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BragilMassoud's library [377 articles]

最近录入 BragilMassoud's 文献库.
  • Fully Automated Molecular Mechanics Based Induced Fit Protein-Ligand Docking Method.
    Journal of chemical information and modeling (25 September 2008)
    by Jürgen Koska, Velin Z Spassov, Allister J Maynard, Lisa Yan, Nic Austin, Paul K Flook, C M Venkatachalam
    posted to flexible_protein docking by BragilMassoud on 2008-10-14 14:05:16 as **
  • Assessment of programs for ligand binding affinity prediction.
    Journal of computational chemistry, Vol. 29, No. 8. (June 2008), pp. 1316-1331.
    by R Kim, J Skolnick
    posted to affinity docking review by BragilMassoud on 2008-07-04 12:58:15 as **
  • Managing bias in ROC curves.
    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
  • How to do an evaluation: pitfalls and traps.
    J Comput Aided Mol Des (23 January 2008)
    by Paul C Hawkins, Gregory L Warren, A G Skillman, Anthony Nicholls
    posted to benchmarks comparison docking by BragilMassoud on 2008-01-27 13:49:59 as ** along with 2 people LamBras thanatos
  • Maximum Common Binding Modes (MCBM): Consensus Docking Scoring Using Multiple Ligand Information and Interaction Fingerprints
    J. Chem. Inf. Model. (23 January 2008)
    by S Renner, S Derksen, S Radestock, F Morchen
    posted to consensus docking similarity by BragilMassoud on 2008-01-25 21:23:42 as ** along with 1 person middledomain
  • Ligand-Protein Docking with Water Molecules
    J. Chem. Inf. Model. (23 January 2008)
    by BC Roberts, RL Mancera
    posted to docking water by BragilMassoud on 2008-01-25 21:23:17 as ** along with 2 people daevans middledomain
  • A Pharmacophore Map of Small Molecule Protein Kinase Inhibitors.
    J Chem Inf Model (17 October 2007)
    by Malcolm J McGregor
    posted to kinase pharmacophore by BragilMassoud on 2007-10-21 13:29:20 as ** along with 1 person hchmani
  • Accelerating molecular modeling applications with graphics processors.
    J Comput Chem (25 September 2007)
    by John E E Stone, James C C Phillips, Peter L L Freddolino, David J J Hardy, Leonardo G G Trabuco, Klaus Schulten
    posted to energyfunctions forcefield gpu by BragilMassoud on 2007-09-28 16:56:49 as ** along with 8 people and 1 group timg ruvido sobolevnrm yalexeev mikaellund OndrejMarsalek npt11tpn afenley baker-group
  • Novel ATP-Competitive Kinesin Spindle Protein Inhibitors.
    J Med Chem, Vol. 50, No. 20. (4 October 2007), pp. 4939-4952.
    by Cynthia A Parrish, Nicholas D Adams, Kurt R Auger, Joelle L Burgess, Jeffrey D Carson, Amita M Chaudhari, Robert A Copeland, Melody A Diamond, Carla A Donatelli, Kevin J Duffy, Leo F Faucette, Jeffrey T Finer, William F Huffman, Erin D Hugger, Jeffrey R Jackson, Steven D Knight, Lusong Luo, Michael L Moore, Ken A Newlander, Lance H Ridgers, Roman Sakowicz, Antony N Shaw, Chiu-Mei M Sung, David Sutton, Kenneth W Wood, Shu-Yun Y Zhang, Michael N Zimmerman, Dashyant Dhanak
    posted to kinesin by BragilMassoud on 2007-09-28 16:56:24 as **
  • Generating Conformer Ensembles Using a Multiobjective Genetic Algorithm.
    J Chem Inf Model (25 September 2007)
    by Mikko J Vainio, Mark S Johnson
    posted to conformaations ligand by BragilMassoud on 2007-09-27 11:35:46 as ** along with 1 person middledomain
  • Torsion Angle Preference and Energetics of Small-Molecule Ligands Bound to Proteins
    J. Chem. Inf. Model. (19 September 2007)
    by MH Hao, O Haq, I Muegge
    posted to conformations ligand structure by BragilMassoud on 2007-09-22 19:28:50 as ** along with 1 person daevans
  • Conformational memories with variable bond angles.
