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Approximately 60% of pathogenic missense mutations lead to functional abnormalities by disrupting molecular interactions. However, although existing $\\Delta \\Delta G$ predictors exhibit strong performance in benchmarks, they suffer from inadequate generalization, a misalignment between evaluation metrics and practical needs, and poor adaptability to complex mutation scenarios. This study systematically assessed eight mainstream predictors, covering both physical energy function-based and machine learning-based methods, and constructed an independent evaluation set. This study employed multi-dimensional metrics, including regression accuracy and classification capability, while also analyzing the performance variations of predictors across different mutation types, stability categories, and microenvironments of protein mutation sites. The results indicate that &amp;gt;60% of predictors (5 out of 8) predictors exhibit a systematic bias toward overestimating mutational instability. In the three-class classification task, predictors demonstrate a limited ability to identify stabilizing mutations ($\\Delta \\Delta G&amp;lt; -0.5$ kcal\/mol), with recall rates &amp;lt;0.1 for this class, and overall predictive efficacy depends on the protein local structure. In summary, this study reveals the limitations of current $\\Delta \\Delta G$ predictors in terms of generalization and adaptability to complex scenarios, thus providing a reference for the optimization and practical application of $\\Delta \\Delta G$ prediction methods. It suggests that future breakthroughs can be achieved by constructing balanced and standardized datasets alongside developing local\u2013global fusion algorithms.<\/jats:p>","DOI":"10.1093\/bib\/bbaf645","type":"journal-article","created":{"date-parts":[[2025,11,18]],"date-time":"2025-11-18T12:46:09Z","timestamp":1763469969000},"source":"Crossref","is-referenced-by-count":0,"title":["Systematic evaluation of predictors for binding free energy changes upon mutations in protein complexes"],"prefix":"10.1093","volume":"26","author":[{"given":"Yu","family":"Zhang","sequence":"first","affiliation":[{"name":"Institute of Artificial Intelligence, School of Informatics, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, National Innovation Platform for Industry-Education Integration in Vaccine Research, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yunjiong","family":"Liu","sequence":"additional","affiliation":[{"name":"Institute of Artificial Intelligence, School of Informatics, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, National Innovation Platform for Industry-Education Integration in Vaccine Research, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yulin","family":"Zhang","sequence":"additional","affiliation":[{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, National Innovation Platform for Industry-Education Integration in Vaccine Research, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ziyang","family":"Wang","sequence":"additional","affiliation":[{"name":"Institute of Artificial Intelligence, School of Informatics, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, National Innovation Platform for Industry-Education Integration in Vaccine Research, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]},{"name":"State Key Laboratory of Vaccines for Infectious Diseases, Xiang An Biomedicine Laboratory, School of Public Health, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoli","family":"Lu","sequence":"additional","affiliation":[{"name":"Information and Networking Center, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province ,","place":["China"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shengxiang","family":"Ge","sequence":"additional","affiliation":[{"name":"National Institute of Diagnostics and Vaccine Development in Infectious Diseases, National Innovation Platform for Industry-Education Integration in Vaccine Research, NMPA Key Laboratory for Research and Evaluation of Infectious Disease Diagnostic Technology, Xiamen University , No. 4221, Xiang'an South Road, Xiang'an District, Xiamen City, 361005, Fujian Province 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