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boris_aguilars library [31 articles]

Nye artikler sendt til boris_aguilars bibliotek.
  • A protein-DNA docking benchmark
    Nucl. Acids Res., Vol. 36, No. 14. (1 August 2008), e88.
    by Marc van Dijk, Alexandre M Bonvin
    posted to docking pka by boris_aguilar on 2008-08-19 21:44:41 as ***** along with 2 people reyez neils
  • A nonlinear elasticity model of macromolecular conformational change induced by electrostatic forces
    Journal of Mathematical Analysis and Applications, Vol. 340, No. 1. (1 April 2008), pp. 135-164.
    by YC Zhou, Michael Holst, Andrew J Mccammon
    posted to general_interest protein_electrostatics structure by boris_aguilar on 2008-08-18 16:31:01 as **** along with 1 person and 1 group sobolevnrm baker-group
  • Accurate prediction of protonation state as a prerequisite for reliable MM-PB(GB)SA binding free energy calculations of HIV-1 protease inhibitors
    Journal of Computational Chemistry, Vol. 29, No. 5. (2008), pp. 673-685.
    by Kitiyaporn Wittayanarakul, Supot Hannongbua, Michael Feig
    posted to docking pka by boris_aguilar on 2008-08-15 18:42:46 as **** along with 4 people and 1 group mijogiffin sobolevnrm dmobley sunhwan baker-group
  • Importance of accurate charges in molecular docking: Quantum mechanical/molecular mechanical (QM/MM) approach
    Journal of Computational Chemistry, Vol. 26, No. 9. (2005), pp. 915-931.
    by Art E Cho, Victor Guallar, Bruce J Berne, Richard Friesner
    posted to docking pka by boris_aguilar on 2008-08-15 16:20:46 as **** along with 1 person and 1 group qaiser_fatmi group
  • Prediction of binding constants of protein ligands: A fast method for the prioritization of hits obtained from de novo design or 3D database search programs
    Journal of Computer-Aided Molecular Design, Vol. 12, No. 4. (1 July 1998), pp. 309-309.
    by Hans-Joachim Böhm
    posted to docking by boris_aguilar on 2008-08-15 15:43:47 as ***
  • 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 docking by boris_aguilar on 2008-08-15 15:37:23 as **** along with 8 people and 2 groups BragilMassoud yongzhao peprovy kazemi sergio_fms carlescorbi robert qaiser_fatmi TSRI_MGL group
  • Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes
    Journal of Computer-Aided Molecular Design, Vol. 11, No. 5. (1997), pp. 425-445.
    by Matthew D Eldridge, Christopher W Murray, Timothy R Auton, Gaia V Paolini, Roger P Mee
    posted to docking drug_design by boris_aguilar on 2008-08-15 00:02:08 as ***
  • A new protein-protein docking scoring function based on interface residue properties
    Bioinformatics, Vol. 23, No. 5. (1 March 2007), pp. 555-562.
    by J Bernauer, J Aze, J Janin, A Poupon
    posted to docking by boris_aguilar on 2008-08-14 23:37:54 as *** along with 2 people bicko chad_davis
  • Calculation of protein-ligand binding affinities.
    Annu Rev Biophys Biomol Struct, Vol. 36 (2007), pp. 21-42.
    by MK Gilson, HX Zhou
    posted to docking drug_design free_energy ligand by boris_aguilar on 2008-08-14 21:22:26 as ***** along with 7 people and 1 group dimka neils hmk ashaytan ras cchang qaiser_fatmi group
  • Signaling Recognition Events with Fluorescent Sensors and Switches.
    Chemical reviews, Vol. 97, No. 5. (5 August 1997), pp. 1515-1566.
    by A. P de Silva, H. Q Gunaratne, Thorfinnur Gunnlaugsson, Allen J Huxley, Colin P McCoy, Jude T Rademacher, Terence E Rice
    posted to biotechnology by boris_aguilar on 2008-08-14 20:59:54 as **
  • Approaches to the Description and Prediction of the Binding Affinity of Small-Molecule Ligands to Macromolecular Receptors
    Angewandte Chemie International Edition, Vol. 41, No. 15. (2002), pp. 2644-2676.
    by Holger Gohlke, Gerhard Klebe
    posted to drug_design free_energy ligand by boris_aguilar on 2008-08-08 21:19:51 as *** along with 3 people kazemi superpyrin LamBras
  • Application of a Theory of Enzyme Specificity to Protein Synthesis.
