Ensemble-based convergence analysis of biomolecular trajectories.

Biophysical Journal
Edward Lyman, Daniel M Zuckerman

Abstract

Assessing the convergence of a biomolecular simulation is an essential part of any careful computational investigation, because many fundamental aspects of molecular behavior depend on the relative populations of different conformers. Here we present a physically intuitive method to self-consistently assess the convergence of trajectories generated by molecular dynamics and related methods. Our approach reports directly and systematically on the structural diversity of a simulation trajectory. Straightforward clustering and classification steps are the key ingredients, allowing the approach to be trivially applied to systems of any size. Our initial study on met-enkephalin strongly suggests that even fairly long trajectories (approximately 50 ns) may not be converged for this small--but highly flexible--system.

References

Dec 6, 1994·Proceedings of the National Academy of Sciences of the United States of America·K SvobodaS M Block
Apr 16, 1998·Protein Science : a Publication of the Protein Society·L S CavesM Karplus
Feb 23, 2002·Science·Elan Zohar EisenmesserDorothee Kern
Mar 23, 2002·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Berk Hess
Mar 28, 2002·Biophysical Journal·Min-yi Shen My, Karl F Freed
Jul 12, 2002·Proteins·Lorna J SmithWilfred F van Gunsteren
Sep 19, 2002·Journal of the American Chemical Society·Carlos SimmerlingAdrian E Roitberg
Jun 21, 2003·Science·Friedrich SchottePhilip A Anfinrud
Dec 18, 2003·Journal of the American Chemical Society·Michele VendruscoloMartin Karplus
Apr 22, 2004·Proceedings of the National Academy of Sciences of the United States of America·Ivano BertiniMaria Antonietta Zoroddu
Dec 21, 2004·The Journal of Chemical Physics·Sidney P Elmer, Vijay S Pande
Sep 17, 2005·The Journal of Chemical Physics·Hideaki FujitaniVijay S Pande
Sep 17, 2005·Science·Philip BradleyDavid Baker
Oct 29, 2005·The Journal of Chemical Physics·Wei ZhangYong Duan

❮ Previous
Next ❯

Citations

May 14, 2010·Journal of Molecular Modeling·Piotr Cysewski, Przemysław Czeleń
Oct 16, 2007·The Journal of Physical Chemistry. B·Edward Lyman, Daniel M Zuckerman
Jul 15, 2009·The Journal of Physical Chemistry. B·Artem B MamonovDaniel M Zuckerman
Apr 13, 2010·The Journal of Physical Chemistry. B·Ying DingDaniel M Zuckerman
Jun 12, 2008·Proceedings of the National Academy of Sciences of the United States of America·F Marty Ytreberg, Daniel M Zuckerman
Jun 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Elodie LaineArnaud Blondel
Jun 28, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·B KnappP Bauer
May 11, 2010·Biochemistry and Cell Biology = Biochimie Et Biologie Cellulaire·Sarah Rauscher, Régis Pomès
Aug 1, 2012·Journal of Bioinformatics and Computational Biology·Biswa Ranjan MeherPradipta Bandyopadhyay
Nov 16, 2011·BMC Bioinformatics·Joshua L PhillipsShawn Newsam
Jan 16, 2009·PloS One·Kresten Lindorff-Larsen, Jesper Ferkinghoff-Borg
Oct 5, 2013·The Journal of Chemical Physics·Nicholas LyleRohit V Pappu
Jan 15, 2016·Journal of Chemical Theory and Computation·Lucas Sawle, Kingshuk Ghosh
Jan 14, 2016·Journal of Chemical Theory and Computation·Nicolas Lenner, Gerald Mathias
Jan 30, 2016·BMC Bioinformatics·Yasaman KaramiAlessandra Carbone
Jul 16, 2008·Journal of Molecular Graphics & Modelling·Won-Joon SonSeokmin Shin
Jan 24, 2007·Proteins·Alan GrossfieldMichael C Pitman
Feb 17, 2015·Evolutionary Applications·Nevra ÖzerTürkan Haliloğlu
Aug 6, 2015·Biophysical Journal·Nicholas LeioattsAlan Grossfield
Apr 16, 2015·Computational Intelligence and Neuroscience·Renata De ParisRodrigo C Barros
Jul 29, 2016·PloS One·Priscila Da Silva Figueiredo Celestino GomesLuba Tchertanov
Jan 22, 2008·The Journal of Chemical Physics·Daniel SindhikaraAdrian E Roitberg
Jan 14, 2017·Journal of Chemical Theory and Computation·Mike Nemec, Daniel Hoffmann
Jun 4, 2016·PloS One·Marcos Tadeu GeraldoNey Lemke
Oct 31, 2012·Journal of Computational Chemistry·Li YangStanley I Sandler
Jun 9, 2009·Journal of Computational Chemistry·Xin ZhangDaniel M Zuckerman
Mar 10, 2011·Journal of Computational Chemistry·Steven LettieriDaniel M Zuckerman
Aug 25, 2010·Journal of Computational Chemistry·Artem B MamonovDaniel M Zuckerman
Dec 12, 2017·Journal of Computational Chemistry·Krishna Kant Singh, Stephane Redon
Dec 18, 2009·Journal of Computational Chemistry·Pu LiuDouglas L Theobald
Jan 21, 2021·International Journal of Molecular Sciences·Maxim StolyarchukLuba Tchertanov

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.