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RamuAnandakrishnans md [94 articles]

Artikler nylig sendt til RamuAnandakrishnans bibliotek klassifisert med nøkkelordet md. You can also see everyone's md.
  • 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
  • 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 **
  • 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 **
  • 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 **
  • 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 **
  • 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 ligand md by RamuAnandakrishnan on 2008-08-03 15:37:26 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 **
  • 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 **
  • 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 implicit_solvent md 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 **
  • 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 electrostatics md by RamuAnandakrishnan on 2008-06-20 23:08:59 as **
  • 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 5 people yalexeev baaden aqeel simone LamBras
  • 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 cutoff electrostatics md 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 electrostatics folding md by RamuAnandakrishnan on 2008-05-28 21:44:59 as ** along with 3 people j3xucite allmensch choonpeng
  • 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 coarse_grain electrostatics md by RamuAnandakrishnan on 2008-05-21 13:42:03 as ** along with 1 person softsimu
  • 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 **
  • 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 **
  • 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 2 people dimka nigham
  • 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 **
  • Testing the Coulomb/Accessible Surface Area solvent model for protein stability, ligand binding, and protein design
    BMC Bioinformatics, Vol. 9 (13 March 2008), 148.
    by Marcel, Anne Lopes, Najette Amara, Christine Bathelt, Thomas Simonson
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-03-13 22:36:35 as ** along with 1 person GeeSharpMinor
  • The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Paul Labute
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2008-02-28 17:07:10 as ** along with 6 people and 1 group onufriev sobolevnrm middledomain sunhwan dmobley GermanErlenkamp baker-group
  • A versatile AMBER-Gaussian QM/MM interface through PUPIL
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Juan Torras, Gustavo, Erik Deumens, SB Trickey, Adrian E Roitberg
    posted to amber md qm_mm by RamuAnandakrishnan on 2008-02-13 14:41:45 as **
  • Coarse-grained force field for the nucleosome from self-consistent multiscaling
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA.
    by Karine Voltz, Joanna Trylska, Valentina Tozzini, Vandana Kurkal-Siebert, Jörg Langowski, Jeremy Smith
    posted to coarse_grain md nucleosome by RamuAnandakrishnan on 2008-02-13 14:39:41 as ** along with 1 person onufriev
  • Computational prediction of the binding site of proteinase 3 to the plasma membrane
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Eric Hajjar, Maja Mihajlovic, Véronique Witko-Sarsat, Themis Lazaridis, Nathalie Reuter
    posted to binding_site electrostatics implicit_solvent ligand md by RamuAnandakrishnan on 2008-01-07 14:43:43 as **
  • Structural and energetic effects of truncating long ranged interactions in ionic and polar fluids
    The Journal of Chemical Physics, Vol. 83, No. 11. (1985), pp. 5897-5908.
    by Charles L Brooks, Montgomery B Pettitt, Martin Karplus
    posted to cutoff md by RamuAnandakrishnan on 2007-12-17 21:27:23 as **
  • Position-resolved free energy of solvation for amino acids in lipid membranes from molecular dynamics simulations
    Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA.
    by Anna CV Johansson, Erik Lindahl
    posted to electrostatics explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-12-16 15:17:13 as ** along with 1 person and 1 group sobolevnrm baker-group
  • HIV-1 protease flaps spontaneously open and reclose in molecular dynamics simulations.
    Proc Natl Acad Sci U S A, Vol. 103, No. 4. (24 January 2006), pp. 915-920.
    by V Hornak, A Okur, RC Rizzo, C Simmerling
    posted to amber implicit_solvent md by RamuAnandakrishnan on 2007-12-14 16:16:11 as ** along with 3 people aqeel allmensch choonpeng
  • The Amber biomolecular simulation programs.
    J Comput Chem, Vol. 26, No. 16. (December 2005), pp. 1668-1688.
    by DA Case, TE Cheatham, T Darden, H Gohlke, R Luo, KM Merz, A Onufriev, C Simmerling, B Wang, RJ Woods
    posted to amber explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-12-14 15:57:53 as ** along with 10 people and 3 groups lna jwm ttjoseph xdeupi tovrstra bilab IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
  • Explicit ion, implicit water solvation for molecular dynamics of nucleic acids and highly charged molecules
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ninad V Prabhu, Manoranjan Panda, Qingyi Yang, Kim A Sharp
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-13 13:11:53 as ** along with 3 people and 1 group sobolevnrm onufriev dimka baker-group
  • The implementation of a fast and accurate QM/MM potential method in Amber
    Journal of Computational Chemistry, Vol. 9999, No. 9999. (2007), NA.
