ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.
Acta crystallographica. Section D, Structural biology
MetadataShow full item record
Croll, T. (2018). ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps.. Acta crystallographica. Section D, Structural biology, 74 (Pt 6), 519-530. https://doi.org/10.1107/s2059798318002425
This paper introduces ISOLDE, a new software package designed to provide an intuitive environment for high-fidelity interactive remodelling/refinement of macromolecular models into electron density maps. ISOLDE combines interactive molecular dynamics flexible fitting with modern molecular graphics visualisation and established structural biology libraries to provide an immersive interface wherein the model constantly acts to maintain physically realistic conformations as the user interacts with it by directly tugging atoms with a mouse or haptic interface or applying/removing restraints. In addition, common validation tasks are accelerated and visualised in real-time. Using the recently-described 3.8Å cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, here I demonstrate how ISOLDE can be used alongside other modern refinement tools to avoid common pitfalls of low-resolution modelling and improve the quality of the final model. A detailed analysis of changes between the initial and final model provides a somewhat sobering insight into the dangers of relying on a small number of validation metrics to judge the quality of a low-resolution model.
Macromolecular Substances, Fungal Proteins, Cryoelectron Microscopy, Models, Molecular, Computer Simulation, Software, Validation Studies as Topic, Molecular Dynamics Simulation, Minichromosome Maintenance Proteins, Data Accuracy
Wellcome Trust (082961/Z/07/A)
Wellcome Trust (082961/Z/07/Z)
Embargo Lift Date
External DOI: https://doi.org/10.1107/s2059798318002425
This record's URL: https://www.repository.cam.ac.uk/handle/1810/277028
Attribution 4.0 International
Licence URL: http://creativecommons.org/licenses/by/4.0/
Recommended or similar items
The following licence files are associated with this item: