Tag docking [at least 200 articles] Export

Recent papers classified by the tag docking.

	Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-Solvent Models: An Evaluation in Protein Kinase and Phosphatase Systems [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 43. (29 October 2009), pp. 14343-14354. by Zunnan Huang, Chung F. Wong posted to protein ligandbinding ligand_binding dynamics docking conformational_flexibility complexformation by anuragsethi on 2009-11-22 05:15:48 as along with 1 person and 1 group jmccammon McCammon
	BioDrugScreen: a computational drug design resource for ranking molecules docked to the human proteome [My Copy] Nucl. Acids Res. (18 November 2009), gkp852. by Liwei Li, Khuchtumur Bum-Erdene, Peter H. Baenziger, et al.Joshua J. Rosen, Jamison R. Hemmert, Joy A. Nellis, Marlon E. Pierce, Samy O. Meroueh posted to docking computationalchemistry by aheilbut on 2009-11-20 21:35:50 as
	Simultaneous prediction of protein folding and docking at high resolution [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 45. (10 November 2009), pp. 18978-18983. by Rhiju Das, Ingemar AndrÃ©, Yang Shen, et al.Yibing Wu, Alexander Lemak, Sonal Bansal, Cheryl H. Arrowsmith, Thomas Szyperski, David Baker posted to unstructured simulation rosetta folding docking das09pdf binding based by paulschlesinger on 2009-11-12 00:10:36 as along with 4 people ahmetbakan apaydin ibuch zwang
	GWIDD: Genome-wide protein docking database [My Copy] Nucl. Acids Res. (9 November 2009), gkp944. by Petras J. Kundrotas, Zhengwei Zhu, Ilya A. Vakser posted to protein-protein modelling genomics docking database by neils on 2009-11-10 22:32:22 as
	High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations [My Copy] PLoS Comput Biol, Vol. 5, No. 10. (9 October 2009), e1000528. by Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, et al.Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji posted to md highthroughput docking bindingaffinities by ibuch on 2009-11-05 09:26:58 as along with 5 people and 1 group klexa skywalkerus02 kentsis reyez barry McCammon
	ISIS: interaction sites identified from sequence. [My Copy] Bioinformatics (Oxford, England), Vol. 23, No. 2. (15 January 2007), pp. e13-16. by Yanay Ofran, Burkhard Rost posted to predict docking coevolution by dfdong on 2009-11-04 03:23:25 as along with 2 people bicko qluo
	Prediction of interface residues in protein-protein complexes by a consensus neural network method: test against NMR data. [My Copy] Proteins. , Vol. 61, No. 1. (1 October 2005), pp. 21-35. by H. Chen, H. X. Zhou posted to predict ml docking complex coevolution by dfdong on 2009-11-04 03:23:02 as along with 2 people qluo karbak
	An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 10. (13 October 2009), pp. 2909-2923. by Roger S. Armen, Jianhan Chen, Charles L. Brooks posted to torsion_angle receptor_flexibility nov09 molecular_dynamics_simulations docking by pmung on 2009-11-04 02:10:39 as
	Docking Ligands into Flexible and Solvated Macromolecules. 5. Force-Field-Based Prediction of Binding Affinities of Ligands to Proteins [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Pablo Englebienne, Nicolas Moitessier posted to solvent prediction nov09 ligand flexibility docking affinity by nickolay on 2009-11-03 20:35:14 as
	Insights into Protein-Protein Interfaces using a Bayesian Network Prediction Method [My Copy] Journal of Molecular Biology, Vol. In Press, Corrected Proof by James R. Bradford, Chris J. Needham, Andrew J. Bulpitt, David R. Westhead posted to predict docking complex by dfdong on 2009-11-03 15:05:10 as along with 8 people and 2 groups barry conkymacro ameetsoni grahamc massivemayhem phoenixzxl marti paolomarcatili structural_bioinformatics Bioinformatics
