arXiv:2605. 21610v2 Announce Type: replace Abstract: Antibody design methods condition on antigen structure to generate complementarity-determining regions (CDR), yet a systematic evaluation of baseline methods reveals that they largely ignore the antigen input.
By Mansoor Ahmed, Murray Patterson
arXiv:2606. 04154v1 Announce Type: cross Abstract: Antibodies neutralize foreign antigens by binding to specific surface regions called epitopes.
By Mansoor Ahmed, Huirong Chai, Haoxin Wang, Hemanth Venkateswara, Murray Patterson
arXiv:2607. 20057v1 Announce Type: cross Abstract: Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules.
By Xiaoliang Shi, Zichen Wang, Runze Ma, Zhongyue Zhang, Shuangjia Zheng
Antibodies are essential proteins that play a central role in immune recognition by binding specific antigen molecules. Although recent protein language models have enabled progress in single-chain protein modeling and generation, they often fall short in antigen-specific antibody design, where effective modeling requires explicit pairing between antibody and antigen, particularly at the epitope level.
arXiv:2605. 21600v2 Announce Type: replace Abstract: Computational antibody CDR design methods condition on antigen structure to generate binding loops.
By Mansoor Ahmed, Spencer VonBank, Nadeem Taj, Sujin Lee, Naila Jan, Murray Patterson
DuaDeep-SeqAffinity is a sequence-only deep learning framework that predicts antibody–antigen binding affinity directly from primary amino acid sequences, eliminating the need for resolved 3D structures. The model processes the antigen and the antibody heavy and light chains as three independent streams, each embedded with a frozen ESM‑2 protein language model and passed through parallel Transformer and CNN branches before late fusion. On a sequence‑disjoint split of the AbRank benchmark, it achieves a Pearson correlation of 0.683, an R² of 0.460, and a pairwise ranking AUC of 0.895, outperforming single‑branch ablations and showing attention to CDR loops and epitope residues.
By Aicha Boutorh, Soumia Bouyahiaoui, Manel Kara Laouar, Sara Belhadj, Nour El Yakine Guendouz, Asma Boutorh