PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL

TL;DR

PyMOLfold is an open-source plugin that integrates AI-based protein and ligand structure prediction directly into PyMOL, streamlining the process from sequence input to 3D visualization within a single platform.

Contribution

It introduces a novel, user-friendly tool that combines advanced protein folding models with structural visualization in PyMOL, simplifying workflows for researchers.

Findings

Enables direct prediction of protein structures from sequences within PyMOL.

Supports ligand placement using SMILES strings alongside protein folding.

Provides an integrated environment for structure prediction and visualization.

Abstract

PyMOLfold is a flexible and open-source plugin designed to seamlessly integrate AI-based protein structure prediction and visualization within the widely used PyMOL molecular graphics system. By leveraging state-of-the-art protein folding models such as ESM3, Boltz-1, and Chai-1, PyMOLfold allows researchers to directly predict protein tertiary structures from amino acid sequences without requiring external tools or complex workflows. Furthermore, with certain models, users can provide a SMILES string of a ligand and have the small molecule placed in the protein structure. This unique capability bridges the gap between computational folding and structural visualization, enabling users to input a primary sequence, perform a folding prediction, and immediately explore the resulting 3D structure within the same intuitive platform.