    by Ross C Walker, Michael F Crowley, David A Case
    posted to amber md qm_mm by RamuAnandakrishnan on 2007-12-11 13:11:59 as ** along with 1 person softsimu
  • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    Nature (18 November 2007)
    by Katherine A Henzler-Wildman, Ming Lei, Vu Thai, Jordan S Kerns, Martin Karplus, Dorothee Kern
    posted to md multi_timescale by RamuAnandakrishnan on 2007-12-10 14:47:57 as ** along with 7 people and 1 group tmmurali allmensch cactus sobolevnrm jlh64 dmobley chenway baker-group
  • Convergence of molecular dynamics simulations of membrane proteins
    Proteins: Structure, Function, and Bioinformatics, Vol. 67, No. 1. (2007), pp. 31-40.
    by Alan Grossfield, Scott E Feller, Michael C Pitman
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-04 22:49:47 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 2007-12-04 22:43:47 as **
  • Theory and applications of the generalized born solvation model in macromolecular simulations
    Biopolymers, Vol. 56, No. 4. (4 December 2001), pp. 275-291.
    by Vickie Tsui, David A Case
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 21:38:04 as ** along with 1 person ttjoseph
  • Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study
    Biophysical Chemistry, Vol. 78, No. 1-2. (5 April 1999), pp. 69-88.
    by PH Hunenberger, JA Mccammon
    posted to electrostatics ewald implicit_solvent md by RamuAnandakrishnan on 2007-12-03 21:02:33 as **
  • Biomolecular simulations: recent developments in force fields, simulations of enzyme catalysis, protein-ligand, protein-protein, and protein-nucleic acid noncovalent interactions.
    Annu Rev Biophys Biomol Struct, Vol. 30 (2001), pp. 211-243.
    by W Wang, O Donini, CM Reyes, PA Kollman
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-03 20:54:28 as ** along with 1 person ibuch
  • Cutoff Size Need Not Strongly Influence Molecular Dynamics Results for Solvated Polypeptides
    Biochemistry, Vol. 44, No. 2. (18 January 2005), pp. 609-616.
    by DAC Beck, RS Armen, V Daggett
    posted to cutoff electrostatics md by RamuAnandakrishnan on 2007-12-03 20:40:03 as **
  • Improving implicit solvent simulations: a Poisson-centric view.
    Curr Opin Struct Biol, Vol. 15, No. 2. (April 2005), pp. 137-143.
    by NA Baker
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 20:08:08 as ** along with 2 people ttjoseph qwermish
  • Generalized born models of macromolecular solvation effects.
    Annu Rev Phys Chem, Vol. 51 (2000), pp. 129-152.
    by D Bashford, DA Case
    posted to electrostatics implicit_solvent md by RamuAnandakrishnan on 2007-12-03 20:02:52 as ** along with 1 person dgront
  • Discretized model of proteins. I. Monte Carlo study of cooperativity in homopolypeptides
    The Journal of Chemical Physics, Vol. 97, No. 12. (1992), pp. 9412-9426.
    by Andrzej Kolinski, Jeffrey Skolnick
    posted to coarse_grain md by RamuAnandakrishnan on 2007-12-03 19:49:55 as **
  • Difficulties with multiple time stepping and fast multipole algorithm in molecular dynamics
    Journal of Computational Chemistry, Vol. 18, No. 14. (1997), pp. 1785-1791.
    by Thomas C Bishop, Robert D Skeel, Klaus Schulten
    posted to ewald md multipole by RamuAnandakrishnan on 2007-12-02 19:22:36 as **
  • Molecular Dynamics Simulations of a Polyalanine Octapeptide under Ewald Boundary Conditions: Influence of Artificial Periodicity on Peptide Conformation
    Journal of Physical Chemistry B, Vol. 104, No. 15. (2000), pp. 3668-3675.
    by W Weber, PH Hunenberger, JA Mccammon
    posted to ewald md by RamuAnandakrishnan on 2007-12-02 18:54:09 as **
  • A generalized reaction field method for molecular dynamics simulations
    The Journal of Chemical Physics, Vol. 102, No. 13. (1995), pp. 5451-5459.
    by Ilario G Tironi, René Sperb, Paul E Smith, Wilfred F van Gunsteren
    posted to electrostatics md by RamuAnandakrishnan on 2007-12-02 18:01:20 as **
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