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Cited by 385

The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.

Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

Open access
Kidmose, Rune Thomas, Juhl, Jonathan, Nissen, Poul, Boesen, Thomas, Karlsen, Jesper Lykkegaard, Pedersen, Bjørn Panyella·2019·IUCrJ
DOI 10.1107/s2052252519007619

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Abstract

Model building into experimental maps is a key element of structural biology, but can be both time consuming and error prone for low-resolution maps. Here we present Namdinator , an easy-to-use tool that enables the user to run a molecular dynamics flexible fitting simulation followed by real-space refinement in an automated manner through a pipeline system. Namdinator will modify an atomic model to fit within cryo-EM or crystallography density maps, and can be used advantageously for both the initial fitting of models, and for a geometrical optimization step to correct outliers, clashes and other model problems. We have benchmarked Namdinator against 39 deposited cryo-EM models and maps, and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and the model-to-map fit and overall model geometry were improved, in several cases substantially. We show that Namdinator is able to model large-scale conformational changes compared to the starting model. Namdinator is a fast and easy tool for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool.

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Show all 5 references

Research works printed but not linked: 20

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Cited by

Metadata

Authors
Kidmose, R. T., Juhl, J., Nissen, P., Boesen, T., Karlsen, J. L., & Pedersen, B. P.
Venue
IUCrJ
Publisher
International Union of Crystallography (IUCr)
Published
2019-06-27
Volume
6
Issue
4
Pages
526-531
ISSN
2052-2525 (ISSN-L)
DOI
10.1107/s2052252519007619
OpenAlex
W2953798760
Cited by
385
References
5
FWCI
16.65
Type
journal article
Language
en
Open access
gold
Licence
Funders
  • H2020 European Research Council (637372)
  • Natur og Univers, Det Frie Forskningsråd (DFF-4002-00052)
  • Aarhus Institute of Advanced Studies, Aarhus Universitet

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