RamuAnandakrishnan's md [103 articles] Export

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	Protein Motions at Zero-Total Angular Momentum: The Importance of Long-Range Correlations [My Copy] Vol. 79, No. 6. (1 December 2000), pp. 2902-2908. by Yaoqi Zhou, Michael Cook, Martin Karplus posted to md energy_conservation by RamuAnandakrishnan on 2009-11-23 02:33:39 as
	Correct virial formulation in the isotropic periodic sum method [My Copy] The Journal of Chemical Physics, Vol. 131, No. 16. (2009), 164103. by Iordan H. Hristov, Reginald Paul, Stephen J. Paddison posted to md by RamuAnandakrishnan on 2009-10-24 01:37:53 as
	Scaling of Multimillion-Atom Biological Molecular Dynamics Simulation on a Petascale Supercomputer [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Roland Schulz, Benjamin Lindner, Loukas Petridis, Jeremy C. Smith posted to md by RamuAnandakrishnan on 2009-09-30 00:03:39 as along with 1 person r2s2
	Evaluating the Performance of the ff99SB Force Field Based on NMR Scalar Coupling Data [My Copy] Vol. 97, No. 3. (5 August 2009), pp. 853-856. by Lauren Wickstrom, Asim Okur, Carlos Simmerling posted to md by RamuAnandakrishnan on 2009-08-12 13:22:40 as
	Free energy simulations reveal a double mutant avian H5N1 virus hemagglutinin with altered receptor binding specificity [My Copy] Journal of Computational Chemistry, Vol. 30, No. 11. (27 August 2009), pp. 1654-1663. by Payel Das, Jingyuan Li, Ajay K. Royyuru, Ruhong Zhou posted to md by RamuAnandakrishnan on 2009-07-29 15:31:13 as along with 3 people oceanwind idoerg zwang
	Molecular dynamics simulation exploration of cooperative migration mechanism of calcium ions in sarcoplasmic reticulum Ca<SUP><FONT SIZE='-1'>2+</FONT></SUP>-ATPase [My Copy] Journal of Computational Chemistry, Vol. 30, No. 13. (2009), pp. 2136-2145. by Yongqi Huang, Huifang Li, Yuxiang Bu posted to md by RamuAnandakrishnan on 2009-07-29 15:11:36 as
	Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles [My Copy] Vol. 14, No. 10. (1 October 2006), pp. 1527-1534. by Filip Lankaa, Richard Lavery, John H. Maddocks posted to md by RamuAnandakrishnan on 2009-07-08 23:16:55 as
	Accelerating molecular dynamic simulation on graphics processing units [My Copy] Journal of Computational Chemistry, Vol. 30, No. 6. (2009), pp. 864-872. by Mark S. Friedrichs, Peter Eastman, Vishal Vaidyanathan, et al.Mike Houston, Scott Legrand, Adam L. Beberg, Daniel L. Ensign, Christopher M. Bruns, Vijay S. Pande posted to gpu md by RamuAnandakrishnan on 2009-02-04 14:40:22 as along with 11 people and 3 groups oteri anuragsethi kevinchannon flbarroso r2s2 iantunbridge ihaque sobolevnrm ruvido massivemayhem barry baker-group structural_bioinformatics McCammon
	Efficient table lookup without inverse square roots for calculation of pair wise atomic interactions in classical simulations [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Lennart Nilsson posted to md by RamuAnandakrishnan on 2008-12-18 15:34:44 as along with 1 person middledomain
	Interplay of local hydrogen-bonding and long-ranged dipolar forces in simulations of confined water [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 49. (December 2008), pp. 19136-19141. by Jocelyn M. Rodgers, John D. Weeks posted to cutoff explicit_solvent md by RamuAnandakrishnan on 2008-12-10 01:53:28 as
	Ten-microsecond MD simulation of a fast-folding WW domain [My Copy] Biophys. J. (13 March 2008), biophysj.108.131565. by Peter L. Freddolino, Feng Liu, Martin H. Gruebele, Klaus Schulten posted to explicit_solvent folding md by RamuAnandakrishnan on 2008-10-09 00:09:39 as along with 7 people and 1 group r2s2 flbarroso doktornoe paulschlesinger skoch3 samjlord biehl Koch_Lab
	Scalable molecular dynamics with NAMD on the IBM Blue Gene/L system [My Copy] IBM Journal of Research and Development, Vol. 52, No. 1/2. (2008), pp. 177-187. by S. Kumar, C. Huang, G. Zheng, et al.E. Bohm, A. Bhatele, J. C. Phillips, H. Yu, L. V. Kalé posted to md by RamuAnandakrishnan on 2008-09-08 19:47:13 as
