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 …

[HTML][HTML] Recent progress in antibody epitope prediction

X Zeng, G Bai, C Sun, B Ma - Antibodies, 2023 - mdpi.com
Recent progress in epitope prediction has shown promising results in the development of
vaccines and therapeutics against various diseases. However, the overall accuracy and …

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 …

The role of force fields and water models in protein folding and unfolding dynamics

ALM Fischer, A Tichy, J Kokot… - Journal of Chemical …, 2024 - ACS Publications
Protein folding is a fascinating, not fully understood phenomenon in biology. Molecular
dynamics (MD) simulations are an invaluable tool to study conformational changes in …

Challenges in antibody structure prediction

ML Fernández-Quintero, J Kokot, F Waibl, ALM Fischer… - MAbs, 2023 - Taylor & Francis
Advances in structural biology and the exponential increase in the amount of high-quality
experimental structural data available in the Protein Data Bank has motivated numerous …

Leveraging artificial intelligence to expedite antibody design and enhance antibody–antigen interactions

DN Kim, AD McNaughton, N Kumar - Bioengineering, 2024 - mdpi.com
This perspective sheds light on the transformative impact of recent computational
advancements in the field of protein therapeutics, with a particular focus on the design and …

Antibodies exhibit multiple paratope states influencing VH–VL domain orientations

ML Fernández-Quintero, ND Pomarici