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

IUCrJ. 2019 Jun 27;6(Pt 4):526-531. doi: 10.1107/S2052252519007619. eCollection 2019 Jul 1.

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.

Keywords: MDFF; automation; cryo-EM; crystallography; flexible fitting; model-fitting; molecular dynamics; molecular dynamics flexible fitting; web services.

Grant support

This work was funded by H2020 European Research Council grant 637372 to Bjørn Panyella Pedersen. Natur og Univers, Det Frie Forskningsråd grant DFF-4002-00052 to Bjørn Panyella Pedersen. Aarhus Institute of Advanced Studies, Aarhus Universitet grant .