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RamuAnandakrishnans library [236 articles]

Nye artikler sendt til RamuAnandakrishnans bibliotek.
  • Dynamics of folded proteins
    Nature, Vol. 267, No. 5612. (16 June 1977), pp. 585-590.
    by Andrew J Mccammon, Bruce R Gelin, Martin Karplus
    posted to md by RamuAnandakrishnan on 2008-07-19 23:40:08 as **
  • Benchmarking pKa prediction
    BMC Biochemistry, Vol. 7 (02 June 2006), 18.
    by Matthew N Davies, Christopher P Toseland, David S Moss, Darren R Flower
    posted to pka by RamuAnandakrishnan on 2008-07-16 19:19:11 as ** along with 3 people bicko cat_worth sim82
  • Improved p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gernot Kieseritzky, EW Knapp
    posted to pka by RamuAnandakrishnan on 2008-07-15 02:47:26 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, Makoto Taiji, Ryutaro Himeno, Haruki Nakamura, Yasushige Yonezawa
    posted to md by RamuAnandakrishnan on 2008-07-15 02:43:13 as **
  • Accurate solution of multi-region continuum biomolecule electrostatic problems using the linearized Poisson-Boltzmann equation with curved boundary elements
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Michael D Altman, Jaydeep P Bardhan, Jacob K White, Bruce Tidor
    posted to implicit_solvent electrostatics by RamuAnandakrishnan on 2008-07-15 02:40:59 as **
  • Accelerating molecular dynamic simulation on the cell processor and playstation 3
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Edgar Luttmann, Daniel L Ensign, Vishal Vaidyanathan, Mike Houston, Noam Rimon, Jeppe Øland, Guha Jayachandran, Mark Friedrichs, Vijay S Pande
    posted to md implicit_solvent by RamuAnandakrishnan on 2008-07-15 02:39:04 as **
  • Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
    Proceedings of the National Academy of Sciences, Vol. 105, No. 27. (2008), 9204.
    by Jory Z Ruscio, Deept Kumar, Maulik Shukla, Michael G Prisant, TM Murali, Alexey V Onufriev
    posted to md by RamuAnandakrishnan on 2008-07-10 03:35:15 as **
  • Electrostatic coupling between retinal isomerization and the ionization state of Glu-204: a general mechanism for proton release in bacteriorhodopsin.
    Biophys. J., Vol. 71, No. 3. (1 September 1996), pp. 1165-1171.
    by RV Sampogna, B Honig
    posted to pka by RamuAnandakrishnan on 2008-07-10 03:19:04 as **
  • A single adenosine with a neutral pKa in the ribosomal peptidyl transferase center.
    Science (New York, N.Y.), Vol. 289, No. 5481. (11 August 2000), pp. 947-950.
    by GW Muth, L Ortoleva-Donnelly, SA Strobel
    posted to pka by RamuAnandakrishnan on 2008-07-10 03:11:40 as **
  • Determination of the pKa values of active-center cysteines, cysteines-32 and -35, in Escherichia coli thioredoxin by Raman spectroscopy
    Biochemistry, Vol. 32, No. 22. (1993), pp. 5800-5808.
    by Huimin Li, Chad Hanson, James A Fuchs, Clare Woodward, George J Thomas
    posted to pka by RamuAnandakrishnan on 2008-07-10 03:08:45 as **
  • Calculation of protein ionization equilibria with conformational sampling: pK<SUB><FONT SIZE='-1'>a</FONT></SUB> of a model leucine zipper, GCN4 and barnase
    Proteins: Structure, Function, and Genetics, Vol. 46, No. 1. (2002), pp. 41-60.
    by Alemayehu A Gorfe, Philippe Ferrara, Amedeo Caflisch, Daniel N Marti, Hans R Bosshard, Ilian Jelesarov
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:55:12 as **
  • pKa calculations for class A beta-lactamases: methodological and mechanistic implications.
    Biophysical journal, Vol. 73, No. 5. (November 1997), pp. 2416-2426.
    by X Raquet, V Lounnas, J Lamotte-Brasseur, JM Frère, RC Wade
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:45:29 as **
  • Improving the accuracy of protein pKa calculations: conformational averaging versus the average structure.
    Proteins, Vol. 33, No. 2. (1 November 1998), pp. 145-158.
    by HW van Vlijmen, M Schaefer, M Karplus
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:41:45 as **
  • A fast and simple method to calculate protonation states in proteins.
