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A pipeline merging AlphaFold2 and crosslinking mass spectrometry (XL-MS) for modeling proteins with multiple conformations. Utilizing two new scores, the monolink probability (MP) and crosslink probability (XLP), we outperformed previous scores on a decoy dataset. Our methodology, guided by real XL-MS data, proved effective in identifying accurate models within AF2 ensembles.

The link to gitlab is here.

Manalastas-Cantos K, Adoni KR, Pfeifer M, Märtens B, Grünewald K, Thalassinos K, Topf M. Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry. Mol. Cell. Proteomics 2024;100724.

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