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RamuAnandakrishnans pka [48 articles]

Artikler nylig sendt til RamuAnandakrishnans bibliotek klassifisert med nøkkelordet pka. You can also see everyone's pka.
  • Improving the Continuum Dielectric Approach to Calculating pKas of Ionizable Groups in Proteins
    J. Phys. Chem., Vol. 100, No. 43. (24 October 1996), pp. 17373-17387.
    by E Demchuk, RC Wade
    posted to pka by RamuAnandakrishnan on 2008-08-11 21:31:04 as ** along with 1 person sim82
  • A simple algorithm for the calculation of multiple site titration curves
    Protein Eng., Vol. 8, No. 3. (1 March 1995), pp. 243-248.
    by Andrej Karshikoff
    posted to pka by RamuAnandakrishnan on 2008-08-03 16:16:30 as **
  • The titration curve of native C reactive protein
    Electrophoresis, Vol. 4, No. 4. (1983), pp. 316-317.
    by Philippe Laurent, Lawrence A Potempa, Henry Gewurz, Barry A Fiedel, Robert C Allen
    posted to pka by RamuAnandakrishnan on 2008-08-03 16:14:21 as **
  • Electrostatic calculations of side-chain pKa values in myoglobin and comparison with NMR data for histidines
    Biochemistry, Vol. 32, No. 31. (1993), pp. 8045-8056.
    by Donald Bashford, David A Case, Claudio Dalvit, Linda Tennant, Peter E Wright
    posted to pka by RamuAnandakrishnan on 2008-07-25 21:10:42 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
  • 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 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
  • 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 3 people and 1 group qaiser_fatmi boris_aguilar tny group
  • 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 **
  • 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 **
  • 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 **
  • pKD: re-designing protein pKa values
    Nucleic Acids Research, Vol. 34, No. web server issue., pp. W48-W51.
    by Barbara M Tynan-Connolly, Jens E Nielsen
    posted to pka electrostatics by RamuAnandakrishnan on 2008-04-28 02:07:11 as **
  • Proton Binding to Proteins: p<i>K</i><sub>a</sub> Calculations with Explicit and Implicit Solvent Models
    J. Am. Chem. Soc., Vol. 126, No. 13. (7 April 2004), pp. 4167-4180.
    by T Simonson, J Carlsson, DA Case
    posted to electrostatics explicit_solvent implicit_solvent pka by RamuAnandakrishnan on 2008-03-28 18:39:53 as ** along with 2 people and 1 group sobolevnrm dmobley 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 pka by RamuAnandakrishnan on 2008-03-28 00:08:51 as ** along with 3 people and 1 group sim82 sobolevnrm boris_aguilar baker-group
  • Analysis of Basic Clustering Algorithms for Numerical Estimation of Statistical Averages in Biomolecules
    Journal of Computational Biology, Vol. 15, No. 2. (2008), pp. 165-184.
    by Ramu Anandakrishnan, Alexey Onufriev
    posted to electrostatics pka statistical_mechanics by RamuAnandakrishnan on 2008-03-03 23:47:30 as ** along with 1 person eskay
  • pH sensitivity of type III secretion system tip proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron P Markham, Susan E Birket, William D Picking, Wendy L Picking, Russell C Middaugh
    posted to electrostatics folding pka by RamuAnandakrishnan on 2008-01-07 14:40:54 as **
  • Protein electrostatics: a review of the equations and methods used to model electrostatic equations in biomolecules--applications in biotechnology.
    Biotechnol Annu Rev, Vol. 9 (2003), pp. 315-395.
    by MT Neves-Petersen, SB Petersen
    posted to electrostatics implicit_solvent pka statistical_mechanics by RamuAnandakrishnan on 2007-11-15 21:40:25 as **
  • Electrostatic properties of protein-protein complexes.
    Biophys J, Vol. 91, No. 5. (September 2006), pp. 1724-1736.
    by PJ Kundrotas, E Alexov
    posted to electrostatics ligand pka by RamuAnandakrishnan on 2007-10-15 15:49:47 as ** along with 1 person choonpeng
  • Protein-protein binding is often associated with changes in protonation state
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Aaron C Mason, Jan H Jensen
    posted to electrostatics ligand pka by RamuAnandakrishnan on 2007-10-12 13:42:54 as **** along with 4 people and 3 groups barry bicko chad_davis sobolevnrm McCammon structural_bioinformatics baker-group
  • PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations
    Nucleic Acids Research, Vol. 35, pp. w522-w525.
    by Todd, Gerhard
    posted to electrostatics pka by RamuAnandakrishnan on 2007-10-04 10:27:52 as ****
  • The Determinants of pKas in Proteins
    Biochemistry, Vol. 35, No. 24. (18 June 1996), pp. 7819-7833.
    by J Antosiewicz, JA Mccammon, MK Gilson
    posted to pka by RamuAnandakrishnan on 2007-09-24 21:17:31 as *****
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