Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard
Open accessAbstract
The PHENIX AutoBuild wizard is a highly automated tool for iterative model building, structure refinement and density modification using RESOLVE model building, RESOLVE statistical density modification and phenix.refine structure refinement. Recent advances in the AutoBuild wizard and phenix.refine include automated detection and application of NCS from models as they are built, extensive model-completion algorithms and automated solvent-molecule picking. Model-completion algorithms in the AutoBuild wizard include loop building, crossovers between chains in different models of a structure and side-chain optimization. The AutoBuild wizard has been applied to a set of 48 structures at resolutions ranging from 1.1 to 3.2 Å, resulting in a mean R factor of 0.24 and a mean free R factor of 0.29. The R factor of the final model is dependent on the quality of the starting electron density and is relatively independent of resolution.
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ARP/Warp and Phenix Autobuild did not create models of as high quality as Phenix Autosolve or MR-Rosetta.
“ARP/Warp19 and Phenix Autobuild20 did not create models of as high quality as Phenix Autosolve or MR-Rosetta, and were thus not analysed in the competition.”
From Determining crystal structures through crowdsourcing and coursework (2016) · cites this paper as [20]
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- Authors
- Terwilliger, T. C., Grosse-Kunstleve, R. W., Afonine, P. V., Moriarty, N. W., Zwart, P. H., Hung, L.-W., Read, R. J., & Adams, P. D.
- Affiliations
- Los Alamos National Laboratory (US)
- Lawrence Berkeley National Laboratory (US)
- University of Cambridge (GB)
- Corresponding author
- Terwilliger, Thomas C.
- Adams, Paul D.
- ORCID
- Venue
- Acta Crystallographica Section D Biological Crystallography
- Published
- 2007-12-04
- Volume
- 64
- Issue
- 1
- Pages
- 61-69
- ISSN
- 0907-4449 (ISSN-L)
- PMC
- PMC2394820
- OpenAlex
- W2127130852
- Cited by
- 1,462
- References
- 1
- Citations by year
- 2026: 53 · 2025: 74 · 2024: 66 · 2023: 92 · 2022: 108 · 2021: 118 · 2020: 136 · 2019: 137 · 2018: 120 · 2017: 112 · 2016: 106 · 2015: 74 · 2014: 87 · 2013: 57 · 2012: 38
- FWCI
- 8.66
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Acta Crystallographica Section D Biological Crystallography (publishedVersion, cc-by)
- Funders
- U.S. Department of Energy (-AC02-05CH11231, Contract No. DE-AC02-05-CH11231, 05CH11231, No. DE-AC02-05-CH11231, DE AC02 05CH11231, DE-AC02-)
- Wellcome Trust
- National Institutes of Health (DE-AC02–05CH11231, GM063210)
- National Institute of General Medical Sciences (P01GM063210)
- Topics
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Inorganic Chemistry › Crystal structures of chemical compounds
- Keywords
- structure refinement, density modification, resolve, model completion, side-chain optimization, electron density
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