biostudies-literatureLiu ZNatural Science Foundation of ShanghaiNational Natural Science Foundation of ChinaNational Key R & D Program of ChinaShanghai Sailing Program1454https://www.ebi.ac.uk/biostudies/studies/S-EPMC9598995biostudies-literatureUnknown11(10)Though AlphaFold2 has attained considerably high precision on protein structure prediction, it is reported that directly inputting coordinates into deep learning networks cannot achieve desirable results on downstream tasks. Thus, how to process and encode the predicted results into effective forms that deep learning models can understand to improve the performance of downstream tasks is worth exploring. In this study, we tested the effects of five processing strategies of coordinates on two single-sequence protein binding site prediction tasks. These five strategies are spatial filtering, the singular value decomposition of a distance map, calculating the secondary structure feature, and the relative accessible surface area feature of proteins. The computational experiment results showed BiologyEvaluation of the Effectiveness of Derived Features of AlphaFold2 on Single-Sequence Protein Binding Site Prediction.PMC9598995nos. 81971292, 82150610506, 1210408881971292No: 21ZR14286001210408821ZR1428600821506105062022ZD0209100No: 19YF140020019YF1400200Li WPan WLiu ZZhen XLiang JYuan KXu FLin GNCai WfalseEvaluation of the Effectiveness of Derived Features of AlphaFold2 on Single-Sequence Protein Binding Site Prediction.Though AlphaFold2 has attained considerably high precision on protein structure prediction, it is reported that directly inputting coordinates into deep learning networks cannot achieve desirable results on downstream tasks. Thus, how to process and encode the predicted results into effective forms that deep learning models can understand to improve the performance of downstream tasks is worth exploring. In this study, we tested the effects of five processing strategies of coordinates on two single-sequence protein binding site prediction tasks. These five strategies are spatial filtering, the singular value decomposition of a distance map, calculating the secondary structure feature, and the relative accessible surface area feature of proteins. The computational experiment results showed 2022-01-01T00:00:00Z2022 Oct2026-06-21T03:08:49.775Z2024-11-19T16:30:07.826ZS-EPMC95989953629035810.3390/biology11101454