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skoddet's library [32 articles]

最近录入 skoddet's 文献库.
  • Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases.
    Journal of chemical information and modeling (19 August 2008)
    by S K Sadiq, David Wright, Simon J Watson, Stefan J Zasada, Ileana Stoica, Peter V Coveney
    posted to hiv by skoddet on 2008-08-26 21:50:32 as ** along with 1 person and 1 group mijogiffin Nielsen group
  • Microwave Activation of Enzymatic Catalysis
    J. Am. Chem. Soc. (10 July 2008)
    by Douglas D Young, Jason Nichols, Robert M Kelly, Alexander Deiters
    posted to catalysis by skoddet on 2008-07-30 15:40:15 as ** along with 1 person katiehumphry
  • An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes.
    J Mol Biol, Vol. 326, No. 4. (28 February 2003), pp. 1239-1259.
    by T Kortemme, AV Morozov, D Baker
    posted to protein structure by skoddet on 2008-07-10 16:17:17 as ** along with 2 people and 1 group lna dgront Nielsen group
  • A ?solvated rotamer? approach to modeling water-mediated hydrogen bonds at protein-protein interfaces
    Proteins: Structure, Function, and Bioinformatics, Vol. 58, No. 4. (2005), pp. 893-904.
    by Lin Jiang, Brian Kuhlman, Tanja Kortemme, David Baker
    posted to protein structure by skoddet on 2008-07-10 16:16:12 as ** along with 3 people apaydin jwm msuarezdiez
  • A simple physical model for binding energy hot spots in protein-protein complexes.
    Proc Natl Acad Sci U S A, Vol. 99, No. 22. (29 October 2002), pp. 14116-14121.
    by T Kortemme, D Baker
    posted to structure-prediction by skoddet on 2008-06-20 15:35:39 as ** along with 5 people and 1 group lna jwm bicko cjeans hmk Nielsen group
  • Computational alanine scanning of protein-protein interfaces.
    Sci STKE, Vol. 2004, No. 219. (10 February 2004)
    by T Kortemme, DE Kim, D Baker
    posted to structure-prediction by skoddet on 2008-06-20 15:34:45 as ** along with 4 people and 6 groups barry sangeetha blackbart joergkurtwegner structural_bioinformatics Bioinformatics Molecular-Modelling Drug-Design Cheminformatics insilicodrug
  • SNPeffect v2.0: a new step in investigating the molecular phenotypic effects of human non synonymous SNPs.
    Bioinformatics (29 June 2006)
    by Joke Reumers, Sebastian Maurer-Stroh, Joost Schymkowitz, Frederic Rousseau
    posted to structure-prediction by skoddet on 2008-06-20 15:33:38 as ** along with 4 people and 3 groups chad_davis caporaso massivemayhem cat_worth structural_bioinformatics biomedical-nlp Nielsen group
  • Joint annotation of coding and non-coding single nucleotide polymorphisms and mutations in the SNPeffect and PupaSuite databases.
    Nucleic Acids Res (17 December 2007)
    by Joke Reumers, Lucia Conde, Ignacio Medina, Sebastian Maurer-Stroh, Joost Van V Durme, Joaquin Dopazo, Frederic Rousseau, Joost Schymkowitz
    posted to no-tag by skoddet on 2008-06-20 15:31:29 as ** along with 1 person and 1 group jyuh Nielsen group
  • 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 hiv pka by skoddet on 2008-06-20 15:29:53 as ** along with 1 person and 1 group boris_aguilar Nielsen group
  • The role of hydrogen bonding in the enzymatic reaction catalyzed by HIV-1 protease.
    Protein science : a publication of the Protein Society, Vol. 13, No. 2. (February 2004), pp. 513-528.
    by J Trylska, P Grochowski, JA McCammon
    posted to hiv pka by skoddet on 2008-06-20 15:29:31 as **
  • Binding pathways of ligands to HIV-1 protease: coarse-grained and atomistic simulations.
