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RamuAnandakrishnan's library [287 articles]

最近录入 RamuAnandakrishnan's ordered by to_read.
  • Pairwise covariance adds little to secondary structure prediction but improves the prediction of non-canonical local structure
    BMC Bioinformatics, Vol. 9 (10 October 2008), 429.
    by Christopher Bystroff, Bobbie-Jo Webb-Robertson
    posted to folding by RamuAnandakrishnan on 2008-10-11 14:59:59 as **
  • Ten-microsecond MD simulation of a fast-folding WW domain
    Biophys. J. (13 March 2008), biophysj.108.131565.
    by Peter L Freddolino, Feng Liu, Martin H Gruebele, Klaus Schulten
    posted to md folding explicit_solvent by RamuAnandakrishnan on 2008-10-09 00:09:39 as ** along with 4 people and 1 group paulschlesinger skoch3 samjlord biehl Koch_Lab
  • The effect of H3K79 dimethylation and H4K20 trimethylation on nucleosome and chromatin structure
    Nat Struct Mol Biol, Vol. 15, No. 10. (October 2008), pp. 1122-1124.
    by Xu Lu, Matthew D Simon, Jayanth V Chodaparambil, Jeffrey C Hansen, Kevan M Shokat, Karolin Luger
    posted to nucleosome by RamuAnandakrishnan on 2008-10-07 00:59:14 as **
  • Very fast prediction and rationalization of p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values for protein-ligand complexes
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2008), NA.
    by Delphine C Bas, David M Rogers, Jan H Jensen
    posted to pka by RamuAnandakrishnan on 2008-10-06 22:28:04 as ** along with 1 person and 1 group sobolevnrm baker-group
  • Very fast empirical prediction and rationalization of protein pKa values.
    Proteins, Vol. 61, No. 4. (1 December 2005), pp. 704-721.
    by H Li, AD Robertson, JH Jensen
    posted to pka by RamuAnandakrishnan on 2008-10-06 22:20:05 as ** along with 6 people and 1 group gisle bicko sim82 barry sunhwan mschofie Bioinformatics
  • Rates of Molecular Evolution Are Linked to Life History in Flowering Plants
    Science, Vol. 322, No. 5898. (3 October 2008), pp. 86-89.
    by Stephen A Smith, Michael J Donoghue
    posted to evolution by RamuAnandakrishnan on 2008-10-04 16:30:41 as ** along with 1 person dinnes
  • A rapid finite difference algorithm, utilizing successive over-relaxation to solve the Poisson-Boltzmann equation
    Journal of Computational Chemistry, Vol. 12, No. 4. (1991), pp. 435-445.
    by Anthony Nicholls, Barry Honig
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-10-03 22:56:36 as **
  • Electrostatic Interactions in Macromolecules: Theory and Applications
    Annual Review of Biophysics and Biophysical Chemistry, Vol. 19, No. 1. (1990), pp. 301-332.
    by KA Sharp, B Honig
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-10-03 22:51:17 as **
  • Protonate3D: Assignment of ionization states and hydrogen coordinates to macromolecular structures
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 999A. (2008), NA.
    by Paul Labute
    posted to pka by RamuAnandakrishnan on 2008-09-16 23:14:47 as ** along with 2 people barry middledomain
  • Molecular Dynamics Simulations of Nucleic Acids with a Generalized Born Solvation Model
    Journal of the American Chemical Society, Vol. 122 (2000), pp. 2489-2498.
    by Vickie Tsui, David A Case
    posted to implicit_explicit gb by RamuAnandakrishnan on 2008-09-09 20:58:55 as **
  • An efficient hybrid explicit/implicit solvent method for biomolecular simulations.
    J Comput Chem, Vol. 25, No. 16. (December 2004), pp. 1967-1978.
    by MS Lee, FR Salsbury, MA Olson
    posted to implicit_explicit by RamuAnandakrishnan on 2008-09-09 20:44:04 as ** along with 1 person jwagoner
  • Comparison of generalized born and poisson models: Energetics and dynamics of HIV protease
    Journal of Computational Chemistry, Vol. 21, No. 4. (2000), pp. 295-309.
    by Laurent David, Ray Luo, Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-09 20:25:06 as **
  • Simulation of the Folding Equilibrium of α-Helical Peptides: A Comparison of the Generalized Born Approximation with Explicit Solvent
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 100, No. 24. (2003), pp. 13934-13939.
    by Hugh Nymeyer, Angel E García
    posted to pb implicit_solvent gb by RamuAnandakrishnan on 2008-09-09 20:14:57 as **
  • AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling
    Journal of Computational Chemistry, Vol. 25, No. 4. (2004), pp. 479-499.
