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onufriev's watchlist [245 articles]

Recent papers matching onufriev's watchlist criteria
  • Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
    Chemical Reviews, Vol. 99, No. 8. (1999), pp. 2161-2200.
    by CJ Cramer, DG Truhlar
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-20 16:47:12 as **
  • Dielectric effects in biopolymers: The theory of ionic saturation revisited
    Biopolymers, Vol. 24, No. 3. (1985), pp. 427-439.
    by BE Hingerty, RH Ritchie, TL Ferrell, JE Turner
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-20 15:23:36 as **
  • Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.
    Protein science : a publication of the Protein Society, Vol. 1, No. 9. (September 1992), pp. 1185-1205.
    by J Guenot, PA Kollman
    posted to md implicit_solvent explicit_solvent by RamuAnandakrishnan on 2008-08-20 15:06:48 as **
  • Automatic parameterization of force field by systematic search and genetic algorithms
    Journal of Computational Chemistry, Vol. 22, No. 12. (2001), pp. 1219-1228.
    by Junmei Wang, Peter A Kollman
    posted to force_field by RamuAnandakrishnan on 2008-08-18 16:01:10 as **
  • Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of alpha/gamma Conformers
    Biophys. J., Vol. 92, No. 11. (1 June 2007), pp. 3817-3829.
    by Alberto Perez, Ivan Marchan, Daniel Svozil, Jiri Sponer, Thomas E Cheatham, Charles A Laughton, Modesto Orozco
    posted to force_field by RamuAnandakrishnan on 2008-08-18 15:48:13 as **
  • Comparison of multiple Amber force fields and development of improved protein backbone parameters
    Proteins: Structure, Function, and Bioinformatics, Vol. 65, No. 3. (2006), pp. 712-725.
    by Viktor Hornak, Robert Abel, Asim Okur, Bentley Strockbine, Adrian Roitberg, Carlos Simmerling
    posted to force_field by RamuAnandakrishnan on 2008-08-18 15:45:45 as ** along with 6 people barry baaden lna allmensch choonpeng kazemi
  • The effects of truncating long-range forces on protein dynamics.
    Proteins, Vol. 6, No. 1. (1989), pp. 32-45.
    by RJ Loncharich, BR Brooks
    posted to md cutoff by RamuAnandakrishnan on 2008-08-18 15:39:56 as **
  • 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 **
  • The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff
    Journal of Computational Chemistry, Vol. 29, No. 12. (2008), pp. 1970-1981.
    by Magdalena Gruziel, Pawel Grochowski, Joanna Trylska
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-03 15:54:27 as ** along with 1 person and 2 groups barry McCammon structural_bioinformatics
  • A molecular mechanics force field for lignin
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Loukas Petridis, Jeremy C Smith
    posted to md ligand by RamuAnandakrishnan on 2008-08-03 15:37:26 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 **
  • 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 **
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