	Interaction-site prediction for protein complexes: a critical assessment [My Copy] Bioinformatics, Vol. 23, No. 17. (1 September 2007), pp. 2203-2209. by Huan-Xiang Zhou, Sanbo Qin posted to predict docking complex by dfdong on 2009-11-03 15:03:56 as along with 14 people jinghu_fandm flbarroso timg phoenixzxl tjimenez bicko malcook zwang cabbagezs niallhaslam carlescorbi marti higueruelo kintoki
	Accurate Prediction of Peptide Binding Sites on Protein Surfaces [My Copy] PLoS Comput Biol, Vol. 5, No. 3. (27 March 2009), e1000335. by Evangelia Petsalaki, Alexander Stark, Eduardo García-Urdiales, Robert B. Russell posted to predict docking complex by dfdong on 2009-11-03 15:02:34 as along with 8 people and 1 group higueruelo pablocarb nickolay phoenixzxl neils idoerg sobolevnrm paulschlesinger baker-group
	Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy. [My Copy] Bioinformatics (Oxford, England), Vol. 25, No. 12. (15 June 2009), pp. 1513-1520. by Nurcan Tuncbag, Attila Gursoy, Ozlem Keskin posted to predict docking complex by dfdong on 2009-11-03 15:02:04 as along with 5 people and 1 group ubcg08l marti apaydin kshameer phoenixzxl structural_bioinformatics
	A Tool for calculating binding-site residues on proteins from PDB Structures [My Copy] BMC Structural Biology, Vol. 9, No. 1. (2009), 52. by Jing Hu, Changhui Yan posted to docking complex by dfdong on 2009-11-03 15:00:56 as along with 3 people balewis peteruetz phoenixzxl
	The interwinding nature of protein-protein interfaces and its implication for protein complex formation [My Copy] Bioinformatics, Vol. 25, No. 23. (1 December 2009), pp. 3108-3113. by Kei Yura, Steven Hayward posted to docking complex by dfdong on 2009-11-03 15:00:25 as along with 4 people kshameer higueruelo tprpip phoenixzxl
	Prediction of protein-protein interaction sites using patch analysis. [My Copy] Journal of molecular biology, Vol. 272, No. 1. (12 September 1997), pp. 133-143. by S. Jones, J. M. Thornton posted to patch docking by dfdong on 2009-11-03 02:18:26 as along with 4 people mgomes cjeans marti bicko
	Principles of protein-protein interactions [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 93, No. 1. (9 January 1996), pp. 13-20. by S. Jones, J. M. Thornton posted to docking complex by dfdong on 2009-11-02 06:56:46 as along with 8 people mgomes sergiun joseolucha boris_aguilar bicko chad_davis Evangelia iris_2001
	Coevolution at protein complex interfaces can be detected by the complementarity trace with important impact for predictive docking [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 22. (3 June 2008), pp. 7708-7713. by Hocine Madaoui, RaphaÃ«l Guerois posted to docking complex coevolution by dfdong on 2009-11-02 06:46:19 as along with 8 people qluo robfsouza RebeccaHamer orr cabbagesofdoom phoenixzxl bicko zwang
	A guest molecule–host cavity fitting algorithm to mine PDB for small molecule targets [My Copy] Biochimica et Biophysica Acta (BBA) - Proteins & Proteomics, Vol. 1764, No. 8. (August 2006), pp. 1320-1324. by William C. Byrem, Stephen C. Armstead, Shunji Kobayashi, Roderic G. Eckenhoff, David M. Eckmann posted to docking by oteri on 2009-11-01 12:43:24 as
	Molecular docking of a series of peptidomimetics in the trypanothione binding site of T. cruzi Trypanothione Reductase [My Copy] Journal of Molecular Graphics and Modelling (31 August 2009) by Samuel S. da Rocha Pita, José J. Cirino, Ricardo B. de Alencastro, Helena C. Castro, Carlos R. Rodrigues, Magaly G. Albuquerque posted to docking by carlosjavierna on 2009-10-31 17:35:04 as
