The EVcouplings Python']Python framework for coevolutionary sequence analysis

被引：173

作者：

Hopf, Thomas A. ^{[1
,2
]}

Green, Anna G. ^{[1
]}

Schubert, Benjamin ^{[1
,2
,3
]}

Mersmann, Sophia ^{[1
]}

Schaerfe, Charlotta P. I. ^{[1
,4
,5
]}

Ingraham, John B. ^{[1
]}

Toth-Petroczy, Agnes ^{[1
]}

Brock, Kelly ^{[1
]}

Riesselman, Adam J. ^{[1
]}

Palmedo, Perry ^{[1
,6
]}

Kang, Chan ^{[1
]}

Sheridan, Robert ^{[7
]}

Draizen, Eli J. ^{[8
]}

Dallago, Christian ^{[1
,2
,9
]}

Sander, Chris ^{[2
,3
]}

Marks, Debora S. ^{[1
]}

机构：

[1] Harvard Med Sch, Dept Syst Biol, Boston, MA 02115 USA

[2] Harvard Med Sch, Dept Cell Biol, Boston, MA 02115 USA

[3] Dana Farber Canc Inst, Dept Biostat & Computat Biol, cBio Ctr, Boston, MA 02215 USA

[4] Univ Tubingen, Ctr Bioinformat, D-72076 Tubingen, Germany

[5] Dept Comp Sci, Appl Bioinformat, D-72076 Tubingen, Germany

[6] MIT, Comp Sci & Artificial Intelligence Lab, 77 Massachusetts Ave, Cambridge, MA 02139 USA

[7] Mem Sloan Kettering Canc Ctr, Computat Biol Ctr, New York, NY 10065 USA

[8] Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22904 USA

[9] Tech Univ Munich, Dept Informat, D-85748 Garching, Germany

来源：

BIOINFORMATICS | 2019年 / 35卷 / 09期

关键词：

RESIDUE CONTACTS; PROTEIN; PREDICTION;

D O I：

10.1093/bioinformatics/bty862

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. Availability and implementation https://github.com/debbiemarkslab/evcouplings

引用

页码：1582 / 1584

页数：3

共 18 条

[1] Learning generative models for protein fold families [J].

Balakrishnan, Sivaraman ;

Kamisetty, Hetunandan ;

Carbonell, Jaime G. ;

Lee, Su-In ;

Langmead, Christopher James .

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2011, 79 (04) :1061-1078

[2] Improved contact prediction in proteins: Using pseudolikelihoods to infer Potts models [J].

Ekeberg, Magnus ;

Lovkvist, Cecilia ;

Lan, Yueheng ;

Weigt, Martin ;

Aurell, Erik .

PHYSICAL REVIEW E, 2013, 87 (01)

[3] Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1 [J].

Figliuzzi, Matteo ;

Jacquier, Herve ;

Schug, Alexander ;

Tenaillon, Oliver ;

Weigt, Martin .

MOLECULAR BIOLOGY AND EVOLUTION, 2016, 33 (01) :268-280

[4] Mutation effects predicted from sequence co-variation [J].

Hopf, Thomas A. ;

Ingraham, John B. ;

Poelwijk, Frank J. ;

Scharfe, Charlotta P. I. ;

Springer, Michael ;

Sander, Chris ;

Marks, Debora S. .

NATURE BIOTECHNOLOGY, 2017, 35 (02) :128-135

[5] Sequence co-evolution gives 3D contacts and structures of protein complexes [J].

Hopf, Thomas A. ;

Schaefe, Charlotta P. I. ;

Rodrigues, Joao P. G. L. M. ;

Green, Anna G. ;

Kohlbacher, Oliver ;

Sander, Chris ;

Bonvin, Alexandre M. J. J. ;

Marks, Debora S. .

ELIFE, 2014, 3

[6] Three-Dimensional Structures of Membrane Proteins from Genomic Sequencing [J].

Hopf, Thomas A. ;

Colwell, Lucy J. ;

Sheridan, Robert ;

Rost, Burkhard ;

Sander, Chris ;

Marks, Debora S. .

CELL, 2012, 149 (07) :1607-1621

[7] MetaPSICOV: combining coevolution methods for accurate prediction of contacts and long range hydrogen bonding in proteins [J].

Jones, David T. ;

Singh, Tanya ;

Kosciolek, Tomasz ;

Tetchner, Stuart .

BIOINFORMATICS, 2015, 31 (07) :999-1006

[8] FreeContact: fast and free software for protein contact prediction from residue co-evolution [J].

Kajan, Laszlo ;

Hopf, Thomas A. ;

Kalas, Matus ;

Marks, Debora S. ;

Rost, Burkhard .

BMC BIOINFORMATICS, 2014, 15

[9] Jupyter Notebooks-a publishing format for reproducible computational workflows [J].

Kluyver, Thomas ;

Ragan-Kelley, Benjamin ;

Perez, Fernando ;

Granger, Brian ;

Bussonnier, Matthias ;

Frederic, Jonathan ;

Kelley, Kyle ;

Hamrick, Jessica ;

Grout, Jason ;

Corlay, Sylvain ;

Ivanov, Paul ;

Avila, Damin ;

Abdalla, Safia ;

Willing, Carol .

POSITIONING AND POWER IN ACADEMIC PUBLISHING: PLAYERS, AGENTS AND AGENDAS, 2016, :87-90

[10] Protein 3D Structure Computed from Evolutionary Sequence Variation [J].

Marks, Debora S. ;

Colwell, Lucy J. ;

Sheridan, Robert ;

Hopf, Thomas A. ;

Pagnani, Andrea ;

Zecchina, Riccardo ;

Sander, Chris .

PLOS ONE, 2011, 6 (12)

← 1 2 →