Open Access

Acta Crystallographica Section D Biological Crystallography, volume 66, issue 2, pages 213-221

PHENIX: a comprehensive Python-based system for macromolecular structure solution

Adams Paul D. ^{1, 2}

Afonine Pavel V. ²

Bunkóczi Gábor ³

Chen Vincent B. ⁴

Davis Ian W. ⁴

Echols Nathaniel ²

Headd Jeffrey J. ⁴

Hung Li-Wei ⁵

Kapral Gary J. ⁴

Grosse-Kunstleve Ralf W. ²

McCoy Airlie J. ³

Moriarty Nigel W. ²

Oeffner Robert ³

Read Randy J. ³

Richardson David C. ⁴

Richardson Jane S. ⁴

Terwilliger Thomas C. ⁵

Zwart Peter H. ²

Hide authors affiliations Show authors affiliations: 5 affiliations

Department of Bioengineering, UC Berkeley, CA 94720, USA |

Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA |

Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Wellcome Trust/MRC Building, Cambridge CB2 0XY, England |

⁴

Department of Biochemistry, Duke University Medical Center, Durham, NC 27710, USA |

⁵

Los Alamos National Laboratory, Los Alamos, NM 87545, USA |

Publication type: Journal Article

Publication date: 2010-01-22

International Union of Crystallography (IUCr)

Journal: Acta Crystallographica Section D Biological Crystallography

Quartile SCImago

—

Quartile WOS

—

Impact factor: —

ISSN: 09074449, 13990047

DOI: 10.1107/S0907444909052925

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PubMed ID: 20124702

General Medicine

Structural Biology

Abstract

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics.PHENIXhas been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.

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1297

Citations by journals

	200 400 600 800 1000 1200 1400
Nature Communications	Nature Communications, 1398, 7.24% Nature Communications 1398 publications, 7.24%
Journal of Biological Chemistry	Journal of Biological Chemistry, 1248, 6.46% Journal of Biological Chemistry 1248 publications, 6.46%
Proceedings of the National Academy of Sciences of the United States of America	Proceedings of the National Academy of Sciences of the United States of America, 751, 3.89% Proceedings of the National Academy of Sciences of the United States of America 751 publications, 3.89%
Nature	Nature, 587, 3.04% Nature 587 publications, 3.04%
Structure	Structure, 581, 3.01% Structure 581 publications, 3.01%
Nucleic Acids Research	Nucleic Acids Research, 525, 2.72% Nucleic Acids Research 525 publications, 2.72%
Scientific Reports	Scientific Reports, 475, 2.46% Scientific Reports 475 publications, 2.46%
eLife	eLife, 434, 2.25% eLife 434 publications, 2.25%
Journal of Molecular Biology	Journal of Molecular Biology, 433, 2.24% Journal of Molecular Biology 433 publications, 2.24%
Journal of Medicinal Chemistry	Journal of Medicinal Chemistry, 401, 2.08% Journal of Medicinal Chemistry 401 publications, 2.08%
Nature Structural and Molecular Biology	Nature Structural and Molecular Biology, 397, 2.06% Nature Structural and Molecular Biology 397 publications, 2.06%
Acta Crystallographica Section D Biological Crystallography	Acta Crystallographica Section D Biological Crystallography, 371, 1.92% Acta Crystallographica Section D Biological Crystallography 371 publications, 1.92%
Science	Science, 363, 1.88% Science 363 publications, 1.88%
Biochemistry	Biochemistry, 360, 1.86% Biochemistry 360 publications, 1.86%
PLoS ONE	PLoS ONE, 352, 1.82% PLoS ONE 352 publications, 1.82%
Acta Crystallographica Section F:Structural Biology Communications	Acta Crystallographica Section F:Structural Biology Communications, 325, 1.68% Acta Crystallographica Section F:Structural Biology Communications 325 publications, 1.68%
Biochemical and Biophysical Research Communications	Biochemical and Biophysical Research Communications, 301, 1.56% Biochemical and Biophysical Research Communications 301 publications, 1.56%
Cell	Cell, 268, 1.39% Cell 268 publications, 1.39%
Molecular Cell	Molecular Cell, 227, 1.18% Molecular Cell 227 publications, 1.18%
Acta Crystallographica Section D: Structural Biology	Acta Crystallographica Section D: Structural Biology, 226, 1.17% Acta Crystallographica Section D: Structural Biology 226 publications, 1.17%
Journal of Virology	Journal of Virology, 209, 1.08% Journal of Virology 209 publications, 1.08%
FEBS Journal	FEBS Journal, 208, 1.08% FEBS Journal 208 publications, 1.08%
Cell Reports	Cell Reports, 197, 1.02% Cell Reports 197 publications, 1.02%
Nature Chemical Biology	Nature Chemical Biology, 196, 1.01% Nature Chemical Biology 196 publications, 1.01%
Journal of Structural Biology	Journal of Structural Biology, 191, 0.99% Journal of Structural Biology 191 publications, 0.99%
Science advances	Science advances, 191, 0.99% Science advances 191 publications, 0.99%
PLoS Pathogens	PLoS Pathogens, 171, 0.89% PLoS Pathogens 171 publications, 0.89%
Proteins: Structure, Function and Genetics	Proteins: Structure, Function and Genetics, 167, 0.86% Proteins: Structure, Function and Genetics 167 publications, 0.86%
Protein Science	Protein Science, 167, 0.86% Protein Science 167 publications, 0.86%
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Citations by publishers