    Proteins, Vol. 36, No. 4. (1 September 1999), pp. 474-483.
    by L Sandberg, O Edholm
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:39:38 as **
  • Optimizing the hydrogen-bond network in Poisson-Boltzmann equation-based pK(a) calculations.
    Proteins, Vol. 43, No. 4. (1 June 2001), pp. 403-412.
    by JE Nielsen, G Vriend
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:35:10 as **
  • A Self-Consistent, Microenvironment Modulated Screened Coulomb Potential Approximation to Calculate pH-Dependent Electrostatic Effects in Proteins
    Biophys. J., Vol. 77, No. 1. (1 July 1999), pp. 3-22.
    by Ernest L Mehler, Frank Guarnieri
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:33:15 as ** along with 1 person sim82
  • Incorporating protein conformational flexibility into the calculation of pH-dependent protein properties.
    Biophysical journal, Vol. 72, No. 5. (May 1997), pp. 2075-2093.
    by EG Alexov, MR Gunner
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:24:53 as ** along with 1 person sim82
  • Prediction of pH-dependent properties of proteins.
    Journal of molecular biology, Vol. 238, No. 3. (6 May 1994), pp. 415-436.
    by J Antosiewicz, JA McCammon, MK Gilson
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:23:31 as **
  • On the evaluation and optimization of protein X-ray structures for pKa calculations.
    Protein science : a publication of the Protein Society, Vol. 12, No. 2. (February 2003), pp. 313-326.
    by JE Nielsen, JA McCammon
    posted to pka by RamuAnandakrishnan on 2008-07-10 02:14:46 as **
  • Crystal structures of Escherichia coli and Lactobacillus casei dihydrofolate reductase refined at 1.7 A resolution. I. General features and binding of methotrexate.
    J Biol Chem, Vol. 257, No. 22. (1982), pp. 13650-13662.
    by JT Bolin, DJ Filman, DA Matthews, RC Hamlin, J Kraut
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:19:19 as **
  • Three-dimensional structures of enzyme-substrate complexes of the hydroxynitrile lyase from Hevea brasiliensis.
    Protein science : a publication of the Protein Society, Vol. 8, No. 10. (October 1999), pp. 1990-2000.
    by J Zuegg, K Gruber, M Gugganig, UG Wagner, C Kratky
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:15:36 as **
  • Hydrogen bonding and catalysis: a novel explanation for how a single amino acid substitution can change the ph optimum of a glycosidase
    Journal of Molecular Biology, Vol. 299, No. 1. (26 May 2000), pp. 255-279.
    by Manish D Joshi, Gary Sidhu, Isabelle Pot, Gary D Brayer, Stephen G Withers, Lawrence P Mcintosh
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:14:49 as **
  • Sugar Ring Distortion in the Glycosyl-Enzyme Intermediate of a Family G/11 Xylanase
    Biochemistry, Vol. 38, No. 17. (27 April 1999), pp. 5346-5354.
    by G Sidhu, SG Withers, NT Nguyen, LP Mcintosh, L Ziser, GD Brayer
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:13:36 as **
  • Structure of chymotrypsin-trifluoromethyl ketone inhibitor complexes: comparison of slowly and rapidly equilibrating inhibitors
    Biochemistry, Vol. 29, No. 33. (1990), pp. 7600-7607.
    by Kenneth Brady, Anzhi Wei, Dagmar Ringe, Robert H Abeles
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:12:42 as **
  • Cyclic HIV Protease Inhibitors: Synthesis, Conformational Analysis, P2/P2' Structure-Activity Relationship, and Molecular Recognition of Cyclic Ureas
    J. Med. Chem., Vol. 39, No. 18. (30 August 1996), pp. 3514-3525.
    by PYS Lam, Y Ru, PK Jadhav, PE Aldrich, GV Delucca, CJ Eyermann, CH Chang, G Emmett, ER Holler, WF Daneker, L Li, PN Confalone, RJ Mchugh, Q Han, R Li, JA Markwalder, SP Seitz, TR Sharpe, LT Bacheler, MM Rayner, RM Klabe, L Shum, DL Winslow, DM Kornhauser, DA Jackson, S Erickson-Viitanen, CN Hodge
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:08:24 as **
  • Structure of HIV-1 protease with KNI-272, a tight-binding transition-state analog containing allophenylnorstatine
    Structure, Vol. 3, No. 6. (June 1995), pp. 581-590.
