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RamuAnandakrishnan's library [201 articles]

Recent papers added to RamuAnandakrishnan's library.
  • 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 2 people jmccammon zwang
  • 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 3 people 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
  • A general method applicable to the search for similarities in the amino acid sequence of two proteins
    Journal of Molecular Biology, Vol. 48, No. 3. (28 March 1970), pp. 443-453.
    by Saul B Needleman, Christian D Wunsch
    posted to genome evolution by RamuAnandakrishnan on 2008-05-05 15:17:53 as ** along with 2 people BioNica adijr
  • Scheffe's More Powerful F-Protected Post Hoc Procedure
    Journal of Educational and Behavioral Statistics, Vol. 25, No. 1. (2000), pp. 13-19.
    by Alan J Klockars, Gregory R Hancock
    posted to statistics genome evolution by RamuAnandakrishnan on 2008-04-29 20:45:51 as **
  • Why highly expressed proteins evolve slowly.
    Proc Natl Acad Sci U S A (21 September 2005)
    by D Allan A Drummond, Jesse D D Bloom, Christoph Adami, Claus O O Wilke, Frances H H Arnold
    posted to genome evolution by RamuAnandakrishnan on 2008-04-29 18:59:09 as ** along with 14 people and 5 groups wilbur balicea rklancer stevanspringer bjorns imouthesmp aprasad dayjm Einat marcius xwbcn penka balabu malcook structural_bioinformatics Nie FAB-lab BioinfoCIPF SGU-CIPF
  • A Combined Empirical and Mechanistic Codon Model
    Molecular Biology and Evolution, Vol. 24, No. 2. (February 2007), pp. 388-397.
    by Doron-Faigenboim, Adi, Pupko, Tal
    posted to genome evolution by RamuAnandakrishnan on 2008-04-29 17:20:40 as **
  • The correlation between relatives on the supposition of mendelian inheritence
    Transactions of the Royal Society of Edinburgh, Vol. 52 (1918), pp. 399-433.
    by RA Fisher
    posted to genome general_interest evolution by RamuAnandakrishnan on 2008-04-28 19:36:47 as **
  • Evolutionary systems biology: links between gene evolution and function
    Current Opinion in Biotechnology, Vol. 17, No. 5. (October 2006), pp. 481-487.
    by Eugene V Koonin, Yuri Wolf
    posted to genome ewald by RamuAnandakrishnan on 2008-04-28 17:41:20 as ** along with 1 person tny
  • The rates of evolution in some ribosomal components
    Journal of Molecular Evolution, Vol. 9, No. 3. (1977), pp. 191-201.
    by Hiroshi Hori, Ken-Ichi Higo, Syozo Osawa
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 17:10:40 as **
  • Fluctuating mutation bias and the evolution of base composition in Drosophila.
    Journal of molecular evolution, Vol. 50, No. 1. (January 2000), pp. 1-10.
    by F Rodríguez-Trelles, R Tarrío, FJ Ayala
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 16:53:07 as **
  • Expected Relationship Between the Silent Substitution Rate and the GC Content: Implications for the Evolution of Isochores
    Journal of Molecular Evolution, Vol. 54, No. 1. (24 January 2002), pp. 129-133.
    by Gwenaël Piganeau, Dominique Mouchiroud, Laurent Duret, Christian Gautier
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 16:31:00 as **
  • The Covariation Between TpA Deficiency, CpG Deficiency, and G+C Content of Human Isochores Is Due to a Mathematical Artifact
    Mol Biol Evol, Vol. 17, No. 11. (1 November 2000), pp. 1620-1625.
    by Laurent Duret, Nicolas Galtier
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 16:22:21 as **
  • Population genetics of duplicated disease-defense genes, hm1 and hm2, in maize (Zea mays ssp. mays L.) and its wild ancestor (Zea mays ssp. parviglumis).
    Genetics, Vol. 162, No. 2. (October 2002), pp. 851-860.
    by L Zhang, AS Peek, D Dunams, BS Gaut
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 15:21:58 as **
  • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
    Nucleic Acids Research, Vol. 34, No. web server issue. (2006), pp. W609-W612.
    by Mikita Suyama, David Torrents, Peer Bork
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 02:15:38 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 **
  • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    Mol Biol Evol (4 May 2007), msm088.
    by Ziheng Yang
    posted to genome evolution by RamuAnandakrishnan on 2008-04-28 01:57:13 as ** along with 7 people and 1 group CharlesM operon akifumi hdopazo BioNica stajich ryanraaum Berkeley Mycology
  • The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 102-105.
    by E Huala, AW Dickerman, M Garcia-Hernandez, D Weems, L Reiser, F LaFond, D Hanley, D Kiphart, M Zhuang, W Huang, LA Mueller, D Bhattacharyya, D Bhaya, BW Sobral, W Beavis, DW Meinke, CD Town, C Somerville, SY Rhee
    posted to genome evolution by RamuAnandakrishnan on 2008-04-27 14:23:44 as ** along with 1 person natstreet
  • Chromosomal location effects on gene sequence evolution in mammals
    Vol. 9, pp. 786-791.