	Massively parallel molecular dynamics simulations of lysozyme unfolding [My Copy] IBM Journal of Research and Development, Vol. 52, No. 1/2. (2008), pp. 19-19. by R. Zhou, M. Eleftheriou, C. C. Hon, R. S. Germain, A. K. Royyuru, B. J. Berne posted to md by RamuAnandakrishnan on 2008-09-08 19:37:40 as
	Anton, a special-purpose machine for molecular dynamics simulation [My Copy] Communications of the ACM, Vol. 51, No. 7. (2008), pp. 91-97. by David E. Shaw, Martin M. Deneroff, Ron O. Dror, et al.Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. 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 [My Copy] 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 4 people gsub kaz229 jheco 6rheology
	Structure and Dynamics of Interphase Chromosomes [My Copy] 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. [My Copy] Protein science : a publication of the Protein Society, Vol. 1, No. 9. (September 1992), pp. 1185-1205. by J. Guenot, P. A. 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. [My Copy] Proteins, Vol. 6, No. 1. (1989), pp. 32-45. by R. J. Loncharich, B. R. Brooks posted to cutoff md by RamuAnandakrishnan on 2008-08-18 15:39:56 as
	A molecular mechanics force field for lignin [My Copy] 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 [My Copy] 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 along with 1 person saravan
	Application of MDGRAPE-3, a special purpose board for molecular dynamics simulations, to periodic biomolecular systems [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Gota Kikugawa, Rossen Apostolov, Narutoshi Kamiya, et al.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 [My Copy] Journal of Computational Chemistry, Vol. 30, No. 2. (2009), pp. 268-274. by Edgar Luttmann, Daniel L. Ensign, Vishal Vaidyanathan, et al.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 along with 2 people cwr choonpeng
	Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin [My Copy] Proceedings of the National Academy of Sciences, Vol. 105, No. 27. (2008), 9204. by Jory Z. Ruscio, Deept Kumar, Maulik Shukla, Michael G. Prisant, T. M. 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 [My Copy] 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 along with 1 person dfgreen
	Molecular dynamics simulations of biomolecules. [My Copy] Nat Struct Biol, Vol. 9, No. 9. (September 2002), pp. 646-652. by M. Karplus, J. A. McCammon posted to md by RamuAnandakrishnan on 2008-06-18 14:55:36 as along with 8 people saravan yxue onufriev adilson_mohr yalexeev baaden aqeel LamBras
	Some fundamental problems for an energy-conserving adaptive-resolution molecular dynamics scheme [My Copy] 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. [My Copy] Science (New York, N.Y.), Vol. 282, No. 5389. (23 October 1998), pp. 740-744. by Y. Duan, P. A. Kollman posted to electrostatics folding md by RamuAnandakrishnan on 2008-05-28 21:44:59 as along with 7 people krapnik flbarroso doktornoe Diego_Prada j3xucite allmensch choonpeng
	Multiscale Simulation of Soft Matter: From Scale Bridging to Adaptive Resolution [My Copy] 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 5 people and 1 group loison whitead flbarroso rok softsimu Jiang Research Group
	Some fundamental problems for an energy conserving adaptive resolution molecular dynamics scheme [My Copy] (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 [My Copy] 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 [My Copy] 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 [My Copy] Chemical Reviews, Vol. 106, No. 5., pp. 1589-1615. by S. A. Adcock, J. A. Mccammon posted to md by RamuAnandakrishnan on 2008-03-26 18:18:28 as
	A Computational Study of Nucleosomal DNA Flexibility [My Copy] 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
