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ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

Open access
Croll, Tristan Ian·2018·Acta Crystallographica Section D Structural Biology

Abstract

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 visualization 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 visualized in real time. Using the recently described 3.8 Å resolution cryo-EM structure of the eukaryotic minichromosome maintenance (MCM) helicase complex as a case study, it is demonstrated 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.

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Cites

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Cited by

Items 101–200 of 208

Metadata

Authors
Croll, T. I.
Venue
Acta Crystallographica Section D Structural Biology
Published
2018-04-11
Volume
74
Issue
6
Pages
519-530
ISSN
2059-7983 (ISSN-L)
OpenAlex
W2801376357
Cited by
2,038
References
7
FWCI
25.66
Type
journal article
Language
en
Open access
hybrid
Licence
Funders
Wellcome Trust (082961/Z/07/Z)

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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

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