    by Eric T Baldwin, Narayana T Bhat, Sergei Gulnik, Beishan Liu, Igor A Topol, Yoshiaki Kiso, Tsutomu Mimoto, Hiroaki Mitsuya, John W Erickson
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:07:16 as **
  • Conserved Folding in Retroviral Proteases: Crystal Structure of a Synthetic HIV-1 Protease
    Science, Vol. 245, No. 4918. (1989), pp. 616-621.
    by Alexander Wlodawer, Maria Miller, Mariusz Jaskólski, Bangalore K Sathyanarayana, Eric Baldwin, Irene T Weber, Linda M Selk, Leigh Clawson, Jens Schneider, Stephen BH Kent
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:05:49 as **
  • The three-dimensional structure of the aspartyl protease from the HIV-1 isolate BRU
    Biochimie, Vol. 73, No. 11. (November 1991), pp. 1391-1396.
    by S Spinelli, QZ Liu, PM Alzari, PH Hirel, RJ Poljak
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:02:29 as **
  • Crystallographic analysis of a complex between human immunodeficiency virus type 1 protease and acetyl-pepstatin at 2.0-A resolution
    J. Biol. Chem., Vol. 265, No. 24. (25 August 1990), pp. 14209-14219.
    by PM Fitzgerald, BM Mckeever, JF Vanmiddlesworth, JP Springer, JC Heimbach, CT Leu, WK Herber, RA Dixon, PL Darke
    posted to pka by RamuAnandakrishnan on 2008-07-09 19:01:41 as **
  • The active site of aspartic proteinases
    FEBS Letters, Vol. 174, No. 1. (20 August 1984), pp. 96-101.
    by Laurence Pearl, Tom Blundell
    posted to pka by RamuAnandakrishnan on 2008-07-09 18:56:46 as **
  • Crystal structures of native and inhibited forms of human cathepsin D: implications for lysosomal targeting and drug design
    PNAS, Vol. 90 (1993), pp. 6796-6800.
    by ET Baldwin, TN Bhat, S Gulnik, MV Hosur, RC Sowder, RE Cachau, J Collins, AM Silva, JW Erickson
    posted to pka by RamuAnandakrishnan on 2008-07-09 18:54:53 as **
  • Conformational switching in an aspartic proteinase
    Nat Struct Mol Biol, Vol. 5, No. 10. (October 1998), pp. 866-871.
    by Angela Y Lee, Sergei V Gulnik, John W Erickson
    posted to pka by RamuAnandakrishnan on 2008-07-09 18:51:06 as **
  • Structure and inhibition of plasmepsin II, a hemoglobin-degrading enzyme from Plasmodium falciparum
    PNAS, Vol. 93 (1996), pp. 10034-10039.
    by AM Silva, AY Lee, SV Gulnik, P Maier, J Collins, TN Bhat, PJ Collins, RE Cachau, KE Luker, IY Gluzman, SE Francis, A Oksman, DE Goldberg, JW Erickson
    posted to pka by RamuAnandakrishnan on 2008-07-09 18:48:38 as **
  • Crystal structure of the novel aspartic proteinase zymogen proplasmepsin II from Plasmodium falciparum
    Nat Struct Mol Biol, Vol. 6, No. 1. (January 1999), pp. 32-37.
    by Nina K Bernstein, Maia M Cherney, Hansruedi Loetscher, Robert G Ridley, Michael N James
    posted to pka by RamuAnandakrishnan on 2008-07-09 18:42:46 as **
  • A generative, probabilistic model of local protein structure
    PNAS, Vol. 105, No. 26. (July 2008), pp. 8932-8937.
    by Wouter Boomsma, Kanti V Mardia, Charles C Taylor, Jesper Ferkinghoff-Borg, Anders Krogh, Thomas Hamelryck
    posted to folding by RamuAnandakrishnan on 2008-07-08 13:37:40 as **
  • 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 pka by RamuAnandakrishnan on 2008-07-03 01:28:17 as ** along with 2 people and 2 groups sobolevnrm skoddet baker-group Nielsen group
  • Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure
    Proceedings of the National Academy of Sciences, Vol. 105, No. 26. (1 July 2008), pp. 8872-8877.
