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Research

Published. Benchmarked. Reproducible.

Peer-reviewed methods that underpin the closed-loop platform. Each citation links to its original source.

Methods we publish.

  1. AsEP — Antibody-specific Epitope Prediction

    Graph-based deep learning benchmarked against published baselines (ICML 2024 Workshop).

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  2. CDR Loop Conformational Analysis

    Structural-bioinformatics analysis of antibody CDR loops upon antigen binding (mAbs 2024).

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  3. Knowledge-Based Retrieval

    The curated complex database powering platform queries.

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Publications

Nature Biotechnology · arXiv · NeurIPS 2024 · mAbsNewest first · each entry links to its source

  1. 2026

    A blinded, prospective benchmark of in silico antibody discovery anchored to experimental affinity and developability

    Erasmus, M. F., Bedinger, D., Hopkins, E., … Denzler, L., Liu, C., … Bradbury, A. R. M. (2026).

    Nature Biotechnology

    AIntibody · Benchmark · Antibody Design

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  1. 2025

    AbRank: A Benchmark Dataset and Metric-Learning Framework for Antibody-Antigen Affinity Ranking

    Liu, C., Pelissier, A., Shao, Y., Denzler, L., Martin, A. C. R., Paige, B., & Rodríguez Martínez, M. (2025).

    Pre-printarXiv

    Benchmark · Affinity Ranking

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  1. 2024

    AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction.

    Liu, C., Denzler, L., Chen, Y., Martin, A., & Paige, B. (2024).

    Advances in Neural Information Processing Systems 37 (NeurIPS 2024) — Datasets and Benchmarks Track

    Deep Learning · AsEP · Benchmark

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  2. Do antibody CDR loops change conformation upon binding?

    Liu, C., Denzler, L. M., Hood, O.E.C., & Martin, A. C. R. (2024).

    mAbs

    Antibody · CDR · mAbs

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Conferences

  1. 2025

    abYcloud — from research to startup

    Presented by Chunan L., University College London · Research Amplified: Harnessing AWS to Power Scientific Innovation — London, UK

    Talk · AWS

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  1. 2024

    C-169: Advancing Antibody-Specific Epitope Prediction with a Graph-Based Approach

    Liu, C. et al. · Intelligent Systems for Molecular Biology (ISMB) 2024 — Montreal, Canada

    Graph · Epitope Prediction

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  2. AsEP: Benchmarking Deep Learning Methods for Antibody-specific Epitope Prediction

    Liu, C. et al. · ICML 2024 Workshop — AI for Science — Vienna, Austria

    ICML · Workshop

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  1. 2023

    B109: Antigen-Specific Antibody Design: Preliminary Progress

    Presented by ChuNan L., University College London · Protein & Antibody Engineering Summit (PEGs) 2023 — Lisbon, Portugal

    Antigen-Specific · PEGs

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Open assets & datasets

Open data

AsEP Benchmark Dataset

Curated antibody-antigen complexes used to benchmark epitope-prediction methods.

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github · biochunan/AsEP-dataset

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