    Chem Biol Drug Des, Vol. 69, No. 1. (January 2007), pp. 5-13.
    by CE Chang, J Trylska, V Tozzini, JA McCammon
    posted to hiv by skoddet on 2008-06-20 15:28:57 as ** along with 1 person and 1 group choonpeng Nielsen group
  • Magnetic resonance imaging of pH in vivo using hyperpolarized 13C-labelled bicarbonate
    Nature (28 May 2008)
    by Ferdia A Gallagher, Mikko I Kettunen, Sam E Day, De-En Hu, Jan H Ardenkjær-Larsen, René, Pernille R Jensen, Magnus Karlsson, Klaes Golman, Mathilde H Lerche, Kevin M Brindle
    posted to pka by skoddet on 2008-06-12 10:09:47 as **
  • Evolutionary analysis of HIV-1 protease inhibitors: Methods for design of inhibitors that evade resistance.
    Proteins, Vol. 48, No. 1. (1 July 2002), pp. 63-74.
    by D Stoffler, MF Sanner, GM Morris, AJ Olson, DS Goodsell
    posted to hiv by skoddet on 2008-06-11 16:52:01 as ** along with 1 group Nielsen group
  • Molecular Analysis of the HIV-1 Resistance Development: Enzymatic Activities, Crystal Structures, and Thermodynamics of Nelfinavir-resistant HIV Protease Mutants
    Journal of Molecular Biology, Vol. 374, No. 4. (7 December 2007), pp. 1005-1016.
    by Milan Kozísek, Jenelle Bray, Pavlína Rezácová, Klára Sasková, Jirí Brynda, Jana Pokorná, Fabrizio Mammano, Lubomír Rulísek, Jan Konvalinka
    posted to hiv by skoddet on 2008-06-11 16:50:39 as ** along with 1 person and 1 group joseph_x_zhou Nielsen group
  • Site-directed mutagenesis of the hinge peptide from the hemagglutinin protein: enhancement of the pH-responsive conformational change
    Protein Engineering, Design and Selection, Vol. 21, No. 6. (1 June 2008), pp. 395-404.
    by Monica Casali, Scott Banta, Carlo Zambonelli, Zaki Megeed, Martin L Yarmush
    posted to pka by skoddet on 2008-05-16 15:22:40 as **
  • Mapping Local Protein Electrostatics by EPR of pH-Sensitive Thiol-Specific Nitroxide
    Biochemistry, Vol. 47, No. 20. (20 May 2008), pp. 5626-5637.
    by Maxim A Voinov, Andres Ruuge, Vladimir A Reznikov, Igor A Grigor’ev, Alex I Smirnov
    posted to nmr pka_values by skoddet on 2008-05-13 11:04:17 as ** along with 1 person and 2 groups sobolevnrm baker-group Nielsen group
  • Comparative study of the prereactive protein kinase A Michaelis complex with Kemptide substrate
    Journal of Computer-Aided Molecular Design, Vol. 21, No. 10. (15 October 2007), pp. 603-615.
    by Manuel Montenegro, Mireia Garcia-Viloca, Àngels González-Lafont, José Lluch
    posted to md pka by skoddet on 2008-05-09 13:25:05 as **
  • Microsecond Molecular Dynamics Simulation Shows Effect of Slow Loop Dynamics on Backbone Amide Order Parameters of Proteins
    J. Phys. Chem. B (1 March 2008)
    by P Maragakis, K Lindorff-Larsen, MP Eastwood, RO Dror, JL Klepeis, IT Arkin, MO Jensen, H Xu, N Trbovic, RA Friesner, AG Palmer, DE Shaw
    posted to md by skoddet on 2008-05-08 16:02:47 as ** along with 1 person and 1 group LamBras Nielsen group
  • Acidic range titration of HEWL using a constant-pH molecular dynamics method
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Miguel Machuqueiro, António M Baptista
    posted to no-tag by skoddet on 2008-04-28 20:24:21 as ** along with 2 people and 1 group sobolevnrm sunhwan baker-group
  • Molecular Dynamics Simulation of the Escherichia coli NikR Protein: Equilibrium Conformational Fluctuations Reveal Interdomain Allosteric Communication Pathways
    Journal of Molecular Biology, Vol. In Press, Corrected Proof
    by Michael J Bradley, Peter T Chivers, Nathan A Baker
    posted to md by skoddet on 2008-04-27 13:46:29 as ** along with 2 people and 2 groups sobolevnrm barry baker-group structural_bioinformatics
  • Correspondences between low-energy modes in enzymes: Dynamics-based alignment of enzymatic functional families
    Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 918-929.