    by Andrew Routh, Sara Sandin, Daniela Rhodes
    posted to nucleosome by RamuAnandakrishnan on 2008-07-02 02:54:34 as **
  • 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 statistical_mechanics pka electrostatics by RamuAnandakrishnan on 2008-06-30 00:49:34 as ** along with 2 people boris_aguilar tny
  • Electrostatic calculations of the pKa values of ionizable groups in bacteriorhodopsin
    Journal of Molecular Biology, Vol. 224, No. 2. (20 March 1992), pp. 473-486.
    by Donald Bashford, Klaus Gerwert
    posted to pka implicit_solvent electrostatics by RamuAnandakrishnan on 2008-06-22 18:37:19 as **
  • Atomic charges derived from electrostatic potentials: A detailed study
    Journal of Computational Chemistry, Vol. 8, No. 6. (1987), pp. 894-905.
    by Lisa E Chirlian, Michelle M Francl
    posted to md electrostatics by RamuAnandakrishnan on 2008-06-20 23:08:59 as **
  • Protein model refinement using an optimized physics-based all-atom force field
    Proceedings of the National Academy of Sciences, Vol. 105, No. 24. (17 June 2008), pp. 8268-8273.
    by Anna Jagielska, Liliana Wroblewska, Jeffrey Skolnick
    posted to folding electrostatics amber by RamuAnandakrishnan on 2008-06-19 12:23:29 as ** along with 3 people and 2 groups barry jmccammon zwang McCammon structural_bioinformatics
  • Molecular dynamics simulations of biomolecules.
    Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652.
    by M Karplus, JA McCammon
    posted to md by RamuAnandakrishnan on 2008-06-18 14:55:36 as ** along with 4 people LamBras baaden aqeel simone
  • Use and misuse of the gene ontology annotations.
    Nature reviews. Genetics (13 May 2008)
    by Seung Yon Rhee, Valerie Wood, Kara Dolinski, Sorin Draghici
    posted to genome by RamuAnandakrishnan on 2008-06-18 12:34:50 as ** along with 18 people and 1 group marck capitall realzhang gjuggler A_Olympia fpattyn cmzmasek djkt renatomilani giovenko tmmurali cabbagesofdoom ptrobajo roys carlk mariakmejia aheilbut jyuh logics of knowledge
  • Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids
    Molecular Simulation, Vol. 34, No. 4. (2008), pp. 349-364.
    by MB Tessier, ML Demarco, AB Yongye, RJ Woods
    posted to ligand force_field amber by RamuAnandakrishnan on 2008-06-17 18:14:43 as **
  • Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme
    Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 76, No. 4. (2007)
    by Luigi Delle Site
    posted to md electrostatics cutoff by RamuAnandakrishnan on 2008-06-02 23:22:52 as **
  • Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution.
    Science, Vol. 282, No. 5389. (23 October 1998), pp. 740-744.
    by Y Duan, PA Kollman
    posted to md folding electrostatics by RamuAnandakrishnan on 2008-05-28 21:44:59 as ** along with 3 people choonpeng j3xucite allmensch
  • Very fast prediction and rationalization of pKa values for protein-ligand complexes
    Proteins, Vol. 9999 (2008)
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to pka ligand electrostatics by RamuAnandakrishnan on 2008-05-25 13:40:07 as **
  • Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution
    Annual Review of Physical Chemistry, Vol. 59, No. 1. (2008), pp. 545-571.
    by Matej Praprotnik, Luigi Delle Site, Kurt Kremer
    posted to md electrostatics coarse_grain by RamuAnandakrishnan on 2008-05-21 13:42:03 as **
  • Improved pKa prediction: Combining empirical and semimicroscopic methods
    Journal of Computational Chemistry, Vol. 9999 (2008)
    by Gernot Kieseritzky, EW Knapp
    posted to pka electrostatics by RamuAnandakrishnan on 2008-05-16 01:53:45 as **
  • Improved Detection of Overrepresentation of Gene-Ontology Annotations with Parent-Child Analysis.
    Bioinformatics (11 September 2007)
    by Steffen Grossmann, Sebastian Bauer, Peter N N Robinson, Martin Vingron
    posted to genome evolution by RamuAnandakrishnan on 2008-05-05 20:35:38 as ** along with 5 people marck sgoetz tmmurali grahamc heliopais
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