PHENIX : building new software for automated crystallographic structure determination
Open accessAbstract
Structural genomics seeks to expand rapidly the number of protein structures in order to extract the maximum amount of information from genomic sequence databases. The advent of several large-scale projects worldwide leads to many new challenges in the field of crystallographic macromolecular structure determination. A novel software package called PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is therefore being developed. This new software will provide the necessary algorithms to proceed from reduced intensity data to a refined molecular model and to facilitate structure solution for both the novice and expert crystallographer.
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The quality indicators for the crystal structures of the Syt1-SNARE complex are well within acceptable ranges indicated by the polygon plot produced by phenix.refine and by the validation report of the deposited structures and diffraction data.
“The quality indicators for the crystal structures of the Syt1-SNARE complex are well within acceptable ranges indicated by the “polygon” plot produced by phenix.refine72 and by the validation report of the deposited structures and diffraction data.”
From Architecture of the synaptotagmin–SNARE machinery for neuronal exocytosis (2015) · cites this paper as [72]
Split into 2 atoms — 1 confirmed, 1 partially supported, 0 disputed, 0 misattributed, 0 unverifiable. Expand the claim to see per-atom verdicts.
Experimental — accuracy not yet measuredElectron density images from x-ray crystallography or cryo-electron microscopy produce proximity constraints representable as networks of atoms linked to other atoms in close spatial proximity.
“At the atomic scale, electron density images generated by x-ray crystallography (Adams et al., 2002; Kleywegt et al., 2004; Yang et al., 2016) or cryo-electron microscopy (cryo-EM) (Chen et al., 2016; Frenz et al., 2017; Hryc et al., 2017) produce proximity constraints that can be represented as networks of atoms (nodes) linked to other atoms determined to be in close spatial proximity (edges).”
From Mapping the multiscale structure of biological systems (2021) · cites this paper as Adams et al., 2002
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- Authors
- Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K., & Terwilliger, T. C.
- Affiliations
- Lawrence Berkeley National Laboratory (US)
- Los Alamos National Laboratory (US)
- Texas A&M University (US)
- University of Cambridge (GB)
- ORCID
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2002-10-21
- Volume
- 58
- Issue
- 11
- Pages
- 1948-1954
- ISSN
- 0907-4449 (ISSN-L)
- OpenAlex
- W2109184569
- Cited by
- 4,361
- References
- 11
- Citations by year
- 2026: 89 · 2025: 156 · 2024: 146 · 2023: 165 · 2022: 183 · 2021: 174 · 2020: 190 · 2019: 231 · 2018: 193 · 2017: 187 · 2016: 216 · 2015: 223 · 2014: 218 · 2013: 277 · 2012: 299
- FWCI
- 5.61
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Crystallographica Section D Biological Crystallography (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OakTrust (Texas A&M University Libraries) (submittedVersion)
- Funders
- U.S. Department of Energy (DE-AC03-?, AC03-76SF00098, DEAC03-76SF00098)
- National Institutes of Health (DE-AC03- 76SF00098)
- National Institute of General Medical Sciences (P01GM063210)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- automated structure determination, macromolecular crystallography, structural genomics, protein structure, intensity data, software package development
- MeSH terms
- Algorithms, Automation, Models, Molecular, Proteins, Software, Molecular Structure, Crystallography, X-Ray, Genomics
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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