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yongzhaos library [160 articles]

Neue Artikel in yongzhaos Bibliothek.
  • Deterministic Sampling methods for Spheres and SO
    (2004)
    by A Yershova, S Lavalle
    posted to sampling by yongzhao on 2007-11-05 18:22:12 as **
  • 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
  • Side-chain flexibility in proteins upon ligand binding
    Proteins: Structure, Function, and Genetics, Vol. 39, No. 3. (2000), pp. 261-268.
    by Rafael Najmanovich, Josef Kuttner, Vladimir Sobolev, Marvin Edelman
    posted to side_chain by yongzhao on 2007-06-29 23:54:07 as **** along with 2 people and 1 group kazemi LamBras TSRI_MGL
  • Pharmacophore Modeling and Three Dimensional Database Searching for Drug Design Using Catalyst: Recent Advances
    pp. 2991-3005.
    by Osman Guner
    posted to library screening by yongzhao on 2007-03-05 21:16:33 as ** along with 1 group TSRI_MGL
  • Trends in Virtual Combinatorial Library Design
    pp. 2095-2101.
    by G Schneider
    posted to library screening by yongzhao on 2007-03-05 21:14:52 as ** along with 1 group TSRI_MGL
  • Structure-based virtual screening of chemical libraries for drug discovery.
    Curr Opin Chem Biol, Vol. 10, No. 3. (June 2006), pp. 194-202.
    by S Ghosh, A Nie, J An, Z Huang
    posted to library screening by yongzhao on 2007-03-05 21:12:00 as *** along with 1 person and 1 group BragilMassoud TSRI_MGL
  • Can Conformational Change Be Described by Only a Few Normal Modes?
    Biophys. J., Vol. 90, No. 5. (1 March 2006), pp. 1583-1593.
    by Paula Petrone, Vijay S Pande
    posted to normal_mode_analysis by yongzhao on 2007-01-29 00:11:25 as ** along with 11 people and 7 groups csrocha BragilMassoud barry dimka aqeel shuns xdeupi choonpeng joergkurtwegner daevans LamBras structural_bioinformatics Bioinformatics TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics LabCompMed
  • Protein flexibility and drug design: how to hit a moving target
    Current Opinion in Chemical Biology, Vol. 6, No. 4. (1 August 2002), pp. 447-452.
    by Heather A Carlson
    posted to review flex by yongzhao on 2007-01-22 19:39:07 as **** along with 1 person and 1 group LamBras TSRI_MGL
  • Decoys for docking.
    J Med Chem, Vol. 48, No. 11. (2 June 2005), pp. 3714-3728.
    by AP Graves, R Brenk, BK Shoichet
    posted to database by yongzhao on 2007-01-17 20:36:55 as ** along with 5 people and 4 groups BragilMassoud dgruiz sangeetha insilico blackbart Bioinformatics TSRI_MGL insilicodrug Computer Aided Drug Design
  • Conformational changes studied by cryo-electron microscopy.
    Nat Struct Biol, Vol. 7, No. 9. (September 2000), pp. 711-714.
    by HR Saibil
    posted to cryoem by yongzhao on 2007-01-17 18:39:26 as ** along with 2 people and 1 group aqeel dgront TSRI_MGL
  • NORMA: a tool for flexible fitting of high-resolution protein structures into low-resolution electron-microscopy-derived density maps
    Acta Crystallographica Section D: Biological Crystallography, Vol. 62, No. 9. (01 September 2006), pp. 1098-1100.
    by Suhre, , Navaza, , Sanejouand, -H
    posted to cryoem by yongzhao on 2007-01-17 18:35:28 as ** along with 4 people and 1 group martainn dawnsong apaydin aqeel TSRI_MGL
  • Normal mode based flexible fitting of high-resolution structure into low-resolution experimental data from cryo-EM.
    J Struct Biol, Vol. 147, No. 3. (September 2004), pp. 315-326.
    by F Tama, O Miyashita, CL Brooks
    posted to cryoem by yongzhao on 2007-01-17 18:30:17 as ** along with 1 person and 1 group aqeel TSRI_MGL
  • Normal mode-based fitting of atomic structure into electron density maps: application to sarcoplasmic reticulum Ca-ATPase.
    Biophys J, Vol. 88, No. 2. (February 2005), pp. 818-827.
    by K Hinsen, N Reuter, J Navaza, DL Stokes, JJ Lacapère
    posted to cryoem by yongzhao on 2007-01-17 18:23:56 as ** along with 1 person and 1 group aqeel TSRI_MGL
  • Critical assessment of the automated AutoDock as a new docking tool for virtual screening.
    Proteins (20 September 2006)
    by Hwangseo Park, Jinuk Lee, Sangyoub Lee
    posted to screening by yongzhao on 2007-01-15 20:54:23 as ** along with 3 people and 1 group BragilMassoud dgruiz insilico 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
  • Development and validation of a modular, extensible docking program: DOCK 5.
