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

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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..

Original languageEnglish
JournalIUCrJ
Volume6
Issue4
Pages (from-to)526-531
Number of pages6
ISSN2052-2525
DOIs
Publication statusPublished - 2019

    Research areas

  • automation, cryo-EM, crystallography, flexible fitting, MDFF, model-fitting, molecular dynamics, molecular dynamics flexible fitting, web services

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ID: 159031191