idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

Borreguero, Jose M.; Islam, Fahima F.; Shrestha, Utsab R.; Petridis, Loukas

doi:10.21105/joss.01007

Title: idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

Abstract

It is estimated that about 30% of the eucariotic proteome consists of intrinsically dis-ordered proteins (IDP’s), yet their presence in public structural databases is severely underrepresented. IDP’s adopt heterogeneous inter-converting conformations with similar probabilities, preventing resolution of structures with X-Ray diffraction techniques. An alternative technique with wide application on IDP systems is small angle scattering(SAS). SAS can measure average structural features of IDP’s when in vitro solution, or even at conditions mimicking protein concentrations found in the cell’s cytoplasm.

Authors:

^[1];

^[1]

Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Publication Date:: Tue Dec 11 00:00:00 EST 2018

Research Org.:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1543227

Grant/Contract Number:: AC05-00OR22725

Resource Type:: Accepted Manuscript

Journal Name:: Journal of Open Source Software

Additional Journal Information:: Journal Volume: 3; Journal Issue: 32; Journal ID: ISSN 2475-9066

Publisher:: Open Source Initiative - NumFOCUS; Copyright - Open Journals

Country of Publication:: United States

Language:: English

Subject:: 97 MATHEMATICS AND COMPUTING

Citation Formats


                    Borreguero, Jose M., Islam, Fahima F., Shrestha, Utsab R., and Petridis, Loukas. idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments.  United States: N. p., 2018. 
Web.  doi:10.21105/joss.01007.

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                    Borreguero, Jose M., Islam, Fahima F., Shrestha, Utsab R., & Petridis, Loukas. idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments.  United States.  https://doi.org/10.21105/joss.01007

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                    Borreguero, Jose M., Islam, Fahima F., Shrestha, Utsab R., and Petridis, Loukas. Tue .  
"idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments".  United States.  https://doi.org/10.21105/joss.01007.  https://www.osti.gov/servlets/purl/1543227.

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@article{osti_1543227,

  title        = {idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments},

  author       = {Borreguero, Jose M. and Islam, Fahima F. and Shrestha, Utsab R. and Petridis, Loukas},

  abstractNote = {It is estimated that about 30% of the eucariotic proteome consists of intrinsically dis-ordered proteins (IDP’s), yet their presence in public structural databases is severely underrepresented. IDP’s adopt heterogeneous inter-converting conformations with similar probabilities, preventing resolution of structures with X-Ray diffraction techniques. An alternative technique with wide application on IDP systems is small angle scattering(SAS). SAS can measure average structural features of IDP’s when in vitro solution, or even at conditions mimicking protein concentrations found in the cell’s cytoplasm.},

  doi          = {10.21105/joss.01007},

  journal      = {Journal of Open Source Software},

  number       = 32,

  volume       = 3,

  place        = {United States},

  year         = {Tue Dec 11 00:00:00 EST 2018},

  month        = {Tue Dec 11 00:00:00 EST 2018}

}

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Works referenced in this record:

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Title: idpflex: Analysis of Intrinsically Disordered Proteins by Comparing Simulations to Small Angle Scattering Experiments

Abstract

Citation Formats

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations conference, January 2016

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features journal, December 1983

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints journal, February 2012

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling journal, January 2006

A solution for the best rotation to relate two sets of vectors journal, September 1976

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories journal, October 2015

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations journal, April 2011

SAXS Ensemble Refinement of ESCRT-III CHMP3 Conformational Transitions journal, January 2011

Characterization of disordered proteins with ENSEMBLE journal, December 2012

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates journal, December 1995

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations
conference, January 2016

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints
journal, February 2012

A Novel Hamiltonian Replica Exchange MD Protocol to Enhance Protein Conformational Space Sampling
journal, January 2006

A solution for the best rotation to relate two sets of vectors
journal, September 1976

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories
journal, October 2015

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations
journal, April 2011

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journal, January 2011

Characterization of disordered proteins with ENSEMBLE
journal, December 2012

CRYSOL – a Program to Evaluate X-ray Solution Scattering of Biological Macromolecules from Atomic Coordinates
journal, December 1995