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	Coarse Point Charge Models For Proteins From Smoothed Molecular Electrostatic Potentials [My Copy] Journal of Chemical Theory and Computation, Vol. 0, No. 0. (0000) by Laurence Leherte, Daniel P. Vercauteren posted to coarse_grain by RamuAnandakrishnan on 2009-11-04 21:01:20 as
	High Local Concentration: A Fundamental Strategy of Life [My Copy] Journal of Molecular Biology (31 October 2009) by Stefan Oehler, Benno Müller-Hill posted to no-tag by RamuAnandakrishnan on 2009-11-04 02:29:09 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
	Efficient nonbonded interactions for molecular dynamics on a graphics processing unit [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Peter Eastman, Vijay S. Pande posted to gpu by RamuAnandakrishnan on 2009-10-22 18:27:12 as along with 1 person klexa
	RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble [My Copy] RNA, Vol. 11, No. 8. (August 2005), pp. 1157-1166. by Y. E. Ding, Chi Y. U. Chan, Charles E. Lawrence posted to folding by RamuAnandakrishnan on 2009-10-22 14:49:16 as
	An image-based reaction field method for electrostatic interactions in molecular dynamics simulations of aqueous solutions [My Copy] The Journal of Chemical Physics, Vol. 131, No. 15. (2009), 154103. by Yuchun Lin, Andrij Baumketner, Shaozhong Deng, Zhenli Xu, Donald Jacobs, Wei Cai posted to implicit_solvent by RamuAnandakrishnan on 2009-10-16 04:17:40 as along with 1 person dlimmer
	Conserving energy during molecular dynamics simulations of water, proteins, and proteins in water [My Copy] Journal of Computational Chemistry, Vol. 11, No. 10. (1990), pp. 1169-1180. by Douglas B. Kitchen, Fumio Hirata, John D. Westbrook, Ronald Levy, David Kofke, Martin Yarmush posted to energy_conservation by RamuAnandakrishnan on 2009-10-02 17:52:16 as
	Correcting mesh-based force calculations to conserve both energy and momentum in molecular dynamics simulations [My Copy] Journal of Computational Physics, Vol. 225, No. 1. (01 July 2007), pp. 1-5. by R. Skeel, D. Hardy, J. Phillips posted to energy_conservation by RamuAnandakrishnan on 2009-10-01 14:31:49 as along with 1 person dmitry_s_yershov
	Universal Solvation Model Based on the Generalized Born Approximation with Asymmetric Descreening [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 9. (8 September 2009), pp. 2447-2464. by Aleksandr V. Marenich, Christopher J. Cramer, Donald G. Truhlar posted to gb by RamuAnandakrishnan on 2009-09-30 00:15:14 as along with 2 people sobolevnrm acpan
	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
	Nucleosome positioning as a determinant of exon recognition [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 9. (16 August 2009), pp. 996-1001. by Hagen Tilgner, Christoforos Nikolaou, Sonja Althammer, et al.Michael Sammeth, Miguel Beato, Juan Valcarcel, Roderic Guigo posted to nucleosome by RamuAnandakrishnan on 2009-09-04 13:49:54 as along with 4 people inesdesantiago sebastien_vigneau fenghezi aalibes
	Dynamics and function of compact nucleosome arrays. [My Copy] Nature structural & molecular biology, Vol. 16, No. 9. (September 2009), pp. 938-944. by Michael G. Poirier, Eugene Oh, Hannah S. Tims, Jonathan Widom posted to nucleosome by RamuAnandakrishnan on 2009-09-04 13:39:10 as along with 1 person sebastien_vigneau
	Accelerating Electrostatic Surface Potential Calculation with Multiscale Approximation on Graphics Processing Units [My Copy] (July 2009) by Ramu Nandakrishnan posted to gpu by RamuAnandakrishnan on 2009-08-12 19:49:06 as
	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
	Time for Computer Science to Grow Up [My Copy] Communications of the ACM, Vol. 52, No. 8., pp. 33-35. by Lance Fortnow edited by M. Communications Of The Ac posted to general_interest by RamuAnandakrishnan on 2009-08-11 13:05:59 as
	Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials [My Copy] Protein Science, Vol. 9999, No. 9999. (2009), NA. by Matsuyuki Shirota, Takashi Ishida, Kengo Kinoshita posted to folding by RamuAnandakrishnan on 2009-08-10 20:26:03 as
	Fast and faster: A designed variant of the B-domain of protein A folds in 3 musec [My Copy] Protein Science, Vol. 13, No. 4. (April 2004), pp. 847-853. by Pooja Arora, Terrence G. Oas, Jeffrey K. Myers posted to folding by RamuAnandakrishnan on 2009-08-08 15:20:06 as along with 1 person apaydin
	R/BHC: fast Bayesian hierarchical clustering for microarray data [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (6 August 2009), 242. by Richard Savage, Katherine Heller, Yang Xu, et al.Zoubin Ghahramani, William Truman, Murray Grant, Katherine Denby, David Wild posted to evolution by RamuAnandakrishnan on 2009-08-07 14:50:08 as along with 10 people and 1 group ptrobajo meanerelk nuin rdiaz guhjy lwaldron rschulz phoenixzxl barriot erexhepa Bioinformatics
	Improving detection of differentially expressed gene sets by applying cluster enrichment analysis to Gene Ontology [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (5 August 2009), 240. by Tao Xu, JianLei Gu, Yan Zhou, LinFang Du posted to evolution by RamuAnandakrishnan on 2009-08-07 03:35:28 as along with 9 people dipenps rdiaz tonamswish guhjy lwaldron dswan barriot kshameer renatomilani
	Approximate atomic surfaces from linear combinations of pairwise overlaps (LCPO) [My Copy] Journal of Computational Chemistry, Vol. 20, No. 2. (1999), pp. 217-230. by Jörg Weiser, Peter S. Shenkin, W. Clark Still posted to gb by RamuAnandakrishnan on 2009-08-04 19:14:30 as along with 1 person mijam
	Stabilization of protein structure by interaction of [alpha]-helix dipole with a charged side chain [My Copy] Nature, Vol. 335, No. 6192. (20 October 1988), pp. 740-743. by Dasa S[breve]ali, Mark Bycroft, Alan R. Fersht posted to pk by RamuAnandakrishnan on 2009-07-31 23:42:22 as
	The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability [My Copy] Biochemistry, Vol. 30, No. 30. (1 July 1991), pp. 7603-7609. by Knut Langsetmo, James A. Fuchs, Clare Woodward posted to pk by RamuAnandakrishnan on 2009-07-31 23:37:50 as
	Linkage of thioredoxin stability to titration of ionizable groups with perturbed pKa [My Copy] Biochemistry, Vol. 30, No. 30. (1 July 1991), pp. 7609-7614. by Knut Langsetmo, James A. Fuchs, Clare Woodward, Kim A. Sharp posted to pk by RamuAnandakrishnan on 2009-07-31 23:36:54 as
	Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II. [My Copy] Science (New York, N.Y.), Vol. 325, No. 5940. (31 July 2009), pp. 626-628. by Courtney Hodges, Lacramioara Bintu, Lucyna Lubkowska, Mikhail Kashlev, Carlos Bustamante posted to nucleosome by RamuAnandakrishnan on 2009-07-31 02:49:22 as along with 7 people and 1 group skoch3 emptyhb jbhiatt pkner absterga leliavski TRHvidsten Koch_Lab
	CLEAN: CLustering Enrichment ANalysis [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (29 July 2009), 234. by Johannes Freudenberg, Vineet Joshi, Zhen Hu, Mario Medvedovic posted to evolution by RamuAnandakrishnan on 2009-07-31 02:40:35 as along with 8 people brianb nuin rdiaz dswan guhjy frohike barriot renatomilani
	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
	The conserved, buried aspartic acid in oxidized Escherichia coli thioredoxin has a pKa of 7.5. Its titration produces a related shift in global stability. [My Copy] Biochemistry, Vol. 30, No. 30. (30 July 1991), pp. 7603-7609. by K. Langsetmo, J. A. Fuchs, C. Woodward posted to pk by RamuAnandakrishnan on 2009-07-28 18:45:42 as