    by Giorgio Matassi, Paul M Sharp, Christian Gautier
    posted to genome evolution by RamuAnandakrishnan on 2008-04-27 02:05:51 as **
  • The proteins of linked genes evolve at similar rates
    Nature, Vol. 407 (2000), pp. 900-903.
    by Elizabeth JB Williams, Laurence D Hurst
    posted to genome evolution by RamuAnandakrishnan on 2008-04-27 00:47:56 as **
  • Evolution by gene duplication: an update
    Trends in Ecology & Evolution, Vol. 18, No. 6. (June 2003), pp. 292-298.
    by Jianzhi Zhang
    posted to genome evolution by RamuAnandakrishnan on 2008-04-26 22:50:31 as ** along with 2 people BioNica ruvido
  • Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Timothy J Giese, Darrin M York
    posted to multipole explicit_solvent electrostatics by RamuAnandakrishnan on 2008-04-24 13:50:18 as ** along with 1 person middledomain
  • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
    Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43.
    by Z Yang, R Nielsen
    posted to evolution genome by RamuAnandakrishnan on 2008-04-21 21:50:04 as ** along with 8 people and 1 group bjorns fernan hdopazo BioNica timflutre Garamonfok ankur_iitg Ema BioinfoCIPF
  • Calculating the electrostatic potential of molecules in solution: Method and error assessment
    Journal of Computational Chemistry, Vol. 9, No. 4. (1988), pp. 327-335.
    by Michael K Gilson, Kim A Sharp, Barry H Honig
    posted to electrostatics implicit_solvent by RamuAnandakrishnan on 2008-04-21 15:11:03 as **
  • Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme
    (17 Sep 2007)
    by L Delle Site
    posted to coarse_grain electrostatics md by RamuAnandakrishnan on 2008-04-16 20:41:19 as **
  • On the optimal contact potential of proteins
    Chemical Physics Letters, Vol. 451, No. 1-3. (17 January 2008), pp. 132-135.
    by Akira R Kinjo, Sanzo Miyazawa
    posted to contact folding by RamuAnandakrishnan on 2008-04-11 14:31:48 as **
  • Local conservation scores without a priori assumptions on neutral substitution rates
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Janis Dingel, Pavol Hanus, Niccolo Leonardi, Joachim Hagenauer, Juergen Zech, Jakob Mueller
    posted to evolution genome by RamuAnandakrishnan on 2008-04-11 14:25:54 as ** along with 3 people and 2 groups aprasad maximilianh cisevol cis-regulatory-evolution BergmanLab
  • VMD: Visual molecular dynamics
    Journal of Molecular Graphics, Vol. 14, No. 1. (February 1996), pp. 33-38.
    by William Humphrey, Andrew Dalke, Klaus Schulten
    posted to structure visualization by RamuAnandakrishnan on 2008-03-28 19:31:15 as ** along with 1 person tji
  • 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
  • Continuum Electrostatics Fails to Describe Ion Permeation in the Gramicidin Channel
    Biophys. J., Vol. 83, No. 3. (1 September 2002), pp. 1348-1360.
    by Scott Edwards, Ben Corry, Serdar Kuyucak, Shin-Ho Chung
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-28 18:31:12 as **
  • Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations
    Journal of Computational Chemistry, Vol. 23, No. 13. (2002), pp. 1211-1219.
    by Pekka Mark, Lennart Nilsson
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2008-03-28 15:22:19 as **
  • Ewald summation techniques in perspective: a survey
    Computer Physics Communications, Vol. 95, No. 2-3. (June 1996), pp. 73-92.
    by Abdulnour Y Toukmaji, John A Board
    posted to electrostatics ewald by RamuAnandakrishnan on 2008-03-28 14:57:44 as ** along with 1 person softsimu
  • 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
  • Molecular Dynamics: Survey of Methods for Simulating the Activity of Proteins
    Chemical Reviews, Vol. 106, No. 5., pp. 1589-1615.
    by SA Adcock, JA Mccammon
    posted to md by RamuAnandakrishnan on 2008-03-26 18:18:28 as **
  • A Computational Study of Nucleosomal DNA Flexibility
    Biophys. J., Vol. 91, No. 11. (1 December 2006), pp. 4121-4132.
    by Jory Z Ruscio, Alexey Onufriev
    posted to md by RamuAnandakrishnan on 2008-03-24 16:53:29 as **
  • Convergence of molecular dynamics simulations of membrane proteins.
    Proteins (22 January 2007)
    by Alan Grossfield, Scott E E Feller, Michael C C Pitman
    posted to electrostatics md by RamuAnandakrishnan on 2008-03-24 14:34:24 as ** along with 1 person dimka
  • Bending of DNA by Asymmetric Charge Neutralization: All-Atom Energy Simulations
    J. Am. Chem. Soc., Vol. 124, No. 17. (1 May 2002), pp. 4838-4847.
    by KM Kosikov, AA Gorin, XJ Lu, WK Olson, GS Manning
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-17 16:06:20 as **
  • Accurate Representation of B-DNA Double Helical Structure with Implicit Solvent and Counterions
    Biophys. J., Vol. 83, No. 1. (1 July 2002), pp. 382-406.
    by Lihua Wang, Brian E Hingerty, AR Srinivasan, Wilma K Olson, Suse Broyde
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-17 16:03:35 as **
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