    J Comput Chem (17 September 2007)
    by Robert M M Whitnell, Dow P P Hurst, Patricia H H Reggio, Frank Guarnieri
    posted to conforamtions mc by BragilMassoud on 2007-09-20 13:45:43 as **
  • Progress in computational protein design.
    Curr Opin Biotechnol (17 July 2007)
    by Shaun M M Lippow, Bruce Tidor
    posted to design protein review structure by BragilMassoud on 2007-09-17 17:58:44 as ** along with 1 person and 1 group msuarezdiez Bioinformatics
  • Visualization software for molecular assemblies
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Thomas D Goddard, Thomas E Ferrin
    posted to protein structure visualization by BragilMassoud on 2007-09-10 13:36:11 as ** along with 4 people and 1 group jyuh sobolevnrm higueruelo dgront baker-group
  • DITOP: drug-induced toxicity related protein database.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007), pp. 1710-1712.
    by Jing-Xian X Zhang, Wei-Juan J Huang, Jing-Hua H Zeng, Wen-Hui H Huang, Yi Wang, Rui Zhao, Bu-Cong C Han, Qing-Feng F Liu, Yu-Zong Z Chen, Zhi-Liang L Ji
    posted to database pharmacology tox by BragilMassoud on 2007-07-29 11:02:28 as ** along with 1 person jyuh
  • On sampling of fragment space.
    J Med Chem, Vol. 50, No. 14. (12 July 2007), pp. 3214-3221.
    by GM Makara
    posted to fragments hts by BragilMassoud on 2007-07-07 15:55:52 as ** along with 1 person daevans
  • Comparison of Topological, Shape, and Docking Methods in Virtual Screening.
    J Chem Inf Model (26 June 2007)
    by Georgia B McGaughey, Robert P Sheridan, Christopher I Bayly, 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
  • Drug repositioning: identifying and developing new uses for existing drugs.
    Nat Rev Drug Discov, Vol. 3, No. 8. (August 2004), pp. 673-683.
    by TT Ashburn, KB Thor
    posted to pharmacology review by BragilMassoud on 2007-06-27 10:21:10 as ** along with 1 person apostola
  • A large-scale computational approach to drug repositioning.
    Genome Inform, Vol. 17, No. 2. (2006), pp. 239-247.
    by YY Li, J An, SJ Jones
    posted to docking inverse_screening by BragilMassoud on 2007-06-27 10:19:14 as ** along with 1 person aheilbut
  • On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: A review.
    J Comput Chem (14 June 2007)
    by Markus Christen, Wilfred F F van Gunsteren
    posted to md review by BragilMassoud on 2007-06-17 12:01:46 as ** along with 4 people dgront rabio somak dmobley
  • Evaluation of docking programs for predicting binding of Golgi alpha-mannosidase II inhibitors: A comparison with crystallography.
    Proteins (7 June 2007)
    by Pablo Englebienne, Hélène Fiaux, Douglas A A Kuntz, Christopher R R Corbeil, Sandrine Gerber-Lemaire, David R R Rose, Nicolas Moitessier
    posted to benchmark docking flexx glide gold by BragilMassoud on 2007-06-10 14:39:26 as **
  • Unbiasing Scoring Functions: A New Normalization and Rescoring Strategy.
    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 **
  • FLIPDock: Docking flexible ligands into flexible receptors.
    Proteins (23 May 2007)
    by Yong Zhao, Michel F F Sanner
    posted to docking flexible_protein by BragilMassoud on 2007-05-28 14:43:46 as ** along with 4 people and 1 group yongzhao kazemi somak LamBras TSRI_MGL
  • Multiple targeted tyrosine kinase inhibition in the clinic: all for one or one for all?
    Eur J Cancer, Vol. 42, No. 10. (July 2006), pp. 1351-1356.
    by MJ de Jonge, J Verweij
    posted to kinases pharmacology specificity by BragilMassoud on 2007-05-14 15:04:18 as **
  • Alternative to Consensus Scoring-A New Approach Toward the Qualitative Combination of Docking Algorithms.
