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Tag docking [559 articles]

Recent papers classified by the tag docking.
  • Docking and scoring with alternative side-chain conformations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Christoph Hartmann, Iris Antes, Thomas Lengauer
    posted to docking scoring by zimbo1 on 2008-08-25 07:41:46 as ** along with 2 people middledomain reyez
  • Computationally Identified Novel Diphenyl- and Phenylpyridine Androgen Receptor Antagonist Structures
    J. Chem. Inf. Model. (20 August 2008)
    by Annu A Söderholm, Johanna Viiliäinen, Pekka T Lehtovuori, Hanna Eskelinen, Daniela Roell, Aria Baniahmad, Tommi H Nyrönen
    posted to androgen docking qsar receptor by zimbo1 on 2008-08-25 08:17:21 as **
  • Supervised Scoring Models with Docked Ligand Conformations for Structure-Based Virtual Screening
    J. Chem. Inf. Model. (9 August 2007)
    by R Teramoto, H Fukunishi
    posted to supervised scoring model docking by zimbo1 on 2008-09-09 08:05:38 as ** along with 1 person daevans
  • A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling
    Journal of Computer-Aided Molecular Design, Vol. 22, No. 11. (1 November 2008), pp. 815-829.
    by Arun, N Gautham
    posted to sampling peptide mols docking conformation by zimbo1 on 2008-10-02 08:35:57 as **
  • Evaluation of Different Virtual Screening Programs for Docking in a Charged Binding Pocket
    J. Chem. Inf. Model. (27 September 2008)
    by Wei Deng, Christophe L Verlinde
    posted to scoring docking charge by zimbo1 on 2008-10-06 08:12:28 as **
  • Using Molecular Docking, 3D-QSAR, and Cluster Analysis for Screening Structurally Diverse Data Sets of Pharmacological Interest
    J. Chem. Inf. Model. (24 September 2008)
    by Osvaldo A Santos-Filho, Artem Cherkasov
    posted to qsar fingerprint docking by zimbo1 on 2008-09-29 09:26:54 as **
  • Improving binding mode predictions by docking into protein-specifically adapted potential fields.
    J Med Chem, Vol. 48, No. 17. (25 August 2005), pp. 5466-5479.
    by S Radestock, M Böhm, H Gohlke
    posted to docking potential_app by yongzhao on 2006-09-08 01:51:42 as **** along with 3 people and 1 group BragilMassoud kazemi naitsabes TSRI_MGL
  • An efficient molecular docking using conformational space annealing.
    J Comput Chem, Vol. 26, No. 1. (15 January 2005), pp. 78-87.
    by K Lee, C Czaplewski, SY Kim, J Lee
    posted to docking by yongzhao on 2005-09-29 06:18:32 as ** along with 1 person and 1 group nachtalp TSRI_MGL
  • Receptor flexibility in de novo ligand design and docking.
    J Med Chem, Vol. 48, No. 21. (20 October 2005), pp. 6585-6596.
    by IL Alberts, NP Todorov, PM Dean
    posted to docking flex side_chain by yongzhao on 2005-10-16 22:24:14 as **** along with 5 people and 1 group BragilMassoud dgruiz apaydin kazemi npt11tpn TSRI_MGL
  • New and fast statistical-thermodynamic method for computation of protein-ligand binding entropy substantially improves docking accuracy
    Journal of Computational Chemistry, Vol. 26, No. 11. (2005), pp. 1089-1095.
    by AM Ruvinsky, AV Kozintsev
    posted to docking reranking by yongzhao on 2006-09-14 22:21:58 as **** along with 1 person and 1 group daevans TSRI_MGL
  • Molecular docking of balanol to dynamics snapshots of protein kinase A.
    Proteins (21 October 2005)
    by Chung F F Wong, Jeremy Kua, Yingkai Zhang, T P P Straatsma, J Andrew A McCammon
    posted to docking multiple by yongzhao on 2005-10-30 23:32:31 as *** along with 1 person and 1 group simone TSRI_MGL
  • A detailed comparison of current docking and scoring methods on systems of pharmaceutical relevance.