    J Comput Aided Mol Des (6 December 2006)
    by Demetri T Moustakas, P T Lang, Scott Pegg, Eric Pettersen, Irwin D Kuntz, Natasja Brooijmans, Robert C Rizzo
    posted to docking_design by yongzhao on 2007-01-11 19:15:50 as ** along with 2 people and 1 group BragilMassoud schlauchi TSRI_MGL
  • Gradient tabu search.
    J Comput Chem, Vol. 28, No. 2. (30 January 2007), pp. 601-611.
    by S Stepanenko, B Engels
    posted to search docking_design by yongzhao on 2007-01-10 00:14:24 as ** along with 1 person and 1 group BragilMassoud 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
  • Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking.
    Proteins (9 November 2006)
    by Sheng-You Y Huang, Xiaoqin Zou
    posted to cross_docking flex multiple potential_app by yongzhao on 2007-01-08 18:29:14 as ***** along with 6 people and 1 group AliceWang BragilMassoud bicko kazemi hmk LamBras TSRI_MGL
  • Structure modeling, ligand binding, and binding affinity calculation (LR-MM-PBSA) of human heparanase for inhibition and drug design.
    Proteins, Vol. 65, No. 3. (15 November 2006), pp. 580-592.
    by Z Zhou, M Bates, JD Madura
    posted to induced_fit by yongzhao on 2007-01-08 17:58:14 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
  • 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
  • Mining the NCI antiviral compounds for HIV-1 integrase inhibitors
    Bioorganic & Medicinal Chemistry, Vol. 14, No. 11. (1 June 2006), pp. 3785-3792.
    by Jinxia Deng, James A Kelley, Joseph J Barchi, Tino Sanchez, Raveendra Dayam, Yves Pommier, Nouri Neamati
    posted to hivin by yongzhao on 2006-12-11 19:08:17 as *** along with 1 group TSRI_MGL
  • HIV-1 integrase inhibitors: a decade of research and two drugs in clinical trial.
    Curr Top Med Chem, Vol. 4, No. 10. (2004), pp. 1059-1077.
    by AA Johnson, C Marchand, Y Pommier
    posted to hivin by yongzhao on 2006-12-11 18:37:56 as ** along with 1 group TSRI_MGL
  • Application of CoMFA and CoMSIA 3D-QSAR and Docking Studies in Optimization of Mercaptobenzenesulfonamides as HIV-1 Integrase Inhibitors
    J. Med. Chem., Vol. 47, No. 2. (15 January 2004), pp. 385-399.
    by CL Kuo, H Assefa, S Kamath, Z Brzozowski, J Slawinski, F Saczewski, JK Buolamwini, N Neamati
    posted to hiv hivin potential_app by yongzhao on 2006-12-11 18:30:24 as ** along with 1 group 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.
    J Mol Biol (29 September 2006)
    by Kannan Gunasekaran, Ruth Nussinov
    posted to potential_app loop by yongzhao on 2006-11-21 19:00:57 as *** along with 8 people and 1 group BragilMassoud dgruiz radestock lna choonpeng weisblum higueruelo nickolay TSRI_MGL
  • Patented HIV-1 Integrase Inhibitors (1998-2005)
    Recent Patents on Anti-Infective Drug Discovery, Vol. 1, No. 1. (January 2006), pp. 1-15.
    by Philippe Cotelle
    posted to hivin by yongzhao on 2006-11-15 23:48:27 as ** along with 1 group TSRI_MGL
  • ROSETTALIGAND: Protein-small molecule docking with full side-chain flexibility.
    Proteins (13 September 2006)
    by Jens Meiler, David Baker
    posted to docking_design side_chain by yongzhao on 2006-11-08 23:55:35 as ** along with 3 people and 1 group BragilMassoud kuhn jwm TSRI_MGL
  • 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
  • Novel transition metal multiple bonding-myth or reality? - A computational study of boryl complexes
    by TR Cundari
    posted to mine by yongzhao on 2006-11-06 23:38:20 as ** along with 1 group TSRI_MGL
  • Design of a Propane Ammoxidation Catalyst Using Artificial Neural Networks and Genetic Algorithms
    Ind. Eng. Chem. Res., Vol. 40, No. 23. (14 November 2001), pp. 5475-5480.
    by T Cundari, J Deng, Y Zhao
    posted to mine by yongzhao on 2006-11-06 23:32:48 as ** along with 1 group TSRI_MGL
  • Novel transition metal multiple bonding--myth or reality?: A computational study of boryl complexes
    Inorganica Chimica Acta, Vol. 345 (10 March 2003), pp. 70-80.
    by Thomas R Cundari, Yong Zhao
    posted to mine by yongzhao on 2006-11-06 23:32:06 as ** along with 1 group TSRI_MGL
  • Hierarchical and multi-resolution representation of protein flexibility.
