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Cited by 1,606Enzyme Structure and FunctionProtein Structure and DynamicsCrystal structures of chemical compounds

Automated macromolecular model building for X-ray crystallography using ARP/wARP version 7

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Langer, Gerrit, Cohen, Serge X, Lamzin, Victor S, Perrakis, Anastassis·2008·Nature Protocols
DOI 10.1038/nprot.2008.91PMC PMC2582149
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Abstract

ARP/wARP is a software suite to build macromolecular models in X-ray crystallography electron density maps. Structural genomics initiatives and the study of complex macromolecular assemblies and membrane proteins all rely on advanced methods for 3D structure determination. ARP/wARP meets these needs by providing the tools to obtain a macromolecular model automatically, with a reproducible computational procedure. ARP/wARP 7.0 tackles several tasks: iterative protein model building including a high-level decision-making control module; fast construction of the secondary structure of a protein; building flexible loops in alternate conformations; fully automated placement of ligands, including a choice of the best-fitting ligand from a 'cocktail'; and finding ordered water molecules. All protocols are easy to handle by a nonexpert user through a graphical user interface or a command line. The time required is typically a few minutes although iterative model building may take a few hours.

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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 [19]

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Cited by

Sorted by citations

Authors
Langer, G., Cohen, S. X., Lamzin, V. S., & Perrakis, A.
Affiliations
  • Deutsches Elektronen-Synchrotron DESY (DE)
  • The Netherlands Cancer Institute (NL)
Corresponding author
Lamzin, Victor S
ORCID
Venue
Nature Protocols
Publisher
Springer Science and Business Media LLC
Published
2008-06-19
Volume
3
Issue
7
Pages
1171-1179
ISSN
  • 1750-2799 (ISSN-L)
  • 1754-2189
DOI
10.1038/nprot.2008.91
PMC
PMC2582149
OpenAlex
W1969672293
Cited by
1,606
References
0
Citations by year
2026: 18 · 2025: 31 · 2024: 49 · 2023: 49 · 2022: 58 · 2021: 69 · 2020: 91 · 2019: 112 · 2018: 92 · 2017: 128 · 2016: 118 · 2015: 150 · 2014: 161 · 2013: 172 · 2012: 128
FWCI
30.44
Type
journal article
Language
en
Open access
Licence
www.springer.com/tdm (tdm)
Locations
  • Nature Protocols (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • HAL (submittedVersion)
Funders
  • Nederlandse Organisatie voor Wetenschappelijk Onderzoek
  • National Institute of General Medical Sciences (R01GM062612, R01 GM62612)
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
automatic model generation, macromolecular structure determination, electron density maps, secondary structure prediction, ordered water molecules, structural genomics, membrane proteins, graphical user interface
MeSH terms
Ligands, Models, Molecular, Proteins, Software, Crystallography, X-Ray, Macromolecular Substances

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