	500 1000 1500 2000 2500 3000 3500 4000
Springer Nature	Springer Nature, 3949, 20.45% Springer Nature 3949 publications, 20.45%
Elsevier	Elsevier, 3388, 17.54% Elsevier 3388 publications, 17.54%
American Chemical Society (ACS)	American Chemical Society (ACS), 1355, 7.02% American Chemical Society (ACS) 1355 publications, 7.02%
American Society for Biochemistry and Molecular Biology	American Society for Biochemistry and Molecular Biology, 1261, 6.53% American Society for Biochemistry and Molecular Biology 1261 publications, 6.53%
International Union of Crystallography (IUCr)	International Union of Crystallography (IUCr), 1173, 6.07% International Union of Crystallography (IUCr) 1173 publications, 6.07%
Wiley	Wiley, 1137, 5.89% Wiley 1137 publications, 5.89%
Proceedings of the National Academy of Sciences (PNAS)	Proceedings of the National Academy of Sciences (PNAS), 751, 3.89% Proceedings of the National Academy of Sciences (PNAS) 751 publications, 3.89%
American Association for the Advancement of Science (AAAS)	American Association for the Advancement of Science (AAAS), 626, 3.24% American Association for the Advancement of Science (AAAS) 626 publications, 3.24%
Public Library of Science (PLoS)	Public Library of Science (PLoS), 623, 3.23% Public Library of Science (PLoS) 623 publications, 3.23%
Oxford University Press	Oxford University Press, 621, 3.22% Oxford University Press 621 publications, 3.22%
American Society for Microbiology	American Society for Microbiology, 450, 2.33% American Society for Microbiology 450 publications, 2.33%
eLife Sciences Publications	eLife Sciences Publications, 434, 2.25% eLife Sciences Publications 434 publications, 2.25%
Multidisciplinary Digital Publishing Institute (MDPI)	Multidisciplinary Digital Publishing Institute (MDPI), 345, 1.79% Multidisciplinary Digital Publishing Institute (MDPI) 345 publications, 1.79%
EMBO press	EMBO press, 165, 0.85% EMBO press 165 publications, 0.85%
Portland Press	Portland Press, 157, 0.81% Portland Press 157 publications, 0.81%
Frontiers Media S.A.	Frontiers Media S.A., 141, 0.73% Frontiers Media S.A. 141 publications, 0.73%
Taylor & Francis	Taylor & Francis, 98, 0.51% Taylor & Francis 98 publications, 0.51%
Royal Society of Chemistry (RSC)	Royal Society of Chemistry (RSC), 98, 0.51% Royal Society of Chemistry (RSC) 98 publications, 0.51%
Cold Spring Harbor Laboratory	Cold Spring Harbor Laboratory, 97, 0.5% Cold Spring Harbor Laboratory 97 publications, 0.5%
Rockefeller University Press	Rockefeller University Press, 76, 0.39% Rockefeller University Press 76 publications, 0.39%
Federation of American Societies for Experimental Biology (FASEB)	Federation of American Societies for Experimental Biology (FASEB), 36, 0.19% Federation of American Societies for Experimental Biology (FASEB) 36 publications, 0.19%
The American Association of Immunologists	The American Association of Immunologists, 34, 0.18% The American Association of Immunologists 34 publications, 0.18%
Biophysical Society	Biophysical Society, 28, 0.14% Biophysical Society 28 publications, 0.14%
American Association for Cancer Research (AACR)	American Association for Cancer Research (AACR), 27, 0.14% American Association for Cancer Research (AACR) 27 publications, 0.14%
The Royal Society	The Royal Society, 22, 0.11% The Royal Society 22 publications, 0.11%
American Society for Pharmacology and Experimental Therapeutics	American Society for Pharmacology and Experimental Therapeutics, 21, 0.11% American Society for Pharmacology and Experimental Therapeutics 21 publications, 0.11%
American Society of Plant Biologists	American Society of Plant Biologists, 19, 0.1% American Society of Plant Biologists 19 publications, 0.1%
Social Science Electronic Publishing	Social Science Electronic Publishing, 18, 0.09% Social Science Electronic Publishing 18 publications, 0.09%
Pleiades Publishing	Pleiades Publishing, 15, 0.08% Pleiades Publishing 15 publications, 0.08%
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Adams P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution // Acta Crystallographica Section D Biological Crystallography. 2010. Vol. 66. No. 2. pp. 213-221.

GOST all authors (up to 50) Copy

Adams P. D., Afonine P. V., Bunkóczi G., Chen V. B., Davis I. W., Echols N., Headd J. J., Hung L., Kapral G. J., Grosse-Kunstleve R. W., McCoy A. J., Moriarty N. W., Oeffner R., Read R. J., Richardson D. C., Richardson J. S., Terwilliger T. C., Zwart P. H. PHENIX: a comprehensive Python-based system for macromolecular structure solution // Acta Crystallographica Section D Biological Crystallography. 2010. Vol. 66. No. 2. pp. 213-221.

RIS |

Cite this

RIS Copy

TY - JOUR

DO - 10.1107/S0907444909052925

UR - https://doi.org/10.1107%2FS0907444909052925

TI - PHENIX: a comprehensive Python-based system for macromolecular structure solution

T2 - Acta Crystallographica Section D Biological Crystallography

AU - Adams, Paul D.

AU - Afonine, Pavel V.

AU - Bunkóczi, Gábor

AU - Chen, Vincent B.

AU - Davis, Ian W.

AU - Echols, Nathaniel

AU - Headd, Jeffrey J.

AU - Hung, Li-Wei

AU - Kapral, Gary J.

AU - Grosse-Kunstleve, Ralf W.

AU - McCoy, Airlie J.

AU - Moriarty, Nigel W.

AU - Oeffner, Robert

AU - Read, Randy J.

AU - Richardson, David C.

AU - Richardson, Jane S.

AU - Terwilliger, Thomas C.

AU - Zwart, Peter H.

PY - 2010

DA - 2010/01/22 00:00:00

PB - International Union of Crystallography (IUCr)

SP - 213-221

IS - 2

VL - 66

PMID - 20124702

SN - 0907-4449

SN - 1399-0047

ER -

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BibTex Copy

@article{2010_Adams,

author = {Paul D. Adams and Pavel V. Afonine and Gábor Bunkóczi and Vincent B. Chen and Ian W. Davis and Nathaniel Echols and Jeffrey J. Headd and Li-Wei Hung and Gary J. Kapral and Ralf W. Grosse-Kunstleve and Airlie J. McCoy and Nigel W. Moriarty and Robert Oeffner and Randy J. Read and David C. Richardson and Jane S. Richardson and Thomas C. Terwilliger and Peter H. Zwart},

title = {PHENIX: a comprehensive Python-based system for macromolecular structure solution},

journal = {Acta Crystallographica Section D Biological Crystallography},

year = {2010},

volume = {66},

publisher = {International Union of Crystallography (IUCr)},

month = {jan},

url = {https://doi.org/10.1107%2FS0907444909052925},

number = {2},

pages = {213--221},

doi = {10.1107/S0907444909052925}

}

MLA

Cite this

MLA Copy

Adams, Paul D., et al. “PHENIX: a comprehensive Python-based system for macromolecular structure solution.” Acta Crystallographica Section D Biological Crystallography, vol. 66, no. 2, Jan. 2010, pp. 213-221. https://doi.org/10.1107%2FS0907444909052925.

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Publisher

International Union of Crystallography (IUCr)

Journal

Acta Crystallographica Section D Biological Crystallography

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Quartile WOS

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ISSN

09074449 (Print)
13990047 (Electronic)