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

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...

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Bibliographic Details
Published in:IUCrJ Vol. 6; no. 4; pp. 526 - 531
Main Authors: Kidmose, Rune Thomas, Juhl, Jonathan, Nissen, Poul, Boesen, Thomas, Karlsen, Jesper Lykkegaard, Pedersen, Bjørn Panyella
Format: Journal Article
Language:English
Published: England International Union of Crystallography 01.07.2019
Subjects:
Automation
Computer simulation
cryo-EM
Crystallography
flexible fitting
MDFF
model-fitting
Molecular dynamics
molecular dynamics flexible fitting
Optimization
Outliers (statistics)
Research Letters
Web services
crystallography
MDFF
automation
web services
molecular dynamics flexible fitting
flexible fitting
molecular dynamics
cryo-EM
model-fitting
ISSN:2052-2525, 2052-2525
Online Access:Get full text
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Summary: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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ISSN:2052-2525
2052-2525
DOI:10.1107/S2052252519007619