    Proteins, Vol. 56, No. 2. (1 August 2004), pp. 235-249.
    by E Perola, WP Walters, PS Charifson
    posted to docking score by yongzhao on 2006-10-30 22:59:14 as ** along with 4 people and 3 groups ramensky BragilMassoud marcius schlauchi TSRI_MGL BioinfoCIPF SGU-CIPF
  • 'Inductive' Charges on Atoms in Proteins: Comparative Docking with the Extended Steroid Benchmark Set and Discovery of a Novel SHBG Ligand.
    J Chem Inf Model, Vol. 45, No. 6. (28 November 2005), pp. 1842-1853.
    by Artem Cherkasov, Zheng Shi, Yvonne Li, Steven J Jones, Magid Fallahi, Geoffrey L Hammond
    posted to docking by yongzhao on 2005-11-30 20:55:11 as ** along with 1 group TSRI_MGL
  • Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function
    Journal of Computational Chemistry, Vol. 19, No. 14. (6 January 1999), pp. 1639-1662.
    by Garrett M Morris, David S Goodsell, Robert S Halliday, Ruth Huey, William E Hart, Richard K Belew, Arthur J Olson
    posted to docking by yongzhao on 2005-10-25 21:31:16 as ***** along with 14 people and 2 groups arlam dgruiz nachtalp P2324548 peprovy tovrstra papatonyhill schlauchi carlescorbi middledomain LamBras andreramme simone UVA_mag_res group TSRI_MGL
  • Flexible protein-protein docking
    Current Opinion in Structural Biology, Vol. 16, No. 2. (April 2006), pp. 194-200.
    by Alexandre MJJ Bonvin
    posted to docking flex by yongzhao on 2006-05-03 00:40:08 as ***** along with 7 people and 3 groups dgruiz aqeel bicko ima sangeetha gloria higueruelo Bioinformatics TSRI_MGL insilicodrug
  • Recent Advances in Docking and Scoring
    Current Computer - Aided Drug Design, Vol. 1, No. 1. (January 2005), pp. 93-102.
    by EM Krovat, T Steindl, T Langer
    posted to docking docking_design review score by yongzhao on 2006-10-30 22:38:36 as **** along with 2 people and 1 group kazemi pmalatino TSRI_MGL
  • Efficient docking of peptides to proteins without prior knowledge of the binding site.
    Protein Sci, Vol. 11, No. 7. (July 2002), pp. 1729-1737.
    by C Hetényi, D van der Spoel
    posted to docking docking_design by yongzhao on 2005-12-12 23:02:44 as **** along with 1 person and 1 group rguenther TSRI_MGL
  • Representing receptor flexibility in ligand docking through relevant normal modes.
    J Am Chem Soc, Vol. 127, No. 26. (6 July 2005), pp. 9632-9640.
    by CN Cavasotto, JA Kovacs, RA Abagyan
    posted to docking normal_mode_analysis by yongzhao on 2005-09-23 23:30:17 as ** along with 6 people and 3 groups BragilMassoud apaydin barry aqeel kazemi LamBras structural_bioinformatics Bioinformatics TSRI_MGL
  • notes Induced Fit in Mouse Acetylcholinesterase upon Binding a Femtomolar Inhibitor: A Molecular Dynamics Study.
    J Med Chem, Vol. 48, No. 26. (29 December 2005), pp. 8155-8162.
    by Sanjib Senapati, Jennifer M Bui, J A McCammon
    posted to docking induced_fit by yongzhao on 2005-12-28 23:54:37 as *** along with 1 group TSRI_MGL
  • A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening.
    J Mol Graph Model, Vol. 18, No. 3. (June 2000)
    by HB Broughton
    posted to docking flex induced_fit screening by yongzhao on 2007-01-03 21:43:02 as ** along with 2 people and 1 group kazemi LamBras TSRI_MGL
  • Further development and validation of empirical scoring functions for structure-based binding affinity prediction.
    J Comput Aided Mol Des, Vol. 16, No. 1. (January 2002), pp. 11-26.
    by R Wang, L Lai, S Wang
    posted to docking docking_design by yongzhao on 2006-09-13 20:11:22 as ***** along with 1 person and 1 group BragilMassoud TSRI_MGL
  • Flexible ligand docking using evolutionary algorithms: investigating the effects of variation operators and local search hybrids
    Biosystems, Vol. 72, No. 1-2. (November 2003), pp. 57-73.
    by Rene Thomsen
    posted to docking ga by yongzhao on 2006-02-23 04:03:16 as *** along with 2 people and 1 group betainverse dgruiz TSRI_MGL
  • Ligand-induced conformational changes: improved predictions of ligand binding conformations and affinities.
    Biophys J, Vol. 84, No. 4. (April 2003), pp. 2273-2281.
    by TM Frimurer, GH Peters, LF Iversen, HS Andersen, NP Møller, OH Olsen
    posted to docking flex by yongzhao on 2006-05-03 21:53:58 as ** along with 3 people and 1 group dgruiz blackbart kazemi TSRI_MGL
  • SODOCK: Swarm optimization for highly flexible protein-ligand docking.
    J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 612-623.
    by HM Chen, BF Liu, HL Huang, SF Hwang, SY Ho
    posted to search docking_design docking by yongzhao on 2007-01-09 23:05:52 as *** along with 2 people and 1 group BragilMassoud dgruiz TSRI_MGL
  • Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects.
    J Med Chem, Vol. 49, No. 2. (26 January 2006), pp. 534-553.
    by Woody Sherman, Tyler Day, Matthew P Jacobson, Richard A Friesner, Ramy Farid
    posted to docking induced_fit by yongzhao on 2006-01-25 02:32:42 as **** along with 4 people and 1 group LamBras BragilMassoud daevans kazemi TSRI_MGL
  • Identification of a minimal subset of receptor conformations for improved multiple conformation docking and two-step scoring.
    J Chem Inf Comput Sci, Vol. 44, No. 1. (b 2004), pp. 88-96.
    by S Yoon, WJ Welsh
    posted to docking docking_design flex by yongzhao on 2006-05-03 22:00:20 as ** along with 1 person and 1 group dgruiz TSRI_MGL
  • FLIPDock: Docking flexible ligands into flexible receptors.
    Proteins (23 May 2007)
    by Yong Zhao, Michel F F Sanner
    posted to cross_docking docking flex induced_fit rotamer_lib side_chain by yongzhao on 2007-07-27 17:59:04 as ** along with 4 people and 1 group BragilMassoud kazemi somak LamBras TSRI_MGL
  • Benchmarking Sets for Molecular Docking
    J. Med. Chem. (26 October 2006)
    by N Huang, BK Shoichet, JJ Irwin
    posted to docking docking_design library potential_app by yongzhao on 2006-10-26 18:11:12 as ** along with 3 people and 1 group ihaque BragilMassoud daevans TSRI_MGL
  • notes Progressive Docking: A Hybrid QSAR/Docking Approach for Accelerating In Silico High Throughput Screening.
    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 screening qsar docking by yongzhao on 2007-01-11 19:25:04 as ** along with 1 person and 1 group BragilMassoud TSRI_MGL
  • Effective handling of induced-fit motion in flexible docking.
    Proteins (10 March 2006)
    by Miho Yamada Y Mizutani, Yoshihiro Takamatsu, Tazuko Ichinose, Kensuke Nakamura, Akiko Itai
    posted to docking docking_design induced_fit by yongzhao on 2006-03-21 18:17:40 as ***** along with 2 people and 1 group BragilMassoud kazemi TSRI_MGL
  • Active site binding modes of HIV-1 integrase inhibitors.
    J Med Chem, Vol. 43, No. 22. (2 November 2000), pp. 4109-4117.
    by CA Sotriffer, H Ni, JA McCammon
    posted to docking hiv by yongzhao on 2005-11-08 01:21:55 as **** along with 1 group TSRI_MGL
  • MolDock: A New Technique for High-Accuracy Molecular Docking.
    J Med Chem, Vol. 49, No. 11. (1 June 2006), pp. 3315-3321.
    by R Thomsen, MH Christensen
    posted to docking docking_design by yongzhao on 2006-06-08 20:23:37 as ** along with 1 person and 1 group BragilMassoud TSRI_MGL
  • Molecular recognition of the inhibitor AG-1343 by HIV-1 protease: conformationally flexible docking by evolutionary programming.
    Chem Biol, Vol. 2, No. 5. (May 1995), pp. 317-324.
    by DK Gehlhaar, GM Verkhivker, PA Rejto, CJ Sherman, DB Fogel, LJ Fogel, ST Freer
    posted to docking score by yongzhao on 2006-06-22 02:36:19 as ** along with 1 group TSRI_MGL
  • A new test set for validating predictions of protein-ligand interaction.
    Proteins, Vol. 49, No. 4. (1 December 2002), pp. 457-471.
    by JW Nissink, C Murray, M Hartshorn, ML Verdonk, JC Cole, R Taylor
    posted to docking potential_app by yongzhao on 2006-06-08 20:25:24 as ** along with 3 people and 1 group BragilMassoud blackbart ramensky TSRI_MGL
  • HIV-reverse transcriptase inhibition: inclusion of ligand-induced fit by cross-docking studies.
    J Med Chem, Vol. 48, No. 1. (13 January 2005), pp. 200-212.
    by R Ragno, S Frasca, F Manetti, A Brizzi, S Massa
    posted to cross_docking docking by yongzhao on 2005-10-20 22:09:00 as **** along with 1 group TSRI_MGL
  • Combining docking and molecular dynamic simulations in drug design.
    Med Res Rev (6 June 2006)
    by Hernán Alonso, Andrey A A Bliznyuk, Jill E E Gready
    posted to docking review by yongzhao on 2006-06-12 23:27:31 as ***** along with 3 people and 1 group aqeel kazemi LamBras TSRI_MGL
  • 1,2,3-triazole as a peptide surrogate in the rapid synthesis of HIV-1 protease inhibitors.
    Chembiochem, Vol. 6, No. 7. (July 2005), pp. 1167-1169.
    by A Brik, J Alexandratos, YC Lin, JH Elder, AJ Olson, A Wlodawer, DS Goodsell, CH Wong
    posted to docking hiv by yongzhao on 2006-01-06 17:26:33 as ** along with 1 group TSRI_MGL
  • Fully flexible low-mode docking: application to induced fit in HIV integrase.
    J Am Chem Soc, Vol. 123, No. 50. (19 December 2001), pp. 12708-12709.
    by GM Keserû, I Kolossváry
    posted to docking hiv by yongzhao on 2005-11-04 15:38:37 as **** along with 1 group TSRI_MGL
  • Enhanced docking with the mining minima optimizer: Acceleration and side-chain flexibility
    Journal of Computational Chemistry, Vol. 23, No. 16. (2002), pp. 1656-1670.
    by Visvaldas Kairys, Michael K Gilson
    posted to cross_docking docking ga search by yongzhao on 2007-01-03 21:51:37 as ** along with 3 people and 2 groups blackbart kazemi arlam TSRI_MGL group
  • Lessons in molecular recognition: the effects of ligand and protein flexibility on molecular docking accuracy.
    J Med Chem, Vol. 47, No. 1. (1 January 2004), pp. 45-55.
    by JA Erickson, M Jalaie, DH Robertson, RA Lewis, M Vieth
    posted to docking potential_app by yongzhao on 2006-03-03 18:41:21 as ** along with 5 people and 3 groups BragilMassoud apaydin sangeetha daevans kazemi Bioinformatics TSRI_MGL insilicodrug
  • Evaluation of docking performance: comparative data on docking algorithms.