    Bioinformatics (18 September 2006)
    by Yong Zhao, Daniel Stoffler, Michel Sanner
    posted to mine by yongzhao on 2006-11-06 23:26:57 as ** along with 4 people and 1 group BragilMassoud dgruiz kazemi LamBras TSRI_MGL
  • ONIOM study of the active species in Pd-phosphine catalyzed coupling reactions
    pp. 121-129.
    by TR Cundari
    posted to mine by yongzhao on 2006-11-06 23:25:17 as ** along with 1 group TSRI_MGL
  • Prediction of binding modes for ligands in the cytochromes P450 and other heme-containing proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 836-844.
    by Stewart B Kirton, Christopher W Murray, Marcel L Verdonk, Richard D Taylor
    posted to p450 by yongzhao on 2006-11-02 01:38:26 as *** along with 1 group 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
  • 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
  • Docking and scoring in virtual screening for drug discovery: methods and applications.
    Nat Rev Drug Discov, Vol. 3, No. 11. (November 2004), pp. 935-949.
    by DB Kitchen, H Decornez, JR Furr, J Bajorath
    posted to screening by yongzhao on 2006-10-30 22:37:00 as ** along with 6 people and 9 groups BragilMassoud dgruiz beapen anita marcius sangeetha Bioinformatics structure-bii TSRI_MGL Atopic_and_Seborrhoeic_Dermatitis Skin_Deep insilicodrug Applied_Bimatics BioinfoCIPF SGU-CIPF
  • M-score: a knowledge-based potential scoring function accounting for protein atom mobility.
    J Med Chem, Vol. 49, No. 20. (5 October 2006), pp. 5903-5911.
    by CY Yang, R Wang, S Wang
    posted to docking_design score by yongzhao on 2006-10-26 18:33:56 as **** along with 1 person and 1 group kazemi 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
  • A review of protein-small molecule docking methods
    Journal of Computer-Aided Molecular Design, Vol. V16, No. 3. (1 March 2002), pp. 151-166.
    by RD Taylor, PJ Jewsbury, JW Essex
    posted to docking_design review by yongzhao on 2006-10-25 00:18:37 as **** along with 1 group TSRI_MGL
  • Principles of docking: An overview of search algorithms and a guide to scoring functions.
    Proteins, Vol. 47, No. 4. (1 June 2002), pp. 409-443.
    by I Halperin, B Ma, H Wolfson, R Nussinov
    posted to docking_design review by yongzhao on 2006-10-24 23:30:31 as ***** along with 20 people and 3 groups timg dgruiz cantupaz apaydin bicko chad_davis ttjoseph nickolay ima sangeetha dgront blackbart gane5h mmuecke kazemi bpagano massivemayhem cjeans Evangelia nigham Bioinformatics TSRI_MGL insilicodrug
  • Dynamite: a simple way to gain insight into protein motions
    Acta Crystallographica Section D: Biological Crystallography, Vol. 60, No. 1. (01 December 2004), pp. 2280-2287.
    by Barrett, , Hall, , Noble,
    posted to conformation_sampling flex by yongzhao on 2006-10-24 02:58:49 as **** along with 3 people and 1 group dimka aqeel choonpeng TSRI_MGL
  • Comparing protein-ligand docking programs is difficult.
    Proteins (3 June 2005)
    by Jason C C Cole, Christopher W W Murray, J Willem M W Nissink, Richard D D Taylor, Robin Taylor
    posted to docking_design review by yongzhao on 2006-10-18 20:51:13 as ***** along with 7 people and 3 groups BragilMassoud dgruiz thaliana sangeetha kzfm peprovy carlescorbi Bioinformatics TSRI_MGL insilicodrug
  • Molecular Symmetry Perception
    J. Chem. Inf. Model., Vol. 44, No. 2. (22 March 2004), pp. 596-600.
    by J Ivanov
    posted to no-tag by yongzhao on 2006-10-14 01:00:19 as ** along with 1 group TSRI_MGL
  • EMAN: semiautomated software for high-resolution single-particle reconstructions.
    J Struct Biol, Vol. 128, No. 1. (1 December 1999), pp. 82-97.
    by SJ Ludtke, PR Baldwin, W Chiu
    posted to cryoem by yongzhao on 2006-10-04 00:22:39 as **** along with 3 people and 3 groups dawnsong jwm faion Radiation_Damage Stressosome TSRI_MGL
  • Current status of virtual screening as analysed by target class.
    Med Chem, Vol. 2, No. 1. (January 2006), pp. 89-112.
    by MJ Stoermer
    posted to screening by yongzhao on 2006-09-20 18:55:14 as ***** along with 1 person and 3 groups marcius TSRI_MGL BioinfoCIPF SGU-CIPF
  • An extensive test of 14 scoring functions using the PDBbind refined set of 800 protein-ligand complexes.
    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 score by yongzhao on 2006-09-20 18:04:05 as ***** along with 1 person and 1 group BragilMassoud 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
  • Discovery of cell-permeable non-peptide inhibitors of beta-secretase by high-throughput docking and continuum electrostatics calculations.
    J Med Chem, Vol. 48, No. 16. (11 August 2005), pp. 5108-5111.
    by D Huang, U Lüthi, P Kolb, K Edler, M Cecchini, S Audetat, A Barberis, A Caflisch
    posted to bace screening by yongzhao on 2006-09-14 02:50:52 as ** along with 1 person and 4 groups joergkurtwegner TSRI_MGL Molecular-Modelling Drug-Design Cheminformatics
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