	Genome wide analysis and comparative docking studies of new diaryl furan derivatives against human cyclooxygenase-2, lipoxygenase, thromboxane synthase and prostacyclin synthase enzymes involved in inflammatory pathway [My Copy] Journal of Molecular Graphics and Modelling (27 August 2009) by P. Nataraj Sekhar, L. Ananda Reddy, Marc De Maeyer, et al.K. Praveen Kumar, Y. S. Srinivasulu, M. S. L. Sunitha, I. S. N. Sphoorthi, G. Jayasree, A. Maruthi Rao, V. S. Kothekar posted to docking by carlosjavierna on 2009-10-31 17:30:09 as
	Induced-fit docking studies of the active and inactive states of protein tyrosine kinases [My Copy] Journal of Molecular Graphics and Modelling, Vol. 28, No. 4. (31 November 2009), pp. 336-346. by Haizhen Zhong, Ly M. Tran, Jenna L. Stang posted to docking by carlosjavierna on 2009-10-31 17:28:31 as
	Assaying phenothiazine derivatives as trypanothione reductase and glutathione reductase inhibitors by theoretical docking and Molecular Dynamics studies [My Copy] Journal of Molecular Graphics and Modelling (23 September 2009) by F. Iribarne, M. Paulino, S. Aguilera, O. Tapia posted to molecular-dynamics-simulations docking by carlosjavierna on 2009-10-31 17:22:52 as
	Fast and accurate predictions of binding free energies using MM-PBSA and MM-GBSA [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Giulio Rastelli, Alberto Del Rio, Gianluca Degliesposti, Miriam Sgobba posted to poisson_boltzman docking by A_Coletta_Thesis to the group Structural Biology Group TorVergata on 2009-10-27 22:07:14 as along with 1 person sobolevnrm
	Influence of Protonation, Tautomeric, and Stereoisomeric States on Protein−Ligand Docking Results [My Copy] Journal of Chemical Information and Modeling, Vol. 0, No. 0. (0000) by Ten, Thomas E. Exner posted to glide drugdiscovery docking charge by snichols15 on 2009-10-21 23:52:13 as along with 1 person ima
	Rational Prediction of the Herbicidal Activities of Novel Protoporphyrinogen Oxidase Inhibitors by Quantitative Structure−Activity Relationship Model Based on Docking-Guided Active Conformation [My Copy] Journal of Agricultural and Food Chemistry, Vol. 57, No. 20. (28 October 2009), pp. 9593-9598. by Beilei Lei, Jiazhong Li, Jing Lu, Juan Du, Huanxiang Liu, Xiaojun Yao posted to qsar molecular-modeling docking by carlosjavierna on 2009-10-21 22:08:56 as
	FRODOCK: a new approach for fast rotational protein-protein docking [My Copy] Bioinformatics, Vol. 25, No. 19. (1 October 2009), pp. 2544-2551. by Jose I. Garzon, Jose R. Lopez-Blanco, Carles Pons, et al.Julio Kovacs, Ruben Abagyan, Juan Fernandez-Recio, Pablo Chacon posted to standalone_tool protein_structure docking by jforment to the group Bioinformatics Core Service on 2009-10-21 14:10:16 as
	PiSQRD: a web server for decomposing proteins into quasi-rigid dynamical domains [My Copy] Bioinformatics, Vol. 25, No. 20. (15 October 2009), pp. 2743-2744. by T. Aleksiev, R. Potestio, F. Pontiggia, S. Cozzini, C. Micheletti posted to domain_movement docking by oteri to the group Structural Biology Group TorVergata on 2009-10-21 11:44:43 as along with 1 person apaydin
	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 rafriesner glide docking by snichols15 on 2009-10-19 01:27:45 as along with 6 people flbarroso BragilMassoud dgruiz daevans LamBras middledomain
	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 rafriesner glide drugdiscovery docking by snichols15 on 2009-10-19 01:26:55 as along with 4 people flbarroso BragilMassoud schlauchi LamBras
	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 rafriesner glide docking by snichols15 on 2009-10-19 01:26:18 as along with 7 people flbarroso BragilMassoud dgruiz cantupaz nachtalp LamBras dbougioukou