    J Chem Inf Model (11 May 2007)
    by Antje Wolf, Marc Zimmermann, Martin Hofmann-Apitius
    posted to autodock consensus docking flexx by BragilMassoud on 2007-05-13 16:47:26 as **
  • Improved sampling methods for molecular simulation.
    Curr Opin Struct Biol, Vol. 17, No. 2. (April 2007), pp. 187-191.
    by H Lei, Y Duan
    posted to math minimization protein review structure by BragilMassoud on 2007-05-08 13:33:48 as ** along with 3 people viktor21614 aqeel allmensch
  • Potential energy functions for protein design.
    Curr Opin Struct Biol (24 March 2007)
    by F Edward E Boas, Pehr B B Harbury
    posted to design energyfunctions protein review structure by BragilMassoud on 2007-05-08 13:32:47 as ** along with 2 people aalibes onufriev
  • Accuracy of binding mode prediction with a cascadic stochastic tunneling method.
    Proteins (11 April 2007)
    by Bernhard Fischer, Serena Basili, Holger Merlitz, Wolfgang Wenzel
    posted to docking mc stun by BragilMassoud on 2007-04-22 16:52:42 as **
  • A simple way to compute protein dynamics without a mechanical model.
    Proteins (13 April 2007)
    by Chien-Hua H Shih, Shao-Wei W Huang, Shih-Chung C Yen, Yan-Long L Lai, Sung-Huan H Yu, Jenn-Kang K Hwang
    posted to nma protein structure by BragilMassoud on 2007-04-20 14:19:53 as ** along with 3 people bicko cactus jlh64
  • From Molecular to Biological Structure and Back.
    J Chem Inf Model (4 April 2007)
    by Danail Bonchev, Gregory A Buck
    posted to graph graphs networks by BragilMassoud on 2007-04-07 12:37:51 as **
  • Quantum chemical investigation of hydrogen-bond strengths and partition into donor and acceptor contributions.
    J Comput Chem (2 April 2007)
    by Stephan Raub, Christel M M Marian
    posted to electrostatics energyfunctions qc by BragilMassoud on 2007-04-07 12:37:03 as **
  • Joint neighbors approximation of macromolecular solvent accessible surface area.
    J Comput Chem (3 April 2007)
    by Georgy Rychkov, Michael Petukhov
    posted to protein solvation structure by BragilMassoud on 2007-04-07 12:36:36 as **
  • On Information and Sufficiency
    The Annals of Mathematical Statistics, Vol. 22, No. 1. (March 1951), pp. 79-86.
    by S Kullback, R Leibler
    posted to math statistics by BragilMassoud on 2007-03-31 17:10:24 as **
  • uBioRSS: Tracking Taxonomic Literature Using RSS.
    Bioinformatics (28 March 2007)
    by Patrick R R Leary, David P P Remsen, Catherine N N Norton, David J J Patterson, Indra Neil N Sarkar
    posted to rss by BragilMassoud on 2007-03-31 14:55:29 as ** along with 3 people and 4 groups jyuh yas kehan biodiversity_conservation Bioinformatics T_lab GrassBase
  • Surflex-Dock 2.1: Robust performance from ligand energetic modeling, ring flexibility, and knowledge-based search.
    J Comput Aided Mol Des (27 March 2007)
    by Ajay N Jain
    posted to docking surflex by BragilMassoud on 2007-03-29 14:44:56 as ** along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
  • The mutual information: detecting and evaluating dependencies between variables.
    Bioinformatics, Vol. 18 Suppl 2 (2002)
    by R Steuer, J Kurths, CO Daub, J Weise, J Selbig
    posted to math statistics by BragilMassoud on 2007-03-17 15:48:49 as ** along with 6 people and 1 group garyfeng anon_pl rsantana wongmld RobMills ebalp ReadingLab
  • Estimating mutual information using B-spline functions - an improved similarity measure for analysing gene expression data
    BMC Bioinformatics, Vol. 5, No. 1. (2004)
    by Carsten Daub, Ralf Steuer, Joachim Selbig, Sebastian Kloska
    posted to math statistics by BragilMassoud on 2007-03-17 15:48:11 as ** along with 1 person mmunson
  • Docking small ligands in flexible binding sites
    Journal of Computational Chemistry, Vol. 19, No. 1. (1998), pp. 21-37.
    by Joannis Apostolakis, Andreas Plückthun, Amedeo Caflisch
    posted to docking flexible_protein mc minimization by BragilMassoud on 2007-03-05 13:48:11 as ** along with 1 person schlauchi
  • A new implicit solvent model for protein-ligand docking.
