Papers › Parapred: antibody paratope prediction using convolutional and recurrent neural networks
Parapred: antibody paratope prediction using convolutional and recurrent neural networks
Edgar Liberis1, Petar Velickovic, Pietro Sormanni, Michele Vendruscolo, Pietro Lio
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.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Tasks
Results from the paper archive 2025-07-28
| Task | Dataset | Model | Metric | Value | Rank at snapshot | Leaderboard | Report |
|---|---|---|---|---|---|---|---|
| Antibody-antigen binding prediction | MIPE | Parapred | AUC-PR | 0.652 | #5 of 7 | Archive leaderboard | report |
| Antibody-antigen binding prediction | MIPE | Parapred | AUC-ROC | 0.868 | #5 of 7 | Archive leaderboard | report |
| Antibody-antigen binding prediction | PECAN | Parapred | AUC-PR | 0.646 | #4 of 5 | Archive leaderboard | report |
| Antibody-antigen binding prediction | PECAN | Parapred | AUC-ROC | 0.930 | #4 of 5 | Archive leaderboard | report |
Ranks are positions in the archive's leaderboards as they stood at the 2025-07-28 snapshot. Results published since then are not among these rows, so a rank here is not a current standing.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections