Bond, Paul S. orcid.org/0000-0002-8465-4823 and Cowtan, Kevin D. orcid.org/0000-0002-0189-1437 (2022) ModelCraft:an advanced automated model-building pipeline using Buccaneer. Acta crystallographica. Section D, Structural biology. pp. 1090-1098. ISSN 2059-7983
Abstract
Interactive model building can be a difficult and time-consuming step in the structure-solution process. Automated model-building programs such as Buccaneer often make it quicker and easier by completing most of the model in advance. However, they may fail to do so with low-resolution data or a poor initial model or map. The Buccaneer pipeline is a relatively simple program that iterates Buccaneer with REFMAC to refine the model and update the map. A new pipeline called ModelCraft has been developed that expands on this to include shift-field refinement, machine-learned pruning of incorrect residues, classical density modification, addition of water and dummy atoms, building of nucleic acids and final rebuilding of side chains. Testing was performed on 1180 structures solved by experimental phasing, 1338 structures solved by molecular replacement using homologues and 2030 structures solved by molecular replacement using predicted AlphaFold models. Compared with the previous Buccaneer pipeline, ModelCraft increased the mean completeness of the protein models in the experimental phasing cases from 91% to 95%, the molecular-replacement cases from 50% to 78% and the AlphaFold cases from 82% to 91%.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Keywords: | automation,Buccaneer,model building,ModelCraft,software,structure solution,X-ray crystallography |
Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Chemistry (York) |
Depositing User: | Pure (York) |
Date Deposited: | 21 Oct 2022 14:10 |
Last Modified: | 21 Jan 2025 18:04 |
Published Version: | https://doi.org/10.1107/S2059798322007732 |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1107/S2059798322007732 |
Related URLs: | |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:192448 |
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Description: ModelCraft: an advanced automated modelbuilding pipeline using Buccaneer
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