Namdinator – automatic molecular dynamics flexible fitting of structural models into cryo-EM and crystallography experimental maps
By R. Kidmose, Jonathan Juhl, P. Nissen, T. Boesen, J. Karlsen, B. P. Pedersen. bioRxiv, 2018
348 citations recorded by the source corpus.
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), or can be run locally as a command-line tool. Synopsis A pipeline tool called Namdinator is presented that enables the user to run a Molecular Dynamics Flexible Fitting (MDFF) simulation in a fully automated manner, both online and locally. This provides a fast and easy way to create suitable initial models for both cryo-EM and crystallography and help fix errors in the final steps of model building.
Subfields: Materials Chemistry, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/44874ce6dfc3188fa70a8beda6ab2c644351c2ae
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In Molecular Biology
Citations in the corpus
- Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex (2022, methodology): “The remainder of the IFT- A integrative model was fit into the map by successive rounds of breaking the structures and refining their fit using Namdinator (Kidmose et al., 2019).”
- Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA (2022, methodology): “The geometries of the intermediate structures were regularized using Phenix geometry minimization tools and molecular dynamics flexible fitting in Namdinator (39), using synthetic electron density maps generated in Chimera as inputs.”