reactifpTM: an accessible reimplementation of actifpTM
Motivation: The actual interface pTM score (actifpTM) is a modified version of the ipTM score that limits the calculation to only those residues at the interface. Whilst actifpTM provides an effective interface quality score, a limiting factor is that it makes use of the predicted aligned error (PAE) with probabilities, information that is generated during a ColabFold run, but not output by the…
Motivation: The actifpTM score, a modified version of the ipTM score, is a commonly used measure for assessing interface quality. However, it relies on predicted aligned error (PAE) with probabilities, which is generated during a ColabFold run but not output by the package or other model prediction software. This limitation has hindered the adoption of actifpTM for software like AlphaFold 2 or AlphaFold 3, as it cannot generate actifpTM scores for their results.
To address this issue, reactifpTM has been developed as a standalone tool. It utilizes standard output files from model prediction software, such as a model and corresponding PAE, to perform an actifpTM-like calculation.
Results: By employing the same underlying principles as actifpTM, reactifpTM uses standard output files from model prediction software to carry out the calculation. When applied to a dataset of 1079 known interfaces in the PDB, strong correlations were observed between the actifpTM and reactifpTM scores.
Availability and implementation: The reactifpTM tool is coded in Python, making it accessible and easy to use. All scripts and associated documentation are available from the GitHub repository at https://github.com/hlasimpk/reactifptm or through the Python Package Index (PyPI) at https://pypi.org/project/reactifptm.
Written by urgent.news from bioRxiv's reporting — not their text. Machine-written — may contain errors; check the original before relying on it.
