Response to “Addressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature”

Résumé fourni par la source

To the Editor, We would like to thank the rigorous dataset inspection work conducted by the author of “Addressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature”. The dataset of enzyme optimal temperature (Topt) used to develop Seq2Topt [1] was obtained from https://github.com/jafetgado/tomer, which was curated by Li et al. 2019 [2] and Gado et al. 2020 [3] from the BRENDA database [4]. In “Addressing flaws in the Seq2Topt dataset for the prediction of enzyme optimal temperature,” the author stated that the Topt values of F9FU71, A9U908, J7HET3, P94368, Q5YXQ1, Q83V33, Q50539, Q50538, Q2WCS9 are erroneously annotated in the dataset used by Seq2Topt. Here, we presented all references associated with these data entries in the BRENDA database in Table 1, and the Topt values of F9FU71, P94368, Q5YXQ1, Q83V33, Q50539, and Q50538 were not found in relevant references [5–9]. Dhar et al. 2013 [10] stated that the Topt values of A9U908 (sodA) and J7HET3 (sodB) were 4°C, but we agree with the critique that no enzyme activity measurements at lower temperatures were conducted to confirm that 4°C was the Topt value of A9U908 and J7HET3. For Q2WCS9, De Angelis et al. 2010 [11] reported that 13°C was the measured Topt value, whereas the critique letter did not provide a source for the claimed measured Topt value of 37°C. Selected nine entries from Seq2Topt dataset. Overall, we concur with the critique that the dataset used to develop enzyme Topt predictive models (and machine learning models for other protein properties) should be carefully reviewed and revised to ensure validity, rather than simply extracting data from established databases such as BRENDA. While such curation may be costly, it remains necessary until a high level of validity is automatically guaranteed by these biochemical databases. Accordingly, future updates of Seq2Topt will be based on a more rigorously vetted dataset. The author declares that there is no conflict of interest. None declared. No new data was generated in this study. This response letter refers to the data provided in the Seq2Topt study [1].

Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.