Kidmose, R. T.; Juhl, J.; Nissen, P.; Boesen, T.; Karlsen, J. L. & Pedersen, B. P. Namdinator: automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps. IUCrJ, 2019, 6, 526-531
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, 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. 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 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 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. is available as a web service (https://namdinator.au.dk), or it can be run locally as a command-line tool.