PHENIX: a comprehensive Python-based system for macromolecular structure solution
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...
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| Published in | Acta crystallographica. Section D, Biological crystallography. Vol. 66; no. 2; pp. 213 - 221 |
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| Main Authors | , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
5 Abbey Square, Chester, Cheshire CH1 2HU, England
International Union of Crystallography
01.02.2010
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| Subjects | |
| Online Access | Get full text |
| ISSN | 1399-0047 0907-4449 1399-0047 |
| DOI | 10.1107/S0907444909052925 |
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| 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. PHENIX has 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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| AbstractList | 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. PHENIX has 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. 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. PHENIX has 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.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. PHENIX has 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. The PHENIX software for macromolecular structure determination is described. 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. PHENIX has 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. 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. PHENIX has 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. |
| Author | Zwart, Peter H. Davis, Ian W. Grosse-Kunstleve, Ralf W. Read, Randy J. Adams, Paul D. Bunkóczi, Gábor Kapral, Gary J. Oeffner, Robert Chen, Vincent B. Echols, Nathaniel Terwilliger, Thomas C. Richardson, Jane S. Headd, Jeffrey J. Richardson, David C. McCoy, Airlie J. Moriarty, Nigel W. Hung, Li-Wei Afonine, Pavel V. |
| Author_xml | – sequence: 1 givenname: Paul D. surname: Adams fullname: Adams, Paul D. – sequence: 2 givenname: Pavel V. surname: Afonine fullname: Afonine, Pavel V. – sequence: 3 givenname: Gábor surname: Bunkóczi fullname: Bunkóczi, Gábor – sequence: 4 givenname: Vincent B. surname: Chen fullname: Chen, Vincent B. – sequence: 5 givenname: Ian W. surname: Davis fullname: Davis, Ian W. – sequence: 6 givenname: Nathaniel surname: Echols fullname: Echols, Nathaniel – sequence: 7 givenname: Jeffrey J. surname: Headd fullname: Headd, Jeffrey J. – sequence: 8 givenname: Li-Wei surname: Hung fullname: Hung, Li-Wei – sequence: 9 givenname: Gary J. surname: Kapral fullname: Kapral, Gary J. – sequence: 10 givenname: Ralf W. surname: Grosse-Kunstleve fullname: Grosse-Kunstleve, Ralf W. – sequence: 11 givenname: Airlie J. surname: McCoy fullname: McCoy, Airlie J. – sequence: 12 givenname: Nigel W. surname: Moriarty fullname: Moriarty, Nigel W. – sequence: 13 givenname: Robert surname: Oeffner fullname: Oeffner, Robert – sequence: 14 givenname: Randy J. surname: Read fullname: Read, Randy J. – sequence: 15 givenname: David C. surname: Richardson fullname: Richardson, David C. – sequence: 16 givenname: Jane S. surname: Richardson fullname: Richardson, Jane S. – sequence: 17 givenname: Thomas C. surname: Terwilliger fullname: Terwilliger, Thomas C. – sequence: 18 givenname: Peter H. surname: Zwart fullname: Zwart, Peter H. |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/20124702$$D View this record in MEDLINE/PubMed https://www.osti.gov/servlets/purl/1625666$$D View this record in Osti.gov |
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| ContentType | Journal Article |
| Copyright | Adams et al. 2010 Adams et al. 2010 2010 |
| Copyright_xml | – notice: Adams et al. 2010 – notice: Adams et al. 2010 2010 |
| CorporateAuthor | Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States) |
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| Snippet | Macromolecular X‐ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are... Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are... The PHENIX software for macromolecular structure determination is described. Macromolecular X-ray crystallography is routinely applied to understand biological... |
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| SubjectTerms | Algorithms BASIC BIOLOGICAL SCIENCES Biochemistry & Molecular Biology Biophysics Crystallography Crystallography, X-Ray - methods Macromolecular Crystallography Models, Molecular PHENIX Python Research Papers Software Design |
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| Title | PHENIX: a comprehensive Python-based system for macromolecular structure solution |
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