    Proc Natl Acad Sci U S A, Vol. 44, No. 2. (February 1958), pp. 98-104.
    by DE Koshland
    posted to ligand pka structure by boris_aguilar on 2008-07-15 21:36:46 as *** along with 5 people apostola robert kazemi nigham sim82
  • pKa's of ionizable groups in proteins: atomic detail from a continuum electrostatic model
    Biochemistry, Vol. 29, No. 44. (1990), pp. 10219-10225.
    by Donald Bashford, Martin Karplus
    posted to implicit_solvation pka poisson-boltzmann by boris_aguilar on 2008-07-15 14:55:19 as *****
  • Ligand-Protein DataBase: Linking Protein-Ligand Complex Structures to Binding Data
    J. Med. Chem., Vol. 44, No. 22. (25 October 2001), pp. 3592-3598.
    by O Roche, R Kiyama, CL Brooks
    posted to drug_design ligand pka structure by boris_aguilar on 2008-07-15 00:44:29 as ***
  • Protein-Protein Docking Benchmark 2.0: an update.
    Proteins, Vol. 60, No. 2. (1 August 2005), pp. 214-216.
    by J Mintseris, K Wiehe, B Pierce, R Anderson, R Chen, J Janin, Z Weng
    posted to ligand pka structure by boris_aguilar on 2008-07-15 00:32:49 as ***** along with 9 people marti aqeel julianm bicko chad_davis ima bluvsh1 selrac Iainios
  • Calculating pKa values in enzyme active sites
    Protein Sci, Vol. 12, No. 9. (1 September 2003), pp. 1894-1901.
    by Jens E Nielsen, Andrew J Mccammon
    posted to pka by boris_aguilar on 2008-06-06 22:56:25 as *** along with 3 people and 1 group tny RamuAnandakrishnan qaiser_fatmi group
  • The Protein Data Bank.
    Nucleic Acids Res, Vol. 28, No. 1. (1 January 2000), pp. 235-242.
    by HM Berman, J Westbrook, Z Feng, G Gilliland, TN Bhat, H Weissig, IN Shindyalov, PE Bourne
    posted to structure by boris_aguilar on 2008-05-30 21:21:20 as ***** along with 23 people and 4 groups nigham lillekatt thaliana dimka kuhn jwm vavi bicko itmeson dgront caporaso condon leelarcombe aengisch debatebob massivemayhem gisle girschick selrac tji higueruelo sebk timg Radiation_Damage Stressosome biomedical-nlp beta
  • Structure and Energetics of Protein-Protein Interactions: The Role of Conformational Heterogeneity in OMTKY3 Binding to Serine Proteases
    Journal of Molecular Biology, Vol. 331, No. 2. (8 August 2003), pp. 497-508.
    by James R Horn, S Ramaswamy, Kenneth P Murphy
    posted to drug_design pka structure by boris_aguilar on 2008-04-23 22:25:39 as ***
  • Histidine pKa shifts and changes of tautomeric states induced by the binding of gallium-protoporphyrin IX in the hemophore HasASM
    Protein Sci, Vol. 11, No. 4. (1 April 2002), pp. 757-765.
    by Nicolas Wolff, Clarisse Deniau, Sylvie Letoffe, Catherine Simenel, Veena Kumar, Igor Stojiljkovic, Cecile Wandersman, Muriel Delepierre, Anne Lecroisey
    posted to drug_design pka structure by boris_aguilar on 2008-04-23 02:17:38 as *** along with 1 person and 1 group qaiser_fatmi group
  • NMR Determination of Lysine pKa Values in the Pol λ Lyase Domain: Mechanistic Implications
    Biochemistry, Vol. 45, No. 6. (14 February 2006), pp. 1785-1794.
    by G Gao, EF Derose, TW Kirby, RE London
    posted to dna drug_design pka by boris_aguilar on 2008-04-23 02:14:52 as ***
  • Ionization states of the catalytic residues in HIV-1 protease
    Nat Struct Mol Biol, Vol. 3, No. 11. (November 1996), pp. 946-950.
    by Ross Smith, Ian M Brereton, Richard Y Chai, Stephen B Kent
    posted to drug_design ligand pka by boris_aguilar on 2008-02-12 17:08:21 as **** along with 1 person and 1 group qaiser_fatmi group
  • Solution NMR Evidence That the HIV-1 Protease Catalytic Aspartyl Groups Have Different Ionization States in the Complex Formed with the Asymmetric Drug KNI-272
    Biochemistry, Vol. 35, No. 31. (6 August 1996), pp. 9945-9950.
    by YX Wang, DI Freedberg, T Yamazaki, PT Wingfield, SJ Stahl, JD Kaufman, Y Kiso, DA Torchia
    posted to drug_design ligand pka by boris_aguilar on 2008-02-12 16:42:13 as ****
  • Molecular flexibility in protein-DNA interactions
    Biosystems, Vol. 85, No. 2. (August 2006), pp. 126-136.
    by Stefan Gunther, Kristian Rother, Cornelius Frommel
    posted to dna ligand structure by boris_aguilar on 2007-12-14 00:28:10 as ****
  • Monte Carlo-based linear Poisson-Boltzmann approach makes accurate salt-dependent solvation free energy predictions possible
    The Journal of Chemical Physics, Vol. 127, No. 18. (2007)
    by Nikolai A Simonov, Michael Mascagni, Marcia O Fenley
    posted to implicit_solvation poisson-boltzmann by boris_aguilar on 2007-12-05 06:46:21 as **** along with 1 person and 1 group sobolevnrm baker-group
  • Optimizing pK<SUB><FONT SIZE='-1'>A</FONT></SUB> computation in proteins with pH adapted conformations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Gernot Kieseritzky, Ernst-Walter Knapp
    posted to analytical_electrostatics pka by boris_aguilar on 2007-12-05 02:27:54 as **** along with 3 people and 1 group sim82 sobolevnrm RamuAnandakrishnan baker-group
  • NPIDB: a Database of Nucleic Acids Protein Interactions
    Bioinformatics, Vol. 23, No. 23. (1 December 2007), pp. 3247-3248.
    by Sergei Spirin, Mikhail Titov, Anna Karyagina, Andrei Alexeevski
    posted to dna drug_design structure by boris_aguilar on 2007-12-04 23:15:25 as **** along with 2 people jyuh tmmurali
  • Anchor residues in protein-protein interactions.
    Proc Natl Acad Sci U S A, Vol. 101, No. 31. (3 August 2004), pp. 11287-11292.
    by D Rajamani, S Thiel, S Vajda, CJ Camacho
    posted to drug_design ligand structure by boris_aguilar on 2007-11-20 16:54:55 as ** along with 3 people and 2 groups barry bicko bluvsh1 structural_bioinformatics Bioinformatics
  • Thermodynamic linkage between the binding of protons and inhibitors to HIV-1 protease
    Protein Sci, Vol. 8, No. 1. (1 January 1999), pp. 180-195.
    by J Trylska, J Antosiewicz, M Geller, Cn Hodge, Rm Klabe, Ms Head, Mk Gilson
    posted to pka by boris_aguilar on 2007-11-13 01:29:53 as *** along with 1 person and 1 group skoddet Nielsen group
  • High-resolution structure prediction and the crystallographic phase problem
    Nature (14 October 2007)
    by Bin Qian, Srivatsan Raman, Rhiju Das, Philip Bradley, Airlie J Mccoy, Randy J Read, David Baker
    posted to structure by boris_aguilar on 2007-11-09 19:27:09 as **** along with 15 people and 2 groups apaydin aheilbut jwm chad_davis eckart_bindewald ffranca dgront massivemayhem cjeans zwang cactus sobolevnrm Ema chenway ardalby baker-group OPIG
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