    by Andrea Zen, Vincenzo Carnevale, Arthur M Lesk, Cristian Micheletti
    posted to nma by skoddet on 2008-04-26 09:04:42 as ** along with 2 people and 1 group edvin tny Nielsen group
  • A buried lysine that titrates with a normal pKa : Role of conformational flexibility at the protein-water interface as a determinant of pKa values
    Protein Sci, Vol. 17, No. 5. (1 May 2008), pp. 833-845.
    by Michael J Harms, Jamie L Schlessman, Michael S Chimenti, Gloria R Sue, Ana Damjanovic, Garcia-Moreno
    posted to electrostatics pka by skoddet on 2008-04-25 21:22:56 as *** along with 2 people and 2 groups sobolevnrm RamuAnandakrishnan baker-group Nielsen group
  • Electrostatic Fields Near the Active Site of Human Aldose Reductase: 1. New Inhibitors and Vibrational Stark Effect Measurements
    Biochemistry (19 January 2008)
    by LJ Webb, SG Boxer
    posted to electrostatics by skoddet on 2008-04-11 10:57:25 as ** along with 1 person higueruelo
  • Local knowledge helps determine protein structures
    Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4533-4534.
    by Michael R Gryk, Jeffrey C Hoch
    posted to nmr structure-prediction by skoddet on 2008-04-11 10:51:06 as ***
  • From the Cover: Consistent blind protein structure generation from NMR chemical shift data
    Proceedings of the National Academy of Sciences, Vol. 105, No. 12. (25 March 2008), pp. 4685-4690.
    by Yang Shen, Oliver Lange, Frank Delaglio, Paolo Rossi, James M Aramini, Gaohua Liu, Alexander Eletsky, Yibing Wu, Kiran K Singarapu, Alexander Lemak, Alexandr Ignatchenko, Cheryl H Arrowsmith, Thomas Szyperski, Gaetano T Montelione, David Baker, Ad Bax
    posted to nmr prediction structure by skoddet on 2008-04-11 10:50:48 as *** along with 5 people and 1 group zwang biehl sunhwan apaydin dgront Nielsen group
  • A finite element framework for computation of protein normal modes and mechanical response
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Mark Bathe
    posted to nma by skoddet on 2008-04-11 10:44:14 as ** along with 2 people and 1 group choonpeng RamuAnandakrishnan Nielsen group
  • A knowledge-based forcefield for protein-protein interface design.
    Proteins, Vol. 70, No. 4. (March 2008), pp. 1540-1550.
    by LA Clark, HW van Vlijmen
    posted to design protein by skoddet on 2008-04-11 10:44:01 as ** along with 1 person and 1 group chad_davis Nielsen group
  • Classifying protein kinase structures guides use of ligand-selectivity profiles to predict inactive conformations: Structure of lck/imatinib complex.
    Proteins (1 October 2007)
    by Marc D D Jacobs, Paul R R Caron, Brian J J Hare
    posted to kinases by skoddet on 2008-04-11 10:43:42 as ** along with 1 person bicko
  • Efficient comprehensive scoring of docked protein complexes using probabilistic support vector machines
    Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 4. (2008), pp. 1367-1378.
    by Oliver Martin, Dietmar Schomburg
    posted to no-tag by skoddet on 2008-04-11 10:43:28 as **
  • Solvent effects in the slow dynamics of proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 70, No. 4. (2008), pp. 1235-1242.
    by Konrad Hinsen, Gerald R Kneller
    posted to no-tag by skoddet on 2008-04-11 10:43:11 as ** along with 2 people choonpeng saravan
  • PDB improvement starts with data deposition [3]
    Science, Vol. 317, No. 5835. (2007), pp. 195-196.
    by RP Joosten, G Vriend
    posted to no-tag by skoddet on 2008-04-09 10:39:09 as read
  • Determination of electrostatic interaction energies and protonation state populations in enzyme active sites
    Journal of Molecular Biology, Vol. In Press, Accepted Manuscript
    by Chresten R Sondergaard, Lawrence P Mcintosh, Gianluca Pollastri, Jens E Nielsen
    posted to electrostatics pka_values by skoddet on 2008-04-06 17:18:28 as read along with 2 people and 2 groups barry sobolevnrm structural_bioinformatics baker-group
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