actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions
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| Format: | Preprint |
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2024
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| _version_ | 1866913621668265984 |
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| author | Varga, Julia K. Ovchinnikov, Sergey Schueler-Furman, Ora |
| author_facet | Varga, Julia K. Ovchinnikov, Sergey Schueler-Furman, Ora |
| contents | One of the main advantages of deep learning models of protein structure, such as Alphafold2, is their ability to accurately estimate the confidence of a generated structural model, which allows us to focus on highly confident predictions.The ipTM score provides a confidence estimate of interchain contacts in protein-protein interactions. However, interactions, in particular motif-mediated interactions, often also contain regions that remain flexible upon binding. These non-interacting flanking regions are assigned low confidence values and will affect iPTM, as it considers all interchain residue pairs, and two models of the same motif-domain interaction, but differing in the length of their flanking regions, would be assigned very different values. Here we propose actifpTM (actual interface pTM), a modified ipTM measure, that focuses on the confident region of an interaction, resulting in a more robust measure of interaction confidence, even when not the full interaction is structured. actifpTM has been incorporated into ColabFold. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2412_15970 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions Varga, Julia K. Ovchinnikov, Sergey Schueler-Furman, Ora Quantitative Methods One of the main advantages of deep learning models of protein structure, such as Alphafold2, is their ability to accurately estimate the confidence of a generated structural model, which allows us to focus on highly confident predictions.The ipTM score provides a confidence estimate of interchain contacts in protein-protein interactions. However, interactions, in particular motif-mediated interactions, often also contain regions that remain flexible upon binding. These non-interacting flanking regions are assigned low confidence values and will affect iPTM, as it considers all interchain residue pairs, and two models of the same motif-domain interaction, but differing in the length of their flanking regions, would be assigned very different values. Here we propose actifpTM (actual interface pTM), a modified ipTM measure, that focuses on the confident region of an interaction, resulting in a more robust measure of interaction confidence, even when not the full interaction is structured. actifpTM has been incorporated into ColabFold. |
| title | actifpTM: a refined confidence metric of AlphaFold2 predictions involving flexible regions |
| topic | Quantitative Methods |
| url | https://arxiv.org/abs/2412.15970 |