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Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
Open accessPublished version of a preprint
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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Metadata
- Authors
- Kidmose, R. T., Juhl, J., Nissen, P., Boesen, T., Karlsen, J. L., & Pedersen, B. P.
- Venue
- IUCrJ
- Published
- 2019-06-27
- Volume
- 6
- Issue
- 4
- Pages
- 526-531
- ISSN
- 2052-2525 (ISSN-L)
- OpenAlex
- W2953798760
- Cited by
- 385
- References
- 5
- FWCI
- 16.65
- Type
- journal article
- Language
- en
- Open access
- gold
- Licence
- creativecommons.org/licenses/by/4.0/legalcode (vor)
- creativecommons.org/licenses/by/4.0/legalcode (tdm)
- 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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- Kidmose, R. T., Juhl, J., Nissen, P., Boesen, T., Karlsen, J. L., & Pedersen, B. P. (2019). Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCrJ. https://doi.org/10.1107/s2052252519007619
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