Emden: A novel method integrating graph and transformer representations for predicting the effect of mutations on clinical drug response

Liu, Zhe; Bao, Yihang; Wang, Weidi; Pan, Liangwei; Wang, Han; Lin, Guan Ning

doi:10.1016/j.compbiomed.2023.107678

Cited by 1 publication

(2 citation statements)

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“…The second research direction involves investigating the practical applications of protein stability predictions, such as forecasting the influence of variations on drug response. This can facilitate the screening of potent drugs [60] and the treatment of cancers caused by unstable proteins.…”

Section: Discussionmentioning

confidence: 99%

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Review of predicting protein stability changes upon variations

Qiu,

Huang,

Cai

2024

Proteomics

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Forecasting alterations in protein stability caused by variations holds immense importance. Improving the thermal stability of proteins is important for biomedical and industrial applications. This review discusses the latest methods for predicting the effects of mutations on protein stability, databases containing protein mutations and thermodynamic parameters, and experimental techniques for efficiently assessing protein stability in high‐throughput settings. Various publicly available databases for protein stability prediction are introduced. Furthermore, state‐of‐the‐art computational approaches for anticipating protein stability changes due to variants are reviewed. Each method's types of features, base algorithm, and prediction results are also detailed. Additionally, some experimental approaches for verifying the prediction results of computational methods are introduced. Finally, the review summarizes the progress and challenges of protein stability prediction and discusses potential models for future research directions.

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Section: Discussionmentioning

confidence: 99%

“…Emden [60] presents a new method that combines transformer and graph representations to forecast the influence of missense variations on drug response. This approach is based entirely on the molecular structure of the drug and protein sequences.…”

Section: Computational Methods For Protein Stability Predictionmentioning

confidence: 99%