    by Emilio Gallicchio, Ronald M Levy
    posted to implicit_solvent gb by RamuAnandakrishnan on 2008-09-09 19:44:55 as ** along with 2 people jwagoner onufriev
  • An analytical approach to computing biomolecular electrostatic potential. I. Derivation and analysis
    The Journal of Chemical Physics, Vol. 129, No. 7. (2008)
    by Andrew T Fenley, John C Gordon, Alexey Onufriev
    posted to pb implicit_solvent by RamuAnandakrishnan on 2008-09-09 16:52:12 as ** along with 2 people afenley agrossfield
  • Accelerated Poisson-Boltzmann calculations for static and dynamic systems
    Journal of Computational Chemistry, Vol. 23, No. 13. (17 July 2002), pp. 1244-1253.
    by Ray Luo, Laurent David, Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:43:42 as **
  • Continuum Electrostatic Energies of Macromolecules in Aqueous Solutions
    J. Phys. Chem. A, Vol. 101, No. 43. (23 October 1997), pp. 8098-8106.
    by M Scarsi, J Apostolakis, A Caflisch
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:27:35 as ** along with 1 person onufriev
  • Theory of electrostatic interactions in macromolecules
    Current Opinion in Structural Biology, Vol. 5, No. 2. (April 1995), pp. 216-223.
    by Michael K Gilson
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:23:25 as **
  • Classical Electrostatics in Biology and Chemistry
    Science, Vol. 268 (1995), pp. 1144-1147.
    by Barry Honig, Anthony Nicholls
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 23:17:00 as ** along with 1 person qwermish
  • Generalized Born Model with a Simple, Robust Molecular Volume Correction
    J. Chem. Theory Comput., Vol. 3, No. 1. (9 January 2007), pp. 156-169.
    by J Mongan, C Simmerling, JA Mccammon, DA Case, A Onufriev
    posted to implicit_solvent by RamuAnandakrishnan on 2008-09-08 22:43:38 as **
  • Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system
    IBM Journal of Research and Development, Vol. 52, No. 1/2. (2008), pp. 177-187.
    by S Kumar, C Huang, G Zheng, E Bohm, A Bhatele, JC Phillips, H Yu, LV Kalé
    posted to md by RamuAnandakrishnan on 2008-09-08 19:47:13 as **
  • Massively parallel molecular dynamics simulations of lysozyme unfolding
    IBM Journal of Research and Development, Vol. 52, No. 1/2. (2008), pp. 19-19.
    by R Zhou, M Eleftheriou, CC Hon, RS Germain, AK Royyuru, BJ Berne
    posted to md by RamuAnandakrishnan on 2008-09-08 19:37:40 as **
  • Anton, a special-purpose machine for molecular dynamics simulation
    Communications of the ACM, Vol. 51, No. 7. (2008), pp. 91-97.
    by David E Shaw, Martin M Deneroff, Ron O Dror, Jeffrey S Kuskin, Richard H Larson, John K Salmon, Cliff Young, Brannon Batson, Kevin J Bowers, Jack C Chao, Michael P Eastwood, Joseph Gagliardo, JP Grossman, Richard C Ho, Douglas J Ierardi, István Kolossváry, John L Klepeis, Timothy Layman, Christine Mcleavey, Mark A Moraes, Rolf Mueller, Edward C Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, Stanley C Wang
    posted to md by RamuAnandakrishnan on 2008-09-08 17:31:52 as **
  • Mesoscopic models of biological membranes
    Physics Reports, Vol. 437, No. 1-2. (December 2006), pp. 1-54.
    by Maddalena Venturoli, Maddalena, Marieke Kranenburg, Berend Smit
    posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 05:02:14 as ** along with 1 person choonpeng
  • Biological and synthetic membranes: What can be learned from a coarse-grained description?
    Physics Reports, Vol. 434, No. 5-6. (November 2006), pp. 113-176.
    by Marcus Muller, Kirill Katsov, Michael Schick
    posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:52:02 as ** along with 1 person loison
  • Usefulness and limitations of normal mode analysis in modeling dynamics of biomolecular complexes.
    Structure (Camb), Vol. 13, No. 3. (March 2005), pp. 373-380.
    by J Ma
    posted to normal_mode_analysis by RamuAnandakrishnan on 2008-09-04 04:46:59 as ** along with 4 people aqeel shuns simone higueruelo
  • Multiscale modeling of biomolecular systems: in serial and in parallel
    Current Opinion in Structural Biology, Vol. In Press, Corrected Proof
    by Gary S Ayton, Will G Noid, Gregory A Voth
    posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:41:43 as ** along with 2 people aqeel choonpeng
  • Coarse-grained models for proteins.
    Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 144-150.
    by V Tozzini
    posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:39:25 as ** along with 7 people baaden aqeel ltrabuco simone cottrell choonpeng iantunbridge
  • Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field
    J. Chem. Theory Comput., Vol. 4, No. 8. (12 August 2008), pp. 1386-1400.
    by Hujun Shen, Cezary Czaplewski, Adam Liwo, Harold A Scheraga
    posted to coarse_grain by RamuAnandakrishnan on 2008-09-04 04:35:01 as **
  • 1 Å crystal structures of B-DNA reveal sequence-specific binding and groove-specific bending of DNA by magnesium and calcium
    Journal of Molecular Biology, Vol. 301, No. 4. (25 August 2000), pp. 915-945.
    by Thang K Chiu, Richard E Dickerson
    posted to structure by RamuAnandakrishnan on 2008-08-29 13:57:46 as **
  • How Well Does Poisson-Boltzmann Implicit Solvent Agree with Explicit Solvent? A Quantitative Analysis
    J. Phys. Chem. B, Vol. 110 (2006), pp. 18680-18687.
    by CH Tan, LJ Yang, R Luo
    posted to explicit_solvent implicit_solvent by RamuAnandakrishnan on 2008-08-26 21:33:39 as **
  • Dynamics of entangled linear polymer melts: A molecular-dynamics simulation
    The Journal of Chemical Physics, Vol. 92, No. 8. (1990), pp. 5057-5086.
    by Kurt Kremer, Gary S Grest
    posted to coarse_grain md nucleosome by RamuAnandakrishnan on 2008-08-23 14:46:45 as ** along with 3 people kaz229 jheco 6rheology
  • Structure and Dynamics of Interphase Chromosomes
    PLoS Comput Biol, Vol. 4, No. 8. (2008), e1000153.
    by Angelo Rosa, Ralf Everaers
    posted to md nucleosome by RamuAnandakrishnan on 2008-08-23 14:35:26 as **
  • Network Legos: Building Blocks of Cellular Wiring Diagrams
    Journal of Computational Biology, Vol. 0, No. 0. (0), pp. 1-16.
    by TM Murali, Corban G Rivera
    posted to no-tag by RamuAnandakrishnan on 2008-08-23 04:52:20 as ** along with 3 people sjcockell tmmurali lptolik
  • Influence of nonlinear electrostatics on transfer energies between liquid phases: Charge burial is far less expensive than Born model
    Proceedings of the National Academy of Sciences, Vol. 105, No. 32. (2008), pp. 11146-11151.
    by Haipeng Gong, Glen Hocky, Karl F Freed
    posted to gb implicit_solvent pka by RamuAnandakrishnan on 2008-08-23 04:45:35 as **
  • An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications
    The Journal of Chemical Physics, Vol. 129, No. 7. (2008)
    by John C Gordon, Andrew T Fenley, Alexey Onufriev
    posted to implicit_solvent by RamuAnandakrishnan on 2008-08-22 23:53:40 as ** along with 1 person agrossfield
  • Comparison of simple potential functions for simulating liquid water
    The Journal of Chemical Physics, Vol. 79, No. 2. (1983), pp. 926-935.
    by William L Jorgensen, Jayaraman Chandrasekhar, Jeffry D Madura, Roger W Impey, Michael L Klein
    posted to force_field by RamuAnandakrishnan on 2008-08-22 23:29:06 as ** along with 8 people and 1 group mleis ttjoseph ffranca easybakemuffin ashaytan r2s2 pavanghatty Diego_Prada CMB
  • A polarizable model of water for molecular dynamics simulations of biomolecules
    Chemical Physics Letters, Vol. 418, No. 1-3. (25 January 2006), pp. 245-249.
    by Guillaume Lamoureux, Edward Harder, Igor V Vorobyov, Benoît Roux, Jr Mackerell
    posted to force_field by RamuAnandakrishnan on 2008-08-22 23:20:17 as **
  • Solution structure of the immunodominant region of protein G of bovine respiratory syncytial virus.
    Biochemistry, Vol. 35, No. 47. (26 November 1996), pp. 14684-14688.
    by JF Doreleijers, JP Langedijk, K Hård, R Boelens, JA Rullmann, WM Schaaper, JT van Oirschot, R Kaptein
    posted to no-tag by RamuAnandakrishnan on 2008-08-21 15:47:47 as **
  • Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics
    Chemical Reviews, Vol. 99, No. 8. (1999), pp. 2161-2200.
    by Christopher J Cramer, Donald G 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 explicit_solvent implicit_solvent md 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 7 people baaden lna allmensch choonpeng kazemi barry GermanErlenkamp
  • 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 cutoff md 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 structural_bioinformatics McCammon
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