	Protein folding roller coaster, one molecule at a time [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 29. (21 July 2009), pp. 11823-11824. by Eugene Shakhnovich posted to folding by RamuAnandakrishnan on 2009-07-23 13:39:39 as along with 1 person paulschlesinger
	How to obtain statistically converged MM/GBSA results [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Samuel Genheden, Ulf Ryde posted to no-tag by RamuAnandakrishnan on 2009-07-14 13:47:41 as along with 3 people and 1 group pmung barry sobolevnrm McCammon
	Error statistics of hidden Markov model and hidden Boltzmann model results [My Copy] BMC Bioinformatics, Vol. 10, No. 1. (2009), 212. by Lee Newberg posted to folding by RamuAnandakrishnan on 2009-07-09 23:48:03 as along with 2 people rdiaz erexhepa
	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
	An <I>N</I> log <I>N</I> approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Ramu Anandakrishnan, Alexey V. Onufriev posted to coarse_grain electrostatics by RamuAnandakrishnan on 2009-07-02 01:04:02 as along with 1 person sobolevnrm
	Fourier transform convolution integrals applied to generalized Born molecular volume [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Thierry Schüpbach, Vincent Zoete, Brice Tsakam-Sotché, Olivier Michielin posted to gb by RamuAnandakrishnan on 2009-06-27 14:26:43 as
	Inferring ideal amino acid interaction forms from statistical protein contact potentials. [My Copy] Proteins, Vol. 59, No. 1. (1 April 2005), pp. 49-57. by P. Pokarowski, A. Kloczkowski, R. L. Jernigan, N. S. Kothari, M. Pokarowska, A. Kolinski posted to folding by RamuAnandakrishnan on 2009-06-21 16:43:58 as along with 3 people mijam krapnik kgutwin
	Algorithmic design of self-assembling structures [My Copy] Proceedings of the National Academy of Sciences, Vol. 106, No. 24. (16 June 2009), pp. 9570-9575. by Henry Cohn, Abhinav Kumar posted to folding statistical_mechanics by RamuAnandakrishnan on 2009-06-19 14:16:05 as along with 2 people Scis0000002 mstumpf
	Molecular determinants of the p<I>K</I><SUB><FONT SIZE='-1'>a</FONT></SUB> values of Asp and Glu residues in staphylococcal nuclease [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Carlos A. Castañeda, Carolyn A. Fitch, Ananya Majumdar, Victor Khangulov, Jamie L. Schlessman, Bertrand E. García-Moreno posted to pk by RamuAnandakrishnan on 2009-06-19 14:06:33 as along with 2 people flbarroso sobolevnrm
	Integrated Assessment of Genomic Correlates of Protein Evolutionary Rate [My Copy] PLoS Comput Biol, Vol. 5, No. 6. (12 June 2009), e1000413. by Yu Xia, Eric A. Franzosa, Mark B. Gerstein posted to evolution by RamuAnandakrishnan on 2009-06-12 18:54:23 as along with 8 people and 1 group aprasad chica biomcgary gjuggler kiekyon michaelbarton djkt bpcusack Journal picks
	Contact prediction in protein modeling. Scoring, folding and refinement of coarse-grained models. [My Copy] BMC Structural Biology, Vol. 8 (11 August 2008), 36. by Dorota Latek, Andrzej Kolinski posted to folding by RamuAnandakrishnan on 2009-06-05 14:50:38 as along with 3 people mcbla sterl0601 j3xucite
	Residue contact-count potentials are as effective as residue-residue contact-type potentials for ranking protein decoys. [My Copy] BMC structural biology, Vol. 8 (08 December 2008), 53. by Dan M. Bolser, Ioannis Filippis, Henning Stehr, Jose Duarte, Michael Lappe posted to folding by RamuAnandakrishnan on 2009-06-05 14:43:24 as along with 3 people tcschen krapnik chad_davis
	Converging concepts of protein folding in vitro and in vivo [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 6. (03 June 2009), pp. 574-581. by F. Ulrich Hartl, Manajit Hayer-Hartl posted to folding by RamuAnandakrishnan on 2009-06-03 14:42:53 as along with 6 people bratwurst skywalkerus02 siggi84 scampos melo_mcr reyez
