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

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 w

SUBMITTER: Kidmose RT 

PROVIDER: S-EPMC6608625 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature