamBras on 2008-09-22 18:17:08 as along with 7 people and 1 group klexa sschurer cen4ik BragilMassoud yongzhao daevans kazemi TSRI_MGL
	Structure-based virtual screening: an overview [My Copy] Drug Discovery Today, Vol. 7, No. 20. (15 October 2002), pp. 1047-1055. by Paul D. Lyne posted to conformers docking drugdesign scoring virtual_screening by LamBras on 2008-09-22 15:19:43 as
	DOCKING AND SCORING IN VIRTUAL SCREENING FOR DRUG DISCOVERY: METHODS AND APPLICATIONS [My Copy] Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949. by Douglas B. Kitchen, Helene Decornez, John R. Furr, Jurgen Bajorath posted to docking scoring virtual_screening by LamBras on 2008-09-22 10:53:23 as along with 5 people and 2 groups Lombardo_7 sangeetha blackbart schlauchi mingzhi Bioinformatics insilicodrug
	Docking of tryptophan analogs to trytophanyl-tRNA synthetase: implications for non-canonical amino acid incorporations. [My Copy] Biological chemistry, Vol. 389, No. 9. (September 2008), pp. 1173-1182. by M. K. Azim, N. Budisa posted to docking homology_modeling trna virtual_screening by LamBras on 2008-09-22 10:51:04 as
	Ligand and structure-based methodologies for the prediction of the activity of G protein-coupled receptor ligands [My Copy] Journal of Computer-Aided Molecular Design by Stefano Costanzi, Irina Tikhonova, T. Harden, Kenneth Jacobson posted to docking gpcr homology_modeling sar virtual_screening by LamBras on 2008-09-16 12:42:59 as
	Principles of flexible protein-protein docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 73, No. 2. (2008), pp. 271-289. by Nelly Andrusier, Efrat Mashiach, Ruth Nussinov, Haim J. Wolfson posted to docking flexibility review by LamBras on 2008-09-16 12:33:50 as along with 3 people and 1 group bicko aqeel csrocha structural_bioinformatics
	Optimization of High Throughput Virtual Screening by Combining Shape-Matching and Docking Methods [My Copy] J. Chem. Inf. Model. (27 February 2008) by H. S. Lee, J. Choi, I. Kufareva, et al.R. Abagyan, A. Filikov, Y. Yang, S. Yoon posted to docking drugdesign virtual_screening by LamBras on 2008-09-08 15:07:34 as along with 1 person 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 cheminformatics docking drugdesign virtual_screening by LamBras on 2008-09-08 15:06:31 as along with 6 people and 1 group BragilMassoud daevans steff83 middledomain ucbcjbm thanatos Computer Aided Drug Design
	Can we use docking and scoring for hit-to-lead optimization? [My Copy] Journal of Computer-Aided Molecular Design, Vol. 22, No. 3. (16 March 2008), pp. 161-168. by Istvan Enyedy, William Egan posted to docking drugdesign virtual_screening by LamBras on 2008-08-26 10:31:24 as
	Structure-based Drug Discovery Using GPCR Homology Modeling: Successful Virtual Screening for Antagonists of the Alpha1A Adrenergic Receptor [My Copy] J. Med. Chem., Vol. 48, No. 4. (24 February 2005), pp. 1088-1097. by A. Evers, T. Klabunde posted to docking gpcr homology_modeling virtual_screening by LamBras on 2008-08-21 16:34:16 as
	Virtual Screening of Biogenic Amine-Binding G-Protein Coupled Receptors: Comparative Evaluation of Protein- and Ligand-Based Virtual Screening Protocols [My Copy] J. Med. Chem., Vol. 48, No. 17. (25 August 2005), pp. 5448-5465. by A. Evers, G. Hessler, H. Matter, T. Klabunde posted to docking gpcr virtual_screening by LamBras on 2008-08-21 16:31:15 as
	Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core. [My Copy] EMBO J, Vol. 22, No. 12. (16 June 2003), pp. 2873-2885. by H. Furukawa, E. Gouaux posted to docking ion_channels nmda nr1 sar by LamBras on 2008-07-20 16:10:50 as
	Improving database enrichment through ensemble docking [My Copy] Journal of Computer-Aided Molecular Design by Shashidhar Rao, Paul Sanschagrin, Jeremy Greenwood, Matthew Repasky, Woody Sherman, Ramy Farid posted to docking ensemble virtual_screening by LamBras on 2008-07-04 11:01:29 as
	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 docking flexibility md by LamBras on 2008-07-04 11:00:17 as along with 6 people and 2 groups karinaecomp oteri jmccammon rbaron higueruelo kazemi Structural Biology Group TorVergata McCammon
	Protein–ligand docking with multiple flexible side chains [My Copy] Journal of Computer-Aided Molecular Design by Yong Zhao, Michel Sanner posted to docking flexibility by LamBras on 2008-07-04 10:59:02 as
	Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function [My Copy] Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1998), pp. 1639-1662. by Garrett M. Morris, David S. Goodsell, Robert S. Halliday, et al.Ruth Huey, William E. Hart, Richard K. Belew, Arthur J. Olson posted to docking forcefield by LamBras on 2008-04-25 14:10:21 as along with 22 people and 2 groups nickolay npt11tpn jamalex joule lna Lombardo_7 karinaecomp oteri A_Coletta_Thesis arlam dgruiz nachtalp P2324548 yongzhao peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain andreramme UVA_mag_res Chang group TSRI_MGL
	MM-GB/SA Rescoring of Docking Poses in Structure-Based Lead Optimization [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 5. (1 May 2008), pp. 958-970. by Cristiano R. W. Guimarães, Mario Cardozo posted to docking scoring by LamBras on 2008-04-24 13:13:03 as along with 1 person tbinbal
	Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. [My Copy] J Med Chem, Vol. 47, No. 7. (25 March 2004), pp. 1750-1759. by T. A. Halgren, R. B. Murphy, R. A. Friesner, et al.H. S. Beard, L. L. Frye, W. T. Pollard, J. L. Banks posted to docking scoring by LamBras on 2008-04-23 10:46:07 as along with 4 people snichols15 flbarroso BragilMassoud schlauchi
	Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. [My Copy] J Med Chem, Vol. 47, No. 7. (25 March 2004), pp. 1739-1749. by R. A. Friesner, J. L. Banks, R. B. Murphy, et al.T. A. Halgren, J. J. Klicic, D. T. Mainz, M. P. Repasky, E. H. Knoll, M. Shelley, J. K. Perry, D. E. Shaw, P. Francis, P. S. Shenkin posted to docking scoring by LamBras on 2008-04-23 10:44:59 as along with 7 people snichols15 flbarroso BragilMassoud dgruiz cantupaz nachtalp dbougioukou
	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 scoring by LamBras on 2008-04-22 12:47:17 as along with 6 people snichols15 flbarroso BragilMassoud dgruiz daevans middledomain
	New insights about HERG blockade obtained from protein modeling, potential energy mapping, and docking studies [My Copy] Bioorganic & Medicinal Chemistry, Vol. 14, No. 9. (1 May 2006), pp. 3160-3173. by Ramy Farid, Tyler Day, Richard A. Friesner, Robert A. Pearlstein posted to docking herg homology_modeling by LamBras on 2008-04-07 15:25:44 as along with 1 person daevans
	Probing ligand binding modes of human cytochrome P450 2J2 by homology modeling, molecular dynamics simulation, and flexible molecular docking [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 71, No. 2. (14 November 2007), pp. 938-949. by Weihua Li, Yun Tang, Hong Liu, Jiagao Cheng, Weiliang Zhu, Hualiang Jiang posted to docking homology_modeling md by LamBras on 2008-03-20 19:37:17 as
	Recommendations for evaluation of computational methods [My Copy] Journal of Computer-Aided Molecular Design by Ajay Jain, Anthony Nicholls posted to docking by LamBras on 2008-03-20 19:23:53 as
	Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 4. (2007), pp. 1599-1608. by Z. Zhou, A. K. Felts, R. A. Friesner, R. M. Levy posted to docking scoring by LamBras on 2008-03-15 16:27:12 as
	FLIPDock: Docking flexible ligands into flexible receptors [My Copy] Proteins (2007) by Yong Zhao, Michel F. Sanner posted to docking flexibility by LamBras on 2008-03-15 16:27:12 as
	Probing flexibility and ?induced-fit? phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 52-66. by Christoph Sotriffer, Oliver Krã¤mer, Gerhard Klebe posted to docking flexibility md by LamBras on 2008-03-15 16:27:11 as
	Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers [My Copy] Proteins: Structure, Function, and Genetics, Vol. 32, No. 2. (1998), pp. 159-174. by Bilha Sandak, Haim Wolfson, Ruth Nussinov posted to conformers docking flexibility by LamBras on 2008-03-15 16:27:11 as
	Molecular docking to ensembles of protein structures [My Copy] J Mol Biol, Vol. 266, No. 2. (1997), pp. 424-440. by R. M. Knegtel, I. D. Kuntz, C. M. Oshiro posted to docking ensemble by LamBras on 2008-03-15 16:27:10 as
	"Soft docking": matching of molecular surface cubes [My Copy] J Mol Biol, Vol. 219, No. 1. (1991), pp. 79-102. by F. Jiang, S. H. Kim posted to docking surface by LamBras on 2008-03-15 16:27:09 as
	Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking [My Copy] Proteins (2006) by Sheng Y. Huang, Xiaoqin Zou posted to docking by LamBras on 2008-03-15 16:27:08 as
	Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors [My Copy] Angewandte Chemie International Edition, Vol. 41, No. 15. (2002), pp. 2644-2676. by Holger Gohlke, Gerhard Klebe posted to docking scoring by LamBras on 2008-03-15 16:27:08 as
