{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T09:50:22Z","timestamp":1775382622271,"version":"3.50.1"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2022,7,27]],"date-time":"2022-07-27T00:00:00Z","timestamp":1658880000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Prediction of protein stability change upon mutation (\u0394\u0394G) is crucial for facilitating protein engineering and understanding of protein folding principles. Robust prediction of protein folding free energy change requires the knowledge of protein three-dimensional (3D) structure. In case, protein 3D structure is not available, one can predict the structure from protein sequence; however, the perspectives of \u0394\u0394G predictions for predicted protein structures are unknown. The accuracy of using 3D structures of the best templates for the \u0394\u0394G prediction is also unclear.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>To investigate these questions, we used a representative set of seven diverse and accurate publicly available tools (FoldX, Eris, Rosetta, DDGun, ACDC-NN, ThermoNet and DynaMut) for stability change prediction combined with AlphaFold or I-Tasser for protein 3D structure prediction. We found that best templates perform consistently better than (or similar to) homology models for all \u0394\u0394G predictors. Our findings imply using the best template structure for the prediction of protein stability change upon mutation if the protein 3D structure is not available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The data are available at https:\/\/github.com\/ivankovlab\/template-vs-model.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac515","type":"journal-article","created":{"date-parts":[[2022,7,27]],"date-time":"2022-07-27T10:49:34Z","timestamp":1658918974000},"page":"4312-4320","source":"Crossref","is-referenced-by-count":21,"title":["Best templates outperform homology models in predicting the impact of mutations on protein stability"],"prefix":"10.1093","volume":"38","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1075-6509","authenticated-orcid":false,"given":"Marina A","family":"Pak","sequence":"first","affiliation":[{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology , Moscow 121205, Russia"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8224-4118","authenticated-orcid":false,"given":"Dmitry N","family":"Ivankov","sequence":"additional","affiliation":[{"name":"Center of Life Sciences, Skolkovo Institute of Science and Technology , Moscow 121205, Russia"}]}],"member":"286","published-online":{"date-parts":[[2022,7,27]]},"reference":[{"key":"2023041408230525900_","article-title":"A structural biology community assessment of AlphaFold 2 applications","author":"Akdel","year":"2021","journal-title":"bioRxiv"},{"key":"2023041408230525900_","doi-asserted-by":"crossref","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool","volume":"215","author":"Altschul","year":"1990","journal-title":"J. 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