Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequence Article Swipe
Zhiwei Nie
,
Yiming Ma
,
Yutian Liu
,
Xiansong Huang
,
Zhihong Liu
,
Yang Peng
,
Fan Xu
,
Feng Yin
,
Zigang Li
,
J. Fu
,
Zhixiang Ren
,
Wenbin Zhang
,
Jie Chen
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbaf319
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbaf319
Predicting the protein stability changes upon mutations is one of the effective ways to improve the efficiency of protein engineering. Here, we propose a dual-view ensemble learning-based framework, DVE-stability, for mutation-induced protein stability change prediction from single sequence. DVE-stability integrates the global and local dependencies of mutations to capture the intramolecular interactions from two views through ensemble learning, in which a structural microenvironment simulation module is designed to indirectly introduce the information of structural microenvironment at the sequence level. DVE-stability achieved state-of-the-art prediction performance on seven single-point mutation benchmark datasets, and comprehensively surpassed other methods on five of them. Furthermore, DVE-stability outperformed other methods comprehensively through zero-shot inference on multiple-point mutation prediction task, demonstrating superior model generalizability to capture the epistasis of multiple-point mutations. More importantly, DVE-stability exhibited superior generalization performance in predicting rare beneficial mutations that are crucial for practical protein directed evolution scenarios. In addition, DVE-stability identified important intramolecular interactions via attention scores, demonstrating interpretable. Overall, DVE-stability provides a flexible and efficient tool for mutation-induced protein stability change prediction in an interpretable ensemble learning manner.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bib/bbaf319
- https://academic.oup.com/bib/article-pdf/26/4/bbaf319/63725431/bbaf319.pdf
- OA Status
- gold
- References
- 65
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4412184079
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- OpenAlex ID
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https://openalex.org/W4412184079Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/bib/bbaf319Digital Object Identifier
- Title
-
Predicting protein stability changes upon mutations with dual-view ensemble learning from single sequenceWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-06-17Full publication date if available
- Authors
-
Zhiwei Nie, Yiming Ma, Yutian Liu, Xiansong Huang, Zhihong Liu, Yang Peng, Fan Xu, Feng Yin, Zigang Li, J. Fu, Zhixiang Ren, Wenbin Zhang, Jie ChenList of authors in order
- Landing page
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https://doi.org/10.1093/bib/bbaf319Publisher landing page
- PDF URL
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https://academic.oup.com/bib/article-pdf/26/4/bbaf319/63725431/bbaf319.pdfDirect link to full text PDF
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YesWhether a free full text is available
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goldOpen access status per OpenAlex
- OA URL
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https://academic.oup.com/bib/article-pdf/26/4/bbaf319/63725431/bbaf319.pdfDirect OA link when available
- Concepts
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Mutation, Stability (learning theory), Benchmark (surveying), Computer science, Epistasis, Ensemble learning, Ensemble forecasting, Artificial intelligence, Sequence (biology), Protein sequencing, Point mutation, Machine learning, Biology, Genetics, Peptide sequence, Geography, Gene, GeodesyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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65Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W2111326065, https://openalex.org/W2147650094, https://openalex.org/W2145317354, https://openalex.org/W2794503008, https://openalex.org/W3035847987, https://openalex.org/W2100538849, https://openalex.org/W3014856454, https://openalex.org/W4206007286, https://openalex.org/W4200321201, https://openalex.org/W3048947632, https://openalex.org/W4394983192, https://openalex.org/W2023490488, https://openalex.org/W2151693654, https://openalex.org/W2125677968, https://openalex.org/W2103459989, https://openalex.org/W3109312535, https://openalex.org/W2324374958, https://openalex.org/W4391308485, https://openalex.org/W4400921915, https://openalex.org/W4403770916, https://openalex.org/W4296032638, https://openalex.org/W3171481040, https://openalex.org/W2262896633, https://openalex.org/W2953906682, https://openalex.org/W2121519777, https://openalex.org/W4388486442, https://openalex.org/W6858130012, https://openalex.org/W4401900858, https://openalex.org/W4327550249, https://openalex.org/W3177828909, https://openalex.org/W2980708516, https://openalex.org/W3116968030, https://openalex.org/W3176047188, https://openalex.org/W3093098684, https://openalex.org/W4224988655, https://openalex.org/W4392549818, https://openalex.org/W6780110802, https://openalex.org/W3146944767, https://openalex.org/W3083008290, https://openalex.org/W4379600237, https://openalex.org/W2767044445, https://openalex.org/W4366823175, https://openalex.org/W3121331573, https://openalex.org/W2003890287, https://openalex.org/W1554288134, https://openalex.org/W2139236870, https://openalex.org/W4233269677, https://openalex.org/W2801256450, https://openalex.org/W2922444498, https://openalex.org/W3205324928, https://openalex.org/W3119518863, https://openalex.org/W4384820649, https://openalex.org/W2950954328, https://openalex.org/W2172034373, https://openalex.org/W3105751341, https://openalex.org/W3093556707, https://openalex.org/W3104081477, https://openalex.org/W4315620405, https://openalex.org/W3117622225, https://openalex.org/W4292002633, https://openalex.org/W2030351692, https://openalex.org/W4386154677, https://openalex.org/W3012929814, https://openalex.org/W4390521376, https://openalex.org/W4387839235 |
| referenced_works_count | 65 |
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