In:
IUCrJ, International Union of Crystallography (IUCr), Vol. 6, No. 4 ( 2019-07-01), p. 526-531
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.
Type of Medium:
Online Resource
ISSN:
2052-2525
DOI:
10.1107/S2052252519007619
DOI:
10.1107/S2052252519007619/eh5002sup1.avi
DOI:
10.1107/S2052252519007619/eh5002sup2.avi
DOI:
10.1107/S2052252519007619/eh5002sup3.pdf
Language:
Unknown
Publisher:
International Union of Crystallography (IUCr)
Publication Date:
2019
detail.hit.zdb_id:
2754953-7
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