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Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix

Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is sim...

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Autores principales: Liebschner, Dorothee, Afonine, Pavel V., Baker, Matthew L., Bunkóczi, Gábor, Chen, Vincent B., Croll, Tristan I., Hintze, Bradley, Hung, Li-Wei, Jain, Swati, McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert D., Poon, Billy K., Prisant, Michael G., Read, Randy J., Richardson, Jane S., Richardson, David C., Sammito, Massimo D., Sobolev, Oleg V., Stockwell, Duncan H., Terwilliger, Thomas C., Urzhumtsev, Alexandre G., Videau, Lizbeth L., Williams, Christopher J., Adams, Paul D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: International Union of Crystallography 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778852/
https://www.ncbi.nlm.nih.gov/pubmed/31588918
http://dx.doi.org/10.1107/S2059798319011471
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author Liebschner, Dorothee
Afonine, Pavel V.
Baker, Matthew L.
Bunkóczi, Gábor
Chen, Vincent B.
Croll, Tristan I.
Hintze, Bradley
Hung, Li-Wei
Jain, Swati
McCoy, Airlie J.
Moriarty, Nigel W.
Oeffner, Robert D.
Poon, Billy K.
Prisant, Michael G.
Read, Randy J.
Richardson, Jane S.
Richardson, David C.
Sammito, Massimo D.
Sobolev, Oleg V.
Stockwell, Duncan H.
Terwilliger, Thomas C.
Urzhumtsev, Alexandre G.
Videau, Lizbeth L.
Williams, Christopher J.
Adams, Paul D.
author_facet Liebschner, Dorothee
Afonine, Pavel V.
Baker, Matthew L.
Bunkóczi, Gábor
Chen, Vincent B.
Croll, Tristan I.
Hintze, Bradley
Hung, Li-Wei
Jain, Swati
McCoy, Airlie J.
Moriarty, Nigel W.
Oeffner, Robert D.
Poon, Billy K.
Prisant, Michael G.
Read, Randy J.
Richardson, Jane S.
Richardson, David C.
Sammito, Massimo D.
Sobolev, Oleg V.
Stockwell, Duncan H.
Terwilliger, Thomas C.
Urzhumtsev, Alexandre G.
Videau, Lizbeth L.
Williams, Christopher J.
Adams, Paul D.
author_sort Liebschner, Dorothee
collection PubMed
description Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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spelling pubmed-67788522019-10-21 Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Liebschner, Dorothee Afonine, Pavel V. Baker, Matthew L. Bunkóczi, Gábor Chen, Vincent B. Croll, Tristan I. Hintze, Bradley Hung, Li-Wei Jain, Swati McCoy, Airlie J. Moriarty, Nigel W. Oeffner, Robert D. Poon, Billy K. Prisant, Michael G. Read, Randy J. Richardson, Jane S. Richardson, David C. Sammito, Massimo D. Sobolev, Oleg V. Stockwell, Duncan H. Terwilliger, Thomas C. Urzhumtsev, Alexandre G. Videau, Lizbeth L. Williams, Christopher J. Adams, Paul D. Acta Crystallogr D Struct Biol Feature Articles Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks. International Union of Crystallography 2019-10-02 /pmc/articles/PMC6778852/ /pubmed/31588918 http://dx.doi.org/10.1107/S2059798319011471 Text en © Liebschner et al. 2019 http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.http://creativecommons.org/licenses/by/4.0/
spellingShingle Feature Articles
Liebschner, Dorothee
Afonine, Pavel V.
Baker, Matthew L.
Bunkóczi, Gábor
Chen, Vincent B.
Croll, Tristan I.
Hintze, Bradley
Hung, Li-Wei
Jain, Swati
McCoy, Airlie J.
Moriarty, Nigel W.
Oeffner, Robert D.
Poon, Billy K.
Prisant, Michael G.
Read, Randy J.
Richardson, Jane S.
Richardson, David C.
Sammito, Massimo D.
Sobolev, Oleg V.
Stockwell, Duncan H.
Terwilliger, Thomas C.
Urzhumtsev, Alexandre G.
Videau, Lizbeth L.
Williams, Christopher J.
Adams, Paul D.
Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title_full Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title_fullStr Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title_full_unstemmed Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title_short Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix
title_sort macromolecular structure determination using x-rays, neutrons and electrons: recent developments in phenix
topic Feature Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778852/
https://www.ncbi.nlm.nih.gov/pubmed/31588918
http://dx.doi.org/10.1107/S2059798319011471
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