	A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening [My Copy] J Mol Graph Model, Vol. 18, No. 3. (2000) by H. B. Broughton posted to docking flexibility virtual_screening by LamBras on 2008-03-15 16:27:08 as
	Incorporating protein flexibility into docking and structure-based drug design [My Copy] pp. 335-349. by Xavier Barril posted to docking flexibility by LamBras on 2008-03-15 16:27:08 as
	Combining docking and molecular dynamic simulations in drug design [My Copy] Med Res Rev (2006) by Hernã¡n Alonso, Andrey A. Bliznyuk, Jill E. Gready posted to docking md by LamBras on 2008-03-15 16:27:08 as
	Multiple protein structures and multiple ligands: effects on the apparent goodness of virtual screening results [My Copy] Journal of Computer-Aided Molecular Design by Robert Sheridan, Georgia Mcgaughey, Wendy Cornell posted to docking virtual_screening by LamBras on 2008-03-10 13:38:00 as
	A new method for ligand docking to flexible receptors by dual alanine scanning and refinement (SCARE) [My Copy] Journal of Computer-Aided Molecular Design by Giovanni Bottegoni, Irina Kufareva, Maxim Totrov, Ruben Abagyan posted to docking flexibility by LamBras on 2008-03-10 13:35:39 as along with 1 person AtoZ
	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 flexibility by LamBras on 2008-02-24 17:12:16 as along with 7 people and 1 group npt11tpn fl karinaecomp BragilMassoud yongzhao kazemi somak TSRI_MGL
	Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors [My Copy] Angewandte Chemie International Edition, Vol. 41, No. 15. (2002), pp. 2644-2676. by Holger Gohlke, Gerhard Klebe posted to docking scoring by LamBras on 2008-02-24 17:11:29 as along with 3 people kazemi superpyrin boris_aguilar
	Comparative Performance of Several Flexible Docking Programs and Scoring Functions: Enrichment Studies for a Diverse Set of Pharmaceutically Relevant Targets [My Copy] Journal of Chemical Information and Modeling, Vol. 47, No. 4. (2007), pp. 1599-1608. by Z. Zhou, A. K. Felts, R. A. Friesner, R. M. Levy posted to docking scoring by LamBras on 2008-02-24 16:55:56 as
	Probing flexibility and ?induced-fit? phenomena in aldose reductase by comparative crystal structure analysis and molecular dynamics simulations [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 56, No. 1. (2004), pp. 52-66. by Christoph A. Sotriffer, Oliver Krämer, Gerhard Klebe posted to docking flexibility md by LamBras on 2008-01-24 15:12:31 as along with 2 people aqeel kazemi
	Molecular docking to ensembles of protein structures. [My Copy] J Mol Biol, Vol. 266, No. 2. (21 February 1997), pp. 424-440. by R. M. Knegtel, I. D. Kuntz, C. M. Oshiro posted to docking ensemble by LamBras on 2007-11-23 12:48:34 as along with 1 person kazemi
	Flexible docking allowing induced fit in proteins: Insights from an open to closed conformational isomers [My Copy] Proteins: Structure, Function, and Genetics, Vol. 32, No. 2. (1998), pp. 159-174. by Bilha Sandak, Haim J. Wolfson, Ruth Nussinov posted to conformers docking flexibility by LamBras on 2007-11-23 12:40:10 as along with 1 person kazemi
	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 by LamBras on 2007-11-23 12:39:46 as along with 8 people and 2 groups nickolay oteri AliceWang BragilMassoud bicko yongzhao kazemi hmk Structural Biology Group TorVergata TSRI_MGL
	"Soft docking": matching of molecular surface cubes. [My Copy] J Mol Biol, Vol. 219, No. 1. (5 May 1991), pp. 79-102. by F. Jiang, S. H. Kim posted to docking by LamBras on 2007-11-23 12:39:34 as along with 1 person kazemi

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flexibility	61
md	61
nmda	58
serinracemase	58
docking	53
virtual_screening	45
adme	30
drugdesign	26
review	19
scoring	18
cheminformatics	14
trna	13
bayesian	12
free_energy	12
ion_channels	12
muscarinic	12
sidechain	12
library_design	10
homology_modeling	9
normal_modes	8
targeted_md	8
nr1	7
rotamers	7
sar	7
conformers	6
gpcr	6
clustering	5
forcefield	5
nmr	5
xray	5
druglike	4
herg	4
proteins	4
surface	4
water_replacement	4
alzheimer	3
chemicalspace	3
ensemble	3
fingerprints	3
hts	3
scaffoldhopping	3
correlation	2
dynamics	2
graph	2
hd	2
lipophilicity	2
mmpbsa	2
pipelining	2
racemase	2
shape	2
similarity	2
allosteric	1
denovo	1
de_novo	1
induced_fit	1
itc	1
m1m2	1
ppb	1
qsar	1
r1	1
schroedinger	1
validation	1
virtuak_screening	1
x-ray	1

LamBras's docking [53 articles] Export

LamBras's tags