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Would be a great merge. |
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Description
The purpose of the PR is to implement the cyclic offset positional encoding in OpenFold. Currently, the residue relative positions are computed linearly, meaning that the sequence is assumed to be a linear peptide. However, this relative positioning does not work well in cyclic peptides. As such, this PR applies the cyclical relative position encoding to allow for better prediction of cyclic species as first reported in the AfCycDesign preprint.
We are showing the result of applying the cyclic offset on the cyclic peptides tested by the AfCycDesign authors (see figure below). We are comparing the RSMD achieved using the standard linear offset with the RSMD achieved using the cyclic offset. The figure shows that for the majority of the peptides the cyclic offset achieved better alignment with the ground truth compared to the linear offset.
We note that we are using the unrelaxed version of the OpenFold output as we have noticed that the relaxed version does not preserve the cyclization bond.