	Assessment of biomolecular force fields for molecular dynamics simulations in a protein crystal [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by Zhongqiao Hu, Jianwen Jiang posted to force_field by RamuAnandakrishnan on 2009-05-29 14:41:37 as
	Statistical potentials extracted from protein structures: how accurate are they? [My Copy] Journal of molecular biology, Vol. 257, No. 2. (29 March 1996), pp. 457-469. by P. D. Thomas, K. A. Dill posted to folding by RamuAnandakrishnan on 2009-05-26 22:40:24 as along with 1 person ashaytan
	Empirical potential function for simplified protein models: Combining contact and local sequence-structure descriptors. [My Copy] Proteins (13 February 2006) by Jinfeng Zhang, Rong Chen, Jie Liang posted to folding by RamuAnandakrishnan on 2009-05-26 22:35:25 as along with 3 people flbarroso wouterboomsma cdeane
	Energetic coupling between DNA bending and base pair opening [My Copy] Proceedings of the National Academy of Sciences of the United States of America, Vol. 85, No. 19. (October 1988), pp. 7231-7235. by J. Ramstein, R. Lavery posted to implicit solvent by RamuAnandakrishnan on 2009-05-19 23:30:24 as
	pH-Dependent Mechanism of Nitric Oxide Release in Nitrophorins 2 and 4 [My Copy] The Journal of Physical Chemistry B, Vol. 113, No. 4. (29 January 2009), pp. 1192-1201. by Jason M. Swails, Yilin Meng, Ann F. Walker, Marcelo A. Marti, Dario A. Estrin, Adrian E. Roitberg posted to constant_ph pk remd by RamuAnandakrishnan on 2009-05-19 21:33:49 as
	The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages [My Copy] Proceedings of the National Academy of Sciences (7 April 2009) by Yuri I. Wolf, Pavel S. Novichkov, Georgy P. Karev, Eugene V. Koonin, David J. Lipman posted to evolution by RamuAnandakrishnan on 2009-05-09 02:16:18 as along with 4 people and 1 group deanmalmgren jjray gjuggler rvosa FAB-lab
	Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber [My Copy] Nature Structural & Molecular Biology, Vol. 16, No. 5. (19 April 2009), pp. 534-540. by Maarten Kruithof, Fan-Tso Chien, Andrew Routh, Colin Logie, Daniela Rhodes, John van Noort posted to nucleosome by RamuAnandakrishnan on 2009-05-07 15:12:31 as along with 1 person ramalldf
	Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 9999, No. 9999. (2009), NA. by Weitao Sun, Jing He posted to folding by RamuAnandakrishnan on 2009-05-07 15:08:10 as along with 1 person and 1 group AliC Orengo Group Journal Picks
	Dynamic folding pathway models of the villin headpiece subdomain (HP-36) structure [My Copy] Journal of Computational Chemistry, Vol. 9999, No. 9999. (2009), NA. by In-Ho Lee, Seung-Yeon Kim, Jooyoung Lee posted to folding by RamuAnandakrishnan on 2009-05-05 13:31:40 as

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implicit_solvation	60
gb	49
molecular_dynamics	36
nucleosome	36
pb	25
protein_folding	24
pka	22
electrostatics	20
dna_bending	19
histone_acetylation	19
dna	18
dna_electrostatics	15
higher_order_chromatin	15
protein_ligand	15
nucleosome_stability	13
dna_ions	12
nucleosome_assembly	11
beyond_pb	8
ions	8
water_models	8
explicit_solvation	7
gb_membrane	7
myoglobin	7
protein_dynamics	7
protein_electrostatics	7
coarse-grain	6
dielectric_in_biopolymers	6
dna_ab	6
dna_nano	5
md_dna	5
pedagogical	5
polyamines	5
surface	5
dna_stacking	4
drug_design	4
multiscale	4
ph	4
phosphorylation	4
rnai	4
image_charge	3
molecular_geometry	3
qmmm	3
rna_sec_structure	3
water_in_biopolymers	3
dna_bend	2
dna_stretching	2
ewald	2
free_energy	2
physics_philosophy	2
br	1
charge_asymmetry	1
classical_mechanics	1
coarse_grain	1
dna_md	1
extremophile	1
hnox	1
monte_carlo	1
non_equilibrium_statmech	1
nucleosome_positioning	1
nucleus	1
performance	1
physics_fundamentals	1
protein_stability	1
time_scale	1
water_molecules	1

onufriev's watchlist [at least 200 articles] Export

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