	Bending of DNA by Asymmetric Charge Neutralization: All-Atom Energy Simulations [My Copy] J. Am. Chem. Soc., Vol. 124, No. 17. (1 May 2002), pp. 4838-4847. by K. M. Kosikov, A. A. Gorin, X. J. Lu, W. K. Olson, G. S. 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 [My Copy] Biophys. J., Vol. 83, No. 1. (1 July 2002), pp. 382-406. by Lihua Wang, Brian E. Hingerty, A. R. 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 [My Copy] 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 [My Copy] 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 [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2008), NA. by Juan Torras, Gustavo, Erik Deumens, S. B. 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 [My Copy] Journal of Computational Chemistry, Vol. 29, No. 9. (2008), pp. 1429-1439. 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 3 people barmak7282 Elena_Zubova onufriev
	Computational prediction of the binding site of proteinase 3 to the plasma membrane [My Copy] 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 [My Copy] 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 [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2007), NA. by Anna C. V. 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. [My Copy] Proc Natl Acad Sci U S A, Vol. 103, No. 4. (24 January 2006), pp. 915-920. by V. Hornak, A. Okur, R. C. Rizzo, C. Simmerling posted to amber implicit_solvent md by RamuAnandakrishnan on 2007-12-14 16:16:11 as along with 3 people dfgreen aqeel allmensch
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by David A. Case, Thomas E. Cheatham, Tom Darden, et al.Holger Gohlke, Ray Luo, Kenneth M. Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J. Woods posted to amber explicit_solvent implicit_solvent md by RamuAnandakrishnan on 2007-12-14 15:57:53 as along with 18 people and 3 groups krapnik csrocha nickolay mmuecke flbarroso charris5 pavanghatty tahereh62 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 [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1113-1130. 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 5 people and 1 group ras Elena_Zubova sobolevnrm onufriev dimka baker-group
	The implementation of a fast and accurate QM/MM potential method in Amber [My Copy] Journal of Computational Chemistry, Vol. 29, No. 7. (2008), pp. 1019-1031. 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 2 people onufriev softsimu
	A hierarchy of timescales in protein dynamics is linked to enzyme catalysis [My Copy] 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 9 people and 1 group Diego_Prada ruvido tmmurali allmensch cactus sobolevnrm jlh64 dmobley chenway baker-group
	Convergence of molecular dynamics simulations of membrane proteins [My Copy] 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 [My Copy] 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 [My Copy] Biopolymers, Vol. 56, No. 4. (4 December 2000), 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 5 people Vadikus oteri flbarroso Lombardo_7 ttjoseph

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md	103
electrostatics	67
pka	57
evolution	57
folding	54
implicit_solvent	52
genome	43
qualifier	26
coarse_grain	22
ligand	14
contact	13
nucleosome	13
force_field	11
gb	11
statistical_mechanics	10
gpu	10
cutoff	10
explicit_solvent	10
pk	9
general_interest	7
molecular_dynamics	6
amber	6
ewald	6
multipole	6
multi_timescale	6
energy_conservation	5
binding_site	4
pb	4
chemical_kinetics	4
numerical_error	3
homology	3
newtons_identity	2
implicit_explicit	2
ulcerative_colitis	2
statistics	2
exponential_function	2
qm_mm	2
structure	2
protein_folding	1
constant_ph	1
parallel_computing	1
docking	1
mult_grid	1
remd	1
implicit	1
capsid	1
pdb	1
mutation_rate	1
thioredoxin	1
visualization	1
chromosome_dynamics	1
volume_integral	1
normal_mode_analysis	1
nucleic_acids	1
myoglobin	1
solvent	1
viral_capsid	1

RamuAnandakrishnan's md [103 articles] Export

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