{"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/message-passing-networks-for-molecules-with","title":"Message Passing Networks for Molecules with Tetrahedral Chirality","arxiv_id":"2012.00094","date":"2020-11-24","proceeding":null,"authors":["Lagnajit Pattanaik","Octavian-Eugen Ganea","Ian Coley","Klavs F. Jensen","William H. Green","Connor W. Coley"],"abstract":"Molecules with identical graph connectivity can exhibit different physical and biological properties if they exhibit stereochemistry-a spatial structural characteristic. However, modern neural architectures designed for learning structure-property relationships from molecular structures treat molecules as graph-structured data and therefore are invariant to stereochemistry. Here, we develop two custom aggregation functions for message passing neural networks to learn properties of molecules with tetrahedral chirality, one common form of stereochemistry. We evaluate performance on synthetic data as well as a newly-proposed protein-ligand docking dataset with relevance to drug discovery. Results show modest improvements over a baseline sum aggregator, highlighting opportunities for further architecture development.","url_abs":"https://arxiv.org/abs/2012.00094v2","url_pdf":"https://arxiv.org/pdf/2012.00094v2.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":"message-passing-networks-for-molecules-with","repo_url":"https://github.com/PattanaikL/chiral_gnn","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2012.00094","mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}