Alharbi, Emad, Calinescu, Radu orcid.org/0000-0002-2678-9260 and Cowtan, Kevin Douglas orcid.org/0000-0002-0189-1437 (2023) Buccaneer model building with neural network fragment selection. Acta crystallographica. Section D, Structural biology. pp. 326-338. ISSN 2059-7983
Abstract
Tracing the backbone is a critical step in protein model building, as incorrect tracing leads to poor protein models. Here, a neural network trained to identify unfavourable fragments and remove them from the model-building process in order to improve backbone tracing is presented. Moreover, a decision tree was trained to select an optimal threshold to eliminate unfavourable fragments. The neural network was tested on experimental phasing data sets from the Joint Center for Structural Genomics (JCSG), recently deposited experimental phasing data sets (from 2015 to 2021) and molecular-replacement data sets. The experimental results show that using the neural network in the Buccaneer protein-model-building software can produce significantly more complete protein models than those built using Buccaneer alone. In particular, Buccaneer with the neural network built protein models with a completeness that was at least 5% higher for 25% and 50% of the original and truncated resolution JCSG experimental phasing data sets, respectively, for 28% of the recently collected experimental phasing data sets and for 43% of the molecular-replacement data sets.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Dates: |
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Institution: | The University of York |
Academic Units: | The University of York > Faculty of Sciences (York) > Computer Science (York) The University of York > Faculty of Sciences (York) > Chemistry (York) |
Depositing User: | Pure (York) |
Date Deposited: | 12 Apr 2023 07:40 |
Last Modified: | 16 Oct 2024 19:06 |
Published Version: | https://doi.org/10.1107/S205979832300181X |
Status: | Published |
Refereed: | Yes |
Identification Number: | 10.1107/S205979832300181X |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:198136 |
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Description: Buccaneer model building with neural network fragment selection
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