Progress and challenges for the machine learning-based design of fit-for-purpose monoclonal antibodies

R Akbar, H Bashour, P Rawat, PA Robert, E Smorodina… - MAbs, 2022 - Taylor & Francis
Although the therapeutic efficacy and commercial success of monoclonal antibodies (mAbs)
are tremendous, the design and discovery of new candidates remain a time and cost …

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 …

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

JA Ruffolo, LS Chu, SP Mahajan, JJ Gray - Nature communications, 2023 - nature.com
Antibodies have the capacity to bind a diverse set of antigens, and they have become critical
therapeutics and diagnostic molecules. The binding of antibodies is facilitated by a set of six …

Antibody structure prediction using interpretable deep learning

JA Ruffolo, J Sulam, JJ Gray - Patterns, 2022 - cell.com
Therapeutic antibodies make up a rapidly growing segment of the biologics market.
However, rational design of antibodies is hindered by reliance on experimental methods for …

Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies

JA Ruffolo, JJ Gray - Biophysical Journal, 2022 - cell.com
1Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA,
2Department of Chemical and Biomolecular Engineering, Johns Hopkins University …

How can we discover developable antibody-based biotherapeutics?

J Bauer, N Rajagopal, P Gupta, P Gupta… - Frontiers in Molecular …, 2023 - frontiersin.org
Antibody-based biotherapeutics have emerged as a successful class of pharmaceuticals
despite significant challenges and risks to their discovery and development. This review …

Antibody variable sequences have a pronounced effect on cellular transport and plasma half-life

A Grevys, R Frick, S Mester, K Flem-Karlsen, J Nilsen… - Iscience, 2022 - cell.com
Monoclonal IgG antibodies are the fastest growing class of biologics, but large differences
exist in their plasma half-life in humans. Thus, to design IgG antibodies with favorable …

A comparison of antibody–antigen complex sequence‐to‐structure prediction methods and their systematic biases

KM McCoy, ME Ackerman, G Grigoryan - Protein Science, 2024 - Wiley Online Library
The ability to accurately predict antibody–antigen complex structures from their sequences
could greatly advance our understanding of the immune system and would aid in the …

Protein structure prediction with mass spectrometry data

SE Biehn, S Lindert - Annual review of physical chemistry, 2022 - annualreviews.org
Knowledge of protein structure is crucial to our understanding of biological function and is
routinely used in drug discovery. High-resolution techniques to determine the three …

[HTML][HTML] Studying the characteristics of nanobody CDR regions based on sequence analysis in combination with 3D structures

TTT Truong, VQ Huynh, NT Vo, HD Nguyen - Journal of Genetic …, 2022 - Elsevier
Background Single-domain antibodies or nanobodies have recently attracted much attention
in research and applications because of their great potential and advantage over …