	Principles of docking: An overview of search algorithms and a guide to scoring functions. [My Copy] Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443. by Inbal Halperin, Buyong Ma, Haim Wolfson, Ruth Nussinov posted to review docking by rabio on 2009-10-12 09:07:45 as along with 25 people and 4 groups ucbcjbm flbarroso csrocha oteri timg dgruiz cantupaz apaydin bicko chad_davis yongzhao ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Structural Biology Group TorVergata Bioinformatics TSRI_MGL insilicodrug
	Hierarchical modeling of protein interactions [My Copy] Journal of Molecular Modeling, Vol. 13, No. 6. (1 July 2007), pp. 691-698. by Mateusz Kurcinski, Andrzej Kolinski posted to docking by rabio on 2009-10-12 09:02:08 as along with 3 people mijam mkurc naitsabes
	Development and validation of a genetic algorithm for flexible docking [My Copy] Journal of Molecular Biology, Vol. 267, No. 3. (04 April 1997), pp. 727-748. by G. Jones posted to docking by ubcg08l on 2009-10-09 15:08:36 as
	Automated docking with grid-based energy evaluation [My Copy] Journal of Computational Chemistry, Vol. 13, No. 4. (1992), pp. 505-524. by Elaine C. Meng, Brian K. Shoichet, Irwin D. Kuntz posted to docking by ubcg08l on 2009-10-09 14:54:02 as along with 3 people nickolay Lombardo_7 middledomain
	ZINC--a free database of commercially available compounds for virtual screening. [My Copy] Journal of chemical information and modeling, Vol. 45, No. 1. (b 2005), pp. 177-182. by John J. Irwin, Brian K. Shoichet posted to docking by ubcg08l on 2009-10-09 14:46:31 as along with 3 people and 3 groups karinaecomp beapen jerome_ucsf_slb Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
	Modern Homology Modeling of G-Protein Coupled Receptors: Which Structural Template to Use? [My Copy] Journal of Medicinal Chemistry, Vol. 52, No. 16. (27 August 2009), pp. 5207-5216. by Juan C. Mobarec, Roberto Sanchez, Marta Filizola posted to theory modeling gpcr docking by xdeupi on 2009-10-08 16:39:12 as along with 2 people dimka reyez
	Pushing Structural Information into the Yeast Interactome by High-Throughput Protein Docking Experiments [My Copy] PLoS Comput Biol, Vol. 5, No. 8. (28 August 2009), e1000490. by Roberto Mosca, Carles Pons, Juan Fernández-Recio, Patrick Aloy posted to structure sep09 protein plos interactions docking by klexa on 2009-10-07 13:47:09 as along with 4 people and 1 group bdessailly zwang phoenixzxl TRHvidsten Orengo Group Journal Picks
	Blind docking of pharmaceutically relevant compounds using RosettaLigand [My Copy] Protein Science, Vol. 18, No. 9. (24 June 2009), pp. 1998-2002. by Ian W. Davis, Kaushik Raha, Martha S. Head, David Baker posted to sep09 protsci ligand drug_discovery docking by klexa on 2009-10-07 13:36:33 as along with 1 person apaydin
	Steering Protein-Ligand Docking with Quantitative NMR Chemical Shift Perturbations. [My Copy] Journal of chemical information and modeling (2 October 2009) by Domingo González-Ruiz, Holger Gohlke posted to nmr docking 2009 by higueruelo on 2009-10-07 12:04:10 as
	Synthesis of new modified truncated peptides and inhibition of glycogen phosphorylase. [My Copy] Journal of peptide science : an official publication of the European Peptide Society, Vol. 15, No. 6. (June 2009), pp. 442-450. by Stephanie S. Schweiker, Wendy A. Loughlin, Christopher L. Brown, Gregory K. Pierens posted to peptide docking by oteri to the group Structural Biology Group TorVergata on 2009-10-06 16:15:43 as
	Docking Ligands on Protein Surfaces: The Case Study of Prion Protein‡ [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2565-2573. by Agata Kranjc, Salvatore Bongarzone, Giulia Rossetti, et al.Xevi Biarnés, Andrea Cavalli, Maria L. Bolognesi, Marinella Roberti, Giuseppe Legname, Paolo Carloni posted to nmr_measurements molecular_simulation docking by pmung on 2009-10-05 19:47:13 as
	Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores [My Copy] Journal of Chemical Information and Modeling, Vol. 48, No. 7. (1 July 2008), pp. 1396-1410. by Caterina Barillari, Gilles Marcou, Didier Rognan posted to theory pharmacology ligands drug docking binding b2ar agonist by xdeupi on 2009-10-05 18:45:05 as along with 3 people tbinbal superpyrin higueruelo
	A model for the solution structure of the rod arrestin tetramer. [My Copy] Structure (London, England : 1993), Vol. 16, No. 6. (June 2008), pp. 924-934. by Susan M. Hanson, Eric S. Dawson, Derek J. Francis, et al.Ned Van Eps, Candice S. Klug, Wayne L. Hubbell, Jens Meiler, Vsevolod V. Gurevich posted to modeling docking arrestin by xdeupi on 2009-10-05 18:41:01 as
	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
	The sensitivity of the results of molecular docking to induced fit effects: application to thrombin, thermolysin and neuraminidase. [My Copy] J Comput Aided Mol Des, Vol. 13, No. 6. (November 1999), pp. 547-562. by C. W. Murray, C. A. Baxter, A. D. Frenkel posted to induced_fit flexibility docking 1999 by klexa on 2009-09-29 23:00:21 as along with 1 person schlauchi
	Comparative evaluation of eight docking tools for docking and virtual screening accuracy. [My Copy] Proteins, Vol. 57, No. 2. (1 November 2004), pp. 225-242. by E. Kellenberger, J. Rodrigo, P. Muller, D. Rognan posted to screening review docking 2004 by klexa on 2009-09-29 22:59:11 as along with 5 people and 2 groups oteri BragilMassoud dgruiz sangeetha schlauchi Bioinformatics insilicodrug
	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 shape screening roc docking 2007 by klexa on 2009-09-29 22:58:53 as along with 7 people LamBras BragilMassoud nachtalp apostola schlauchi daevans thanatos
	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 scaffold fragment fingerprints docking 2007 by klexa on 2009-09-29 22:58:10 as along with 8 people RebeccaHamer richardbickerton nanonan BragilMassoud peprovy schlauchi massivemayhem sithmein
	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 ligand flexibility docking binding 1998 by klexa on 2009-09-29 22:57:39 as along with 3 people karinaecomp BragilMassoud schlauchi

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protein	157
review	108
screening	106
structure	92
drug	80
ligand	67
scoring	65
binding	56
flexibility	46
algorithms	40
protein-protein	34
drug_design	33
interaction	33
docking_prog	32
energyfunctions	31
protein-ligand	31
protein_structure	30
ppi	29
virtual_screening	28
prediction	27
algorithm	26
modeling	25
bioinformatics	24
protein_ligand	22
affinity	21
autodock	21
flexible	20
nmr	20
docking_design	18
glide	18
gpcr	18
rna	18
complexes	17
pharmacology	17
flexible_protein	16
md	16
2009	15
induced_fit	15
interface	15
modelling	15
molecular	15
homology	14
pka	14
computational	13
function	13
gold	13
kinases	13
ligands	13
solvation	13
biology	12
database	12
disease	12
flex	12
nma	12
protein_docking	12
score	12
simulation	12
flexx	11
fragments	11
hts	11
molecular_dynamics	11
software	11
virtual	11
2007	10
complex	10
conformation	10
design	10
dna	10
dockingscore	10
dynamics	10
free_energy	10
hdock	10
potential_app	10
proj_assembly	10
qsar	10
sbdd	10
biophysics	9
drug-design	9
fragment	9
interactions	9
pharmacophore	9
receptor	9
structural_bioinformatics	9
1paper	8
benchmark	8
electrostatics	8
hiv	8
programs	8
protein_dynamics	8
protein_protein	8
surflex	8
validation	8
virtualscreening	8
cheminformatics	7
db	7
dockingpose	7
ga	7
library	7
md_simulation	7
model	7

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