Machine-designed biotherapeutics: opportunities, feasibility and advantages of deep learning in computational antibody discovery

W Wilman, S Wróbel, W Bielska… - Briefings in …, 2022 - academic.oup.com
Antibodies are versatile molecular binders with an established and growing role as
therapeutics. Computational approaches to develo** and designing these molecules are …

Assessing developability early in the discovery process for novel biologics

ML Fernández-Quintero, A Ljungars, F Waibl, V Greiff… - MAbs, 2023 - Taylor & Francis
Beyond potency, a good developability profile is a key attribute of a biological drug.
Selecting and screening for such attributes early in the drug development process can save …

Accelerating Bayesian optimization for biological sequence design with denoising autoencoders

S Stanton, W Maddox, N Gruver… - International …, 2022 - proceedings.mlr.press
Bayesian optimization (BayesOpt) is a gold standard for query-efficient continuous
optimization. However, its adoption for drug design has been hindered by the discrete, high …

Machine learning optimization of candidate antibody yields highly diverse sub-nanomolar affinity antibody libraries

L Li, E Gupta, J Spaeth, L Shing, R Jaimes… - Nature …, 2023 - nature.com
Therapeutic antibodies are an important and rapidly growing drug modality. However, the
design and discovery of early-stage antibody therapeutics remain a time and cost-intensive …

Regression transformer enables concurrent sequence regression and generation for molecular language modelling

J Born, M Manica - Nature Machine Intelligence, 2023 - nature.com
Despite tremendous progress of generative models in the natural sciences, their
controllability remains challenging. One fundamentally missing aspect of molecular or …

In vivo neutralization of coral snake venoms with an oligoclonal nanobody mixture in a murine challenge model

M Benard-Valle, Y Wouters, A Ljungars… - Nature …, 2024 - nature.com
Oligoclonal mixtures of broadly-neutralizing antibodies can neutralize complex compositions
of similar and dissimilar antigens, making them versatile tools for the treatment of eg …

The RESP AI model accelerates the identification of tight-binding antibodies

J Parkinson, R Hard, W Wang - Nature communications, 2023 - nature.com
High-affinity antibodies are often identified through directed evolution, which may require
many iterations of mutagenesis and selection to find an optimal candidate. Deep learning …

End-to-end meta-bayesian optimisation with transformer neural processes

A Maraval, M Zimmer, A Grosnit… - Advances in Neural …, 2023 - proceedings.neurips.cc
Meta-Bayesian optimisation (meta-BO) aims to improve the sample efficiency of Bayesian
optimisation by leveraging data from related tasks. While previous methods successfully …

Antibody optimization enabled by artificial intelligence predictions of binding affinity and naturalness

S Bachas, G Rakocevic, D Spencer, AV Sastry, R Haile… - BioRxiv, 2022 - biorxiv.org
Traditional antibody optimization approaches involve screening a small subset of the
available sequence space, often resulting in drug candidates with suboptimal binding …

Ai models for protein design are driving antibody engineering

MF Chungyoun, JJ Gray - Current opinion in biomedical engineering, 2023 - Elsevier
Therapeutic antibody engineering seeks to identify antibody sequences with specific binding
to a target and optimized drug-like properties. When guided by deep learning, antibody …