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

By T. Croll. 2018

1,782 citations recorded by the source corpus.

ISOLDE is an interactive molecular-dynamics environment for rebuilding models against experimental cryo-EM or crystallographic maps. Analysis of its results reinforces the need for great care when validating models built into low-resolution data.

Subfields: Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Materials Chemistry

1. Paul D. Adams
2. Randy J. Read
3. Pavel V. Afonine
4. T. C. Terwilliger
5. Yang Zhang
6. T. Croll
7. Nigel W. Moriarty
8. David Baker

In Molecular Biology

1. Yang Zhang
2. Randy J. Read
3. Paul D. Adams
4. David Baker
5. Pavel V. Afonine
6. T. C. Terwilliger
7. Andriy Kryshtafovych
8. T. Croll

Citations in the corpus

• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, methodology): “(vi) ISOLDE (Croll, 2018) is a plugin to UCSF ChimeraX (Goddard et al., 2018) for improving low-resolution cryo-EM or crystal structures.”
• Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, background): “The identification of these problems is not straightforward, and it is an important aspect of the ISOLDE interface.(22) The ability to “nudge” residues along a chain has now also been added into Coot, allowing quick generation of alternative hypotheses for the register of residues which the user can”
• Evaluation of model refinement in CASP13 (2019, background): “22 The problem in essence is that in any physically The question of how to handle refinement of single domains culled from their context in larger complexes is a challenging one with no easy answers.”
• Structure and dynamics of the CGRP receptor in apo and peptide-bound forms (2021, methodology): “6), the protein backbone was flexibly fitted into the illustrated map frames using Isolde (53), implemented in ChimeraX.”
• The human coronavirus HCoV-229E S-protein structure and receptor binding (2019, methodology): “To 576 improve the geometry of the atomic model, molecular dynamics-assisted model building was 577 carried out in ChimeraX (64) using the ISOLDE tool (65).”
• UCSF ChimeraX: Structure visualization for researchers, educators, and developers (2020, methodology): “…by local direct exploration (ISOLDE) plugin to ChimeraX for interactive dynamics-assisted structure building into cryo-EM and crystallographic maps 24 (https://isolde.cimr.cam. ac.uk) has already been cited in over 30 publications, including two focused on proteins from severe acute respiratory…”
• Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms (2020, methodology): “A uthor M anuscript A uthor M anuscript A uthor M anuscript A uthor M anuscript REAGENT or RESOURCE SOURCE IDENTIFIER pProEX-Htb-CtISWI77-Δ-722 Chittori et al., 2019 https://academic.oup.com/nar/ article/47/17/9400/5545016 Software and Algorithms Relion 3.0 Zivanov et al., 2018 https://github.com/3d”
• Comparative host-coronavirus protein interaction networks reveal pan-viral disease mechanisms. (2020, positive): “0 (73) using the plugin for UCSF ChimeraX (74).”
• DNSN-1 recruits GINS for CMG helicase assembly during DNA replication initiation in C. elegans (2023, positive): “To improve the fit of the model to our cryoEM density, COOT (68) was used to remove regions of the proteins for which density was not resolved before using an iterative combination of ISOLDE (71) [within UCSF ChimeraX (70, 72)] and COOT to adjust and refine models to density on a residue-by-residue ”