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bioRxiv · 10.1101/2021.07.27.453972

Can AlphaFold2 predict protein-peptide complex structures accurately?

Ko, J.·Lee, J.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWIn this preprint, we investigated whether AlphaFold2, AF2, can predict protein-peptide complex structures only with sequence information. We modeled the structures of 203 protein-peptide complexes from the PepBDB DB and 183 from the PepSet. The structures were modeling with concatenated sequences of receptors and peptides via poly-glycine linker. We found that for more than half of the test cases, AF2 predicted the bound structures of peptides with good accuracy, C-RMSD of a peptide < 3.0 [A]. For about 40% of cases, the peptide structures were modeled with an accuracy of C-RMSD < 2.0 [A]. Our benchmark results clearly show that AF2 has a great potential to be applied to various higher-order structure prediction tasks.

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Ko, J., Lee, J.. 2021-07-27. Can AlphaFold2 predict protein-peptide complex structures accurately?. https://doi.org/10.1101/2021.07.27.453972

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