{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/pymolfold-interactive-protein-and-ligand","title":"PyMOLfold: Interactive Protein and Ligand Structure Prediction in PyMOL","arxiv_id":"2502.00508","date":"2025-02-01","proceeding":null,"authors":["Colby T. Ford","Samee Ullah","Dinler Amaral Antunes","Tarsis Gesteira Ferreira"],"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.","url_abs":"https://arxiv.org/abs/2502.00508v1","url_pdf":"https://arxiv.org/pdf/2502.00508v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"pymolfold-interactive-protein-and-ligand","repo_url":"https://github.com/colbyford/pymolfold","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"prediction","task_name":"Prediction"},{"task_slug":"protein-folding","task_name":"Protein Folding"},{"task_slug":"protein-structure-prediction","task_name":"Protein Structure Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}