Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
| Autor: | Rune Thomas Kidmose, Jonathan Juhl, Poul Nissen, Thomas Boesen, Jesper Lykkegaard Karlsen, Bjørn Panyella Pedersen |
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| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: | |
| Zdroj: | IUCrJ, Vol 6, Iss 4, Pp 526-531 (2019) |
| Druh dokumentu: | article |
| ISSN: | 2052-2525 20522525 |
| DOI: | 10.1107/S2052252519007619 |
| Popis: | 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. |
| Databáze: | Directory of Open Access Journals |
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