Dec 23, 2018

Namdinator - Automatic Molecular Dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps

BioRxiv : the Preprint Server for Biology
Rune Thomas KidmoseBjørn Panyella Pedersen

Abstract

Model building into experimental maps is a key element of structural biology, but can be both time consuming and error-prone. Here we present Namdinator, an easy-to-use tool that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation 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 models and maps from cryo-EM and observe model improvements in 34 of these cases (87%). Clashes between atoms were reduced, and 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 way to create suitable initial models for both cryo-EM and crystallography. It can fix model errors in the final steps of model building, and is usable for structural model builders at all skill levels. Namdinator is available as a web service (https://namdinator.au.dk...Continue Reading

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Mentioned in this Paper

Molecular_function
Fitness Centers
Electron Microscopy
Simulation
Crystallography

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