    J Med Chem, Vol. 47, No. 3. (29 January 2004), pp. 558-565.
    by M Kontoyianni, LM McClellan, GS Sokol
    posted to docking docking_design potential_app by yongzhao on 2006-02-23 21:56:40 as ** along with 4 people and 5 groups marcius sangeetha insilico schuwi Bioinformatics TSRI_MGL insilicodrug BioinfoCIPF SGU-CIPF
  • Protein-ligand docking: Current status and future challenges.
    Proteins (21 July 2006)
    by Sérgio Filipe F Sousa, Pedro Alexandrino A Fernandes, Maria João J Ramos
    posted to autodock docking by yongzhao on 2006-11-07 19:07:30 as ** along with 8 people and 2 groups BragilMassoud peprovy kazemi sergio_fms carlescorbi robert boris_aguilar qaiser_fatmi TSRI_MGL group
  • Comparison of automated docking programs as virtual screening tools.
    J Med Chem, Vol. 48, No. 4. (24 February 2005), pp. 962-976.
    by MD Cummings, RL DesJarlais, AC Gibbs, V Mohan, EP Jaeger
    posted to docking screening by yongzhao on 2005-12-08 18:41:56 as *** along with 3 people and 3 groups BragilMassoud sangeetha kazemi Bioinformatics TSRI_MGL insilicodrug
  • HADDOCK: a protein-protein docking approach based on biochemical or biophysical information.
    J Am Chem Soc, Vol. 125, No. 7. (19 February 2003), pp. 1731-1737.
    by C Dominguez, R Boelens, AM Bonvin
    posted to docking haddock protein-protein by yalexeev on 2008-02-01 11:09:14 as ** along with 6 people betainverse dgruiz bicko bluvsh1 gloria ruvido
  • Docking and scoring protein complexes: CAPRI 3rd Edition
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Marc F Lensink, Raúl Méndez, Shoshana J Wodak
    posted to docking protein-protein by yalexeev on 2008-02-01 11:06:58 as ** along with 7 people bicko chad_davis ruvido cjeans carlescorbi middledomain timg
  • ZDOCK predictions for the CAPRI challenge.
    Proteins, Vol. 52, No. 1. (1 July 2003), pp. 68-73.
    by R Chen, W Tong, J Mintseris, L Li, Z Weng
    posted to docking protein-protein zdock by yalexeev on 2008-02-01 11:01:52 as ** along with 1 person ffranca
  • Mechanisms of Inter- and Intramolecular Communication in GPCRs and G Proteins
    J. Am. Chem. Soc. (12 March 2008)
    by F Raimondi, M Seeber, PG Debenedetti, F Fanelli
    posted to activation docking gpcr gproteins by xdeupi on 2008-05-03 17:09:50 as ** along with 1 person paulschlesinger
  • notes Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations
    Journal of Molecular Biology, Vol. 331, No. 1. (1 August 2003), pp. 281-299.
    by Jeffrey J Gray, Stewart Moughon, Chu Wang, Ora Schueler-Furman, Brian Kuhlman, Carol A Rohl, David Baker
    posted to dimer docking modeling theory by xdeupi on 2008-04-07 14:18:56 as ** along with 4 people ima bluvsh1 selrac timg
  • notes Protein-Protein Docking with Backbone Flexibility
    Journal of Molecular Biology, Vol. 373, No. 2. (19 October 2007), pp. 503-519.
    by Chu Wang, Philip Bradley, David Baker
    posted to docking flexibility modeling theory by xdeupi on 2008-04-07 14:23:45 as ** along with 3 people and 2 groups barry jwm Ema structural_bioinformatics Bioinformatics
  • Structure of a β1-adrenergic G-protein-coupled receptor
    Nature (25 June 2008)
    by Tony Warne, Maria J Serrano-Vega, Jillian G Baker, Rouslan Moukhametzianov, Patricia C Edwards, Richard Henderson, Andrew GW Leslie, Christopher G Tate, Gebhard FX Schertler
    posted to xray structure ligands drug docking binding b2ar by xdeupi on 2008-09-16 10:15:17 as ** along with 2 people and 2 groups merj TonyIvetac LabCompMed McCammon
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