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bioRxiv · 10.1101/2025.10.03.680230

PymolFold: A PyMOL Plugin for API-driven Structure Prediction and Quality Assessment

Deng, Y.·Sun, J.
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Abstract

Deep learning has transformed protein structure prediction, yet many experimental scientists face barriers in accessing state-of-the-art (SOTA) models due to technical complexity and hardware requirements. To address this, we present PymolFold, an open-source PyMOL plugin that seamlessly integrates cutting edge API-based protein structure predictors such as ESM-3 and Boltz2 into the molecular visualization environment. PymolFold supports both graphical and command-line interfaces for flexible usage and incorporates PXMeter, an open-source Python package for quantitative evaluation of protein structure predictions against reference data. Together, these features establish a unified "predict-visualize-analyze" workflow, lowering technical entry barriers and broadening access to advanced structural modeling. PymolFold is freely available at https://github.com/jinyuansun/PymolFold.

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Deng, Y., Sun, J.. 2025-10-07. PymolFold: A PyMOL Plugin for API-driven Structure Prediction and Quality Assessment. https://doi.org/10.1101/2025.10.03.680230

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