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:2603. 13431v3 Announce Type: replace-cross Abstract: Computational antibody design has seen rapid methodological progress, with dozens of deep generative methods proposed in the past three years, yet the field lacks a standardized benchmark for fair comparison and model development.
By Mansoor Ahmed, Nadeem Taj, Imdad Ullah Khan, Hemanth Venkateswara, 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
arXiv:2609.00518v1 Announce Type: new
Abstract: Antibody-specific language models pretrained via masked language modeling (MLM) learn representations that are critical for downstream sequence design...
By Ayan Goel, Thomas A. Walton, Amirali Aghazadeh
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
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