{"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/parapred-antibody-paratope-prediction-using","title":"Parapred: antibody paratope prediction using convolutional and recurrent neural networks","arxiv_id":null,"date":"2018-04-16","proceeding":"Bioinformatics 2018 4","authors":["Edgar Liberis1","Petar Velickovic","Pietro Sormanni","Michele Vendruscolo","Pietro Lio"],"abstract":"Motivation: Antibodies play essential roles in the immune system of vertebrates and are powerful tools in research and diagnostics. While hypervariable regions of antibodies, which are responsible for binding, can be readily identified from their amino acid sequence, it remains challenging to accurately pinpoint which amino acids will be in contact with the antigen (the paratope). Results: In this work, we present a sequence-based probabilistic machine learning algorithm for paratope prediction, named Parapred. Parapred uses a deep-learning architecture to leverage features from both local residue neighbourhoods and across the entire sequence. The method significantly improves on the current state-of-the-art methodology, and only requires a stretch of amino acid sequence corresponding to a hypervariable region as an input, without any information about the antigen. We further show that our predictions can be used to improve both speed and accuracy of a rigid docking algorithm. Availability and implementation: The Parapred method is freely available as a webserver at http:// www-mvsoftware.ch.cam.ac.uk/and for download at https://github.com/eliberis/parapred. Contact: el398@cam.ac.uk or ps589@cam.ac.uk Supplementary information: Supplementary information is available at Bioinformatics online.","url_abs":"https://academic.oup.com/bioinformatics/article/34/17/2944/4972995","url_pdf":"https://academic.oup.com/bioinformatics/article-pdf/34/17/2944/50581998/bioinformatics_34_17_2944.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":"parapred-antibody-paratope-prediction-using","repo_url":"https://github.com/eliberis/parapred","is_official":0,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"tf","reach":null}],"tasks":[{"task_slug":"antibody-antigen-binding-prediction","task_name":"Antibody-antigen binding prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[{"leaderboard":"/sota/antibody-antigen-binding-prediction-on-mipe","task":"Antibody-antigen binding prediction","dataset":"MIPE","model":"Parapred","rank_in_archive_order":5,"of":7,"metrics":{"AUC-PR":"0.652","AUC-ROC":"0.868"},"uses_additional_data":false},{"leaderboard":"/sota/antibody-antigen-binding-prediction-on-pecan","task":"Antibody-antigen binding prediction","dataset":"PECAN","model":"Parapred","rank_in_archive_order":4,"of":5,"metrics":{"AUC-PR":"0.646","AUC-ROC":"0.930"},"uses_additional_data":false}],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}