DOI: 10.1371/journal.pone.0039918. Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations

10.1371/journal.pone.0039918

Crossref journal-article

Public Library of Science (PLoS)

PLoS ONE (340)

Bibliography

Piana, S., Lindorff-Larsen, K., Dirks, R. M., Salmon, J. K., Dror, R. O., & Shaw, D. E. (2012). Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations. PLoS ONE, 7(6), e39918.

Authors 6

Stefano Piana (first)
Kresten Lindorff-Larsen (additional)
Robert M. Dirks (additional)
John K. Salmon (additional)
Ron O. Dror (additional)
David E. Shaw (additional)

References 39 Referenced 89

10.1016/j.sbi.2009.03.004 / Curr Opin Struct Biol / Long-timescale molecular dynamics simulations of protein structure and function. by JL Klepeis (2009)
10.1126/science.1187409 / Science / Atomic-level characterization of the structural dynamics of proteins. by DE Shaw (2010)
10.1145/2063384.2063465 / Copernicus: a new paradigm for parallel adaptive molecular dynamics. Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC11). by S Pronk (2011)
10.1021/ja106936n / J Am Chem Soc / Atomistic folding simulations of the five-helix bundle protein λ(6−85). by GR Bowman (2011)
10.1016/j.jmgm.2010.06.010 / J Mol Graph Model / GPU-accelerated molecular modeling coming of age. by JE Stone (2011)
10.1085/jgp.200910373 / J Gen Physiol / Exploring atomic resolution physiology on a femtosecond to millisecond timescale using molecular dynamics simulations. by RO Dror (2010)
10.1007/s10822-011-9497-y / J Comput Aided Mol Des / Let’s get honest about sampling. by DL Mobley (2012)
10.1002/jcc.540150702 / J Comp Chem / New spherical-cutoff methods for long-range forces in macromolecular simulation. by PJ Steinbach (1994)
10.1146/annurev.biophys.28.1.155 / Annu Rev Biophys Biomol Struct / Molecular dynamics simulations of biomolecules: long-range electrostatic effects. by C Sagui (1999)
10.1021/bi0486381 / Biochemistry / Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. by DAC Beck (2005)
10.1016/S0006-3495(00)76405-8 / Biophys J / On the truncation of long-range electrostatic interactions in DNA. by J Norberg (2000)
10.1063/1.3558787 / J Chem Phys / Communication: shifted forces in molecular dynamics. by S Toxvaerd (2011)
10.1063/1.2354486 / J Chem Phys / Dynamical motions of lipids and a finite size effect in simulations of bilayers. by JB Klauda (2006)
10.1016/S0006-3495(03)75094-2 / Biophys J / Molecular dynamics simulations of lipid bilayers: major artifacts due to truncating electrostatic interactions. by M Patra (2003)
10.1021/jp9614658 / J Phys Chem / Effect of electrostatic force truncation on interfacial and transport properties of water. by SE Feller (1996)
10.1002/jcc.20828 / J Comput Chem / Effects of long-range electrostatic forces on simulated protein folding kinetics. by A Robertson (2008)
10.1016/j.jmb.2006.03.034 / J Mol Biol / Sub-microsecond protein folding. by J Kubelka (2006)
10.1002/jcc.10349 / J Comput Chem / A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. by Y Duan (2003)
10.1016/j.bpj.2011.03.051 / Biophys J / How robust are protein folding simulations with respect to force field parameterization? by S Piana (2011)
10.1073/pnas.1010880108 / Proc Natl Acad Sci U S A / Quantitative comparison of villin headpiece subdomain simulations and triplet–triplet energy transfer experiments. by KA Beauchamp (2011)
10.1016/j.jmb.2007.09.069 / J Mol Biol / Heterogeneity even at the speed limit of folding: large-scale molecular dynamics study of a fast-folding variant of the villin headpiece. by DL Ensign (2007)
10.1063/1.2206581 / J Chem Phys / Is the Ewald summation still necessary? Pairwise alternatives to the accepted standard for long-range electrostatics. by CJ Fennell (2006)
{'key': 'ref23', 'article-title': 'Millisecond-scale molecular dynamics simulations on Anton. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC09).', 'author': 'DE Shaw', 'year': '2009'} / Millisecond-scale molecular dynamics simulations on Anton. In Proceedings of the ACM/IEEE Conference on Supercomputing (SC09). by DE Shaw (2009)
10.1371/journal.pone.0032131 / PLoS ONE / Systematic validation of protein force fields against experimental data. by K Lindorff-Larsen (2012)
10.1063/1.1839571 / J Chem Phys / Gaussian split Ewald: a fast Ewald mesh method for molecular simulation. by Y Shan (2005)
10.1126/science.1208351 / Science / How fast-folding proteins fold. by K Lindorff-Larsen (2011)
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10.1103/PhysRevA.31.1695 / Phys Rev A / Canonical dynamics: equilibrium phase-space distributions. by WG Hoover (1985)
10.1063/1.463137 / J Chem Phys / Reversible multiple time scale molecular dynamics. by M Tuckerman (1992)
10.1063/1.2431176 / J Chem Phys / A common, avoidable source of error in molecular dynamics integrators. by RA Lippert (2007)
10.1063/1.467468 / J Chem Phys / Constant pressure molecular dynamics algorithms. by GJ Martyna (1994)
10.1063/1.440484 / J Chem Phys / The stable states picture of chemical reactions. I. Formulation for rate constants and initial condition effects. by SH Northrup (1980)
10.1021/jp0761665 / J Phys Chem B / Coarse master equations for peptide folding dynamics. by N-V Buchete (2008)
10.1021/jp0735987 / J Phys Chem B / Accurate and efficient corrections for missing dispersion interactions in molecular simulations. by MR Shirts (2007)
10.1038/35018538 / Nature / Optimal shapes of compact strings. by A Maritan (2000)
10.1021/ja209931w / J Am Chem Soc / Structure and dynamics of an unfolded protein examined by molecular dynamics simulation. by K Lindorff-Larsen (2012)
10.1021/j100358a012 / J Phys Chem / Acceleration of convergence for lattice sums. by N Karasawa (1989)
10.1063/1.457480 / J Chem Phys / Error estimates on averages of correlated data. by H Flyvbjerg (1989)
10.1002/prot.340230412 / Proteins / Knowledge-based protein secondary structure assignment. by D Frishman (1995)

Dates

Type	When
Created	13 years, 1 month ago (June 29, 2012, 5:40 p.m.)
Deposited	6 years, 10 months ago (Oct. 22, 2018, 11:26 a.m.)
Indexed	3 weeks, 6 days ago (Aug. 2, 2025, 12:32 a.m.)
Issued	13 years, 2 months ago (June 29, 2012)
Published	13 years, 2 months ago (June 29, 2012)
Published Online	13 years, 2 months ago (June 29, 2012)

Funders 0

None

BibTeX

@article{Piana_2012, title={Evaluating the Effects of Cutoffs and Treatment of Long-range Electrostatics in Protein Folding Simulations}, volume={7}, ISSN={1932-6203}, url={http://dx.doi.org/10.1371/journal.pone.0039918}, DOI={10.1371/journal.pone.0039918}, number={6}, journal={PLoS ONE}, publisher={Public Library of Science (PLoS)}, author={Piana, Stefano and Lindorff-Larsen, Kresten and Dirks, Robert M. and Salmon, John K. and Dror, Ron O. and Shaw, David E.}, editor={Verma, Chandra}, year={2012}, month=jun, pages={e39918} }

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