Literature DB >> 23233655

Characterization of disordered proteins with ENSEMBLE.

Mickaël Krzeminski1, Joseph A Marsh, Chris Neale, Wing-Yiu Choy, Julie D Forman-Kay.   

Abstract

UNLABELLED: ENSEMBLE is a computational approach for determining a set of conformations that represents the structural ensemble of a disordered protein based on input experimental data. The disordered protein can be an unfolded or intrinsically disordered state. Here, we introduce the latest version of the program, which has been enhanced to facilitate its general release and includes an intuitive user interface, as well as new approaches to treat data and analyse results.
AVAILABILITY AND IMPLEMENTATION: ENSEMBLE is a program implemented in C and embedded in a Perl wrapper. It is supported on main Linux distributions. Source codes and installation files, including a detailed example, can be freely downloaded at http://abragam.med.utoronto.ca/∼JFKlab.

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Year:  2012        PMID: 23233655     DOI: 10.1093/bioinformatics/bts701

Source DB:  PubMed          Journal:  Bioinformatics        ISSN: 1367-4803            Impact factor:   6.937


  51 in total

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Journal:  Chem Rev       Date:  2015-03-19       Impact factor: 60.622

2.  The combined force field-sampling problem in simulations of disordered amyloid-β peptides.

Authors:  James Lincoff; Sukanya Sasmal; Teresa Head-Gordon
Journal:  J Chem Phys       Date:  2019-03-14       Impact factor: 3.488

3.  Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure.

Authors:  F Marty Ytreberg; Wade Borcherds; Hongwei Wu; Gary W Daughdrill
Journal:  Intrinsically Disord Proteins       Date:  2015-02-03

4.  Direct observation of structure and dynamics during phase separation of an elastomeric protein.

Authors:  Sean E Reichheld; Lisa D Muiznieks; Fred W Keeley; Simon Sharpe
Journal:  Proc Natl Acad Sci U S A       Date:  2017-05-15       Impact factor: 11.205

5.  Conformational Dynamics of the Partially Disordered Yeast Transcription Factor GCN4.

Authors:  Paul Robustelli; Nikola Trbovic; Richard A Friesner; Arthur G Palmer
Journal:  J Chem Theory Comput       Date:  2013-11-01       Impact factor: 6.006

Review 6.  Integrative, dynamic structural biology at atomic resolution--it's about time.

Authors:  Henry van den Bedem; James S Fraser
Journal:  Nat Methods       Date:  2015-04       Impact factor: 28.547

7.  Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model.

Authors:  Amir Mazouchi; Zhenfu Zhang; Abdullah Bahram; Gregory-Neal Gomes; Hong Lin; Jianhui Song; Hue Sun Chan; Julie D Forman-Kay; Claudiu C Gradinaru
Journal:  Biophys J       Date:  2016-04-12       Impact factor: 4.033

8.  Structure of an Intrinsically Disordered Stress Protein Alone and Bound to a Membrane Surface.

Authors:  John Atkinson; Matthew W Clarke; Josephine M Warnica; Kelly F Boddington; Steffen P Graether
Journal:  Biophys J       Date:  2016-08-09       Impact factor: 4.033

Review 9.  Dynamic Protein Interaction Networks and New Structural Paradigms in Signaling.

Authors:  Veronika Csizmok; Ariele Viacava Follis; Richard W Kriwacki; Julie D Forman-Kay
Journal:  Chem Rev       Date:  2016-02-29       Impact factor: 60.622

10.  A Metastable Contact and Structural Disorder in the Estrogen Receptor Transactivation Domain.

Authors:  Yi Peng; Shufen Cao; Janna Kiselar; Xiangzhu Xiao; Zhanwen Du; An Hsieh; Soobin Ko; Yinghua Chen; Prashansa Agrawal; Wenwei Zheng; Wuxian Shi; Wei Jiang; Lin Yang; Mark R Chance; Witold K Surewicz; Matthias Buck; Sichun Yang
Journal:  Structure       Date:  2018-12-20       Impact factor: 5.006

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