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PREreview of Deep Geometric Framework to Predict Antibody-Antigen Binding Affinity

by Randa Salah Gomaa Mahmoud
Published
DOI
10.5281/zenodo.12661726
License
CC BY 4.0

The goal of the study was to develop a general deep model that is not confined to a specific family of antigens. The proposed network was trained on a curated dataset comprising antibody-antigen pairs for HIV, MERS, flu virus, etc. The authors observed a significant improvement in the mean absolute error compared to existing state-of-the-art models.

Major issues

  • The statistical analysis section that includes the tests used for comparison and correlation, the program used to evaluate these tests, and the level of significance should be mentioned.

  • In Table 2: the mean absolute error (MAE) and mean squared error (MSE) are presented but no statistical comparisons were performed to assess if the differences are statistically significant.

  • Page3, 2nd column last paragraph:  Authors said “From Table 2, it is evident that our final Combined-V2 model outperforms all the considered state-of-the-art approaches at least by a margin of 10.6% while improving the performance of our individual sequence-based and structure-based models by 5.6% and 6.8%, respectively.” The mentioned percentages are not presented in the table

  • Page 3, 2nd column last paragraph: why authors examined both the Pearson correlation coefficient and Spearman’s correlation coefficient. Also, the p-value should be mentioned to assess the significance.

  • Page 4, 2nd column, Table 3: the mean absolute error (MAE) is presented as an indicator of performance but no statistical comparisons were performed to assess if the differences are statistically significant. This is also for table 4,5,7,8

Minor issues

  • Page1, Introduction section, 2nd column, 2nd paragraph: identify the abbreviation (IC50) as half-maximal inhibitory concentration

  • Page2, 1st column, 2nd paragraph:  the name of the author of reference (6) should be added as follows: In the study done by Shan et al, (6)

  • The correct Citation of reference 1: Lu RM, Hwang YC, Liu IJ, Lee CC, Tsai HZ, Li HJ, Wu HC. Development of therapeutic antibodies for the treatment of diseases. J Biomed Sci. 2020 Jan 2;27(1):1. doi: 10.1186/s12929-019-0592-z.

  • The correct citation of reference 2: Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD. Molecular docking and structure-based drug design strategies. Molecules. 2015 Jul 22;20(7):13384-421. doi: 10.3390/molecules200713384.

  • The previous citation should be applied to all references

  • Reference 23 is a repetition of reference 7

  • Reference 35 is a repetition of reference 30

Competing interests

The author declares that they have no competing interests.