    Proteins (28 February 2007)
    by Antonio Morreale, Rubén Gil-Redondo, Angel R R Ortiz
    posted to docking electrostatics energyfunctions by BragilMassoud on 2007-03-04 13:30:32 as **
  • Identifying allosteric fluctuation transitions between different protein conformational states as applied to Cyclin Dependent Kinase 2
    BMC Bioinformatics, Vol. 8 (07 February 2007), 45.
    by Jenny Gu, Philip E Bourne
    posted to flexible_protein kinases by BragilMassoud on 2007-02-21 13:27:55 as ** along with 2 people lna aqeel
  • Improved evolutionary optimization from genetically adaptive multimethod search
    PNAS, Vol. 104, No. 3. (16 January 2007), pp. 708-711.
    by Jasper A Vrugt, Bruce A Robinson
    posted to ga optimization by BragilMassoud on 2007-02-20 14:36:53 as ** along with 1 person noby
  • Gaussian docking functions
    Biopolymers, Vol. 68, No. 1. (2003), pp. 76-90.
    by Mark R Mcgann, Harold R Almond, Anthony Nicholls, Andrew J Grant, Frank K Brown
    posted to docking energyfunctions openeye by BragilMassoud on 2007-02-19 11:10:26 as ** along with 1 person ima
  • Ligand-protein inverse docking and its potential use in the computer search of protein targets of a small molecule.
    Proteins, Vol. 43, No. 2. (1 May 2001), pp. 217-226.
    by YZ Chen, DG Zhi
    posted to inversescreening by BragilMassoud on 2007-02-18 14:49:57 as ** along with 1 person and 2 groups sangeetha Bioinformatics insilicodrug
  • Diverse, high-quality test set for the validation of protein-ligand docking performance.
    J Med Chem, Vol. 50, No. 4. (22 February 2007), pp. 726-741.
    by MJ Hartshorn, ML Verdonk, G Chessari, SC Brewerton, WT Mooij, PN Mortenson, CW Murray
    posted to benchmark docking by BragilMassoud on 2007-02-18 12:24:11 as ** along with 8 people GermanErlenkamp massivemayhem higueruelo daevans ramensky hmk superpyrin thanatos
  • Self-organizing superimposition algorithm for conformational sampling.
    J Comput Chem (13 February 2007)
    by Fangqiang Zhu, Dimitris K K Agrafiotis
    posted to conformations ligand structure by BragilMassoud on 2007-02-16 16:59:37 as ** along with 1 person superpyrin
  • Supervised Consensus Scoring for Docking and Virtual Screening.
    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.
    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
  • Mechanism of inactivation of ornithine transcarbamoylase by Ndelta -(N'-Sulfodiaminophosphinyl)-L-ornithine, a true transition state analogue? Crystal structure and implications for catalytic mechanism.
    J Biol Chem, Vol. 275, No. 26. (30 June 2000), pp. 20012-20019.
    by DB Langley, MD Templeton, BA Fields, RE Mitchell, CA Collyer
    posted to robert by BragilMassoud on 2007-02-15 00:05:49 as **
  • Dijkstra's algorithm
    pp. 595-599.
    by TH Cormen, CE Leiserson, RL Rivest, C Stein
    posted to algorithm graph robert by BragilMassoud on 2007-02-14 18:53:03 as **
  • The Automatic Detection of Chemical Reaction Sites.
    Journal of Chemical Information and Computer Sciences, Vol. 18, No. 3. (1978), pp. 154-159.
    by Michael F Lynch, Peter Willett
    posted to robert by BragilMassoud on 2007-02-14 14:40:42 as **
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