The EVcouplings Python framework for coevolutionary sequence analysis

Bioinformatics
Thomas A HopfDebora S Marks

Abstract

Coevolutionary sequence analysis has become a commonly used technique for de novo prediction of the structure and function of proteins, RNA, and protein complexes. We present the EVcouplings framework, a fully integrated open-source application and Python package for coevolutionary analysis. The framework enables generation of sequence alignments, calculation and evaluation of evolutionary couplings (ECs), and de novo prediction of structure and mutation effects. The combination of an easy to use, flexible command line interface and an underlying modular Python package makes the full power of coevolutionary analyses available to entry-level and advanced users. https://github.com/debbiemarkslab/evcouplings.

References

Jan 1, 2009·Proceedings of the National Academy of Sciences of the United States of America·Martin WeigtTerence Hwa
Jan 27, 2011·Proteins·Sivaraman BalakrishnanChristopher James Langmead
Nov 23, 2011·Proceedings of the National Academy of Sciences of the United States of America·Faruck MorcosMartin Weigt
Dec 14, 2011·PloS One·Debora S MarksChris Sander
Feb 16, 2013·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Magnus EkebergErik Aurell
Mar 29, 2014·BMC Bioinformatics·László KajánBurkhard Rost
Nov 7, 2014·PLoS Computational Biology·Marcin J SkwarkArne Elofsson
Oct 9, 2015·Molecular Biology and Evolution·Matteo FigliuzziMartin Weigt
Apr 19, 2016·Cell·Caleb WeinrebDebora S Marks
Jan 17, 2017·Nature Biotechnology·Thomas A HopfDebora S Marks
Apr 4, 2017·Bioinformatics·Felix SimkovicDaniel J Rigden

❮ Previous
Next ❯

Citations

Apr 21, 2020·BioMed Research International·Chao FangHan Wang
Jul 23, 2019·PeerJ·Adam J Hockenberry, Claus O Wilke
Aug 10, 2020·Molecular Biology and Evolution·Jorge Fernandez-de-Cossio-DiazAndrea Pagnani
Oct 4, 2020·Communications Biology·Nash D RochmanEugene V Koonin
Dec 11, 2020·BMC Evolutionary Biology·Manuel SeefelderStefan Kochanek
Jan 16, 2021·Science·Brian HieBryan Bryson
Nov 3, 2020·F1000Research·Roc ReguantNicholas Paul Gauthier
Feb 27, 2021·PLoS Computational Biology·Alex Hawkins-HookerDavid Bikard
Mar 25, 2021·Protein Science : a Publication of the Protein Society·Caitlyn L McCaffertyEdward M Marcotte
Dec 12, 2020·Insect Biochemistry and Molecular Biology·Eugenia ChartschenkoMathias Beller
Apr 24, 2021·The Protein Journal·Dwaipayan ChaudhuriKalyan Giri
May 15, 2021·Journal of Molecular Biology·Hena SandhuGunnar von Heijne
Jun 5, 2021·Bioinformatics·Guilherme F BottinoLeandro Martínez
Jul 1, 2021·Proceedings of the National Academy of Sciences of the United States of America·Alexander S GarrussGeorge M Church
Jun 18, 2021·Current Opinion in Structural Biology·Charlotte W van NoortAlexandre M J J Bonvin
Jul 2, 2021·Acta Crystallographica. Section D, Structural Biology·B MylemansA R D Voet

❮ Previous
Next ❯

Related Concepts

Related Feeds

Researcher Network:CZI Neurodegeneration Challenge

The Neurodegeneration Challenge Network aims to provide funding for and to bring together researchers studying neurodegenerative diseases. Find the latest research from the NDCN grantees here.