Transformer technology in molecular science

J Jiang, L Ke, L Chen, B Dou, Y Zhu… - Wiley …, 2024 - Wiley Online Library
A transformer is the foundational architecture behind large language models designed to
handle sequential data by using mechanisms of self‐attention to weigh the importance of …

Generative AI: driving productivity and scientific breakthroughs in pharmaceutical R&D

G Doron, S Genway, M Roberts, S Jasti - Drug Discovery Today, 2024 - Elsevier
Highlights•Generative AI accelerates discovery, improves targets, and boosts R&D
productivity.•Smarter assistants and generative biology in Horizon 1 revolutionize R&D …

New Horizons: Pioneering Pharmaceutical R&D with Generative AI from lab to the clinic--an industry perspective

G Doron, S Genway, M Roberts, S Jasti - ar** the strategic vision for R&D across
industries. The unique challenges of pharmaceutical R&D will see applications of generative …

Deep learning-based design and experimental validation of a medicine-like human antibody library

N Rajagopal, U Choudhary, K Tsang… - Briefings in …, 2025 - academic.oup.com
Antibody generation requires the use of one or more time-consuming methods, namely
animal immunization, and in vitro display technologies. However, the recent availability of …

[HTML][HTML] A Comprehensive Overview of Recent Advances in Generative Models for Antibodies

F Meng, N Zhou, G Hu, R Liu, Y Zhang, M **g… - Computational and …, 2024 - Elsevier
Therapeutic antibodies are an important class of biopharmaceuticals. With the rapid
development of deep learning methods and the increasing amount of antibody data …

HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer

X Xu, C Xu, W He, L Wei, H Li, J Zhou, R Zhang… - …, 2024 - academic.oup.com
Motivation Macrocyclic peptides hold great promise as therapeutics targeting intracellular
proteins. This stems from their remarkable ability to bind flat protein surfaces with high …

Development and experimental validation of computational methods for human antibody affinity enhancement

J Li, L Liao, C Zhang, K Huang, P Zhang… - Briefings in …, 2024 - academic.oup.com
High affinity is crucial for the efficacy and specificity of antibody. Due to involving high-
throughput screens, biological experiments for antibody affinity maturation are time …

[HTML][HTML] Improving antibody optimization ability of generative adversarial network through large language model

W Zhao, X Luo, F Tong, X Zheng, J Li, G Zhao… - Computational and …, 2023 - Elsevier
Generative adversarial networks (GANs) have successfully generated functional protein
sequences. However, traditional GANs often suffer from inherent randomness, resulting in a …

Leveraging Large Language Models to Predict Antibody Biological Activity Against Influenza A Hemagglutinin

E Barkan, I Siddiqui, KJ Cheng, A Golts… - arxiv preprint arxiv …, 2025 - arxiv.org
Monoclonal antibodies (mAbs) represent one of the most prevalent FDA-approved
modalities for treating autoimmune diseases, infectious diseases, and cancers. However …

ProteinRL: Reinforcement learning with generative protein language models for property-directed sequence design

M Sternke, J Karpiak - NeurIPS 2023 Generative AI and Biology …, 2023 - openreview.net
The overarching goal of protein engineering is the design and optimization of proteins
customized for specific purposes. Generative protein language models (PLMs) allow …