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Parapred: antibody paratope prediction using convolutional and recurrent neural networks.

Accepted version
Peer-reviewed

Type

Article

Change log

Authors

Liberis, Edgar 
Velickovic, Petar 
Vendruscolo, Michele  ORCID logo  https://orcid.org/0000-0002-3616-1610
Liò, Pietro 

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. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

Description

Keywords

Algorithms, Amino Acid Sequence, Antibodies, Binding Sites, Antibody, Deep Learning, Machine Learning, Models, Molecular, Neural Networks, Computer

Journal Title

Bioinformatics

Conference Name

Journal ISSN

1367-4803
1367-4811

Volume Title

34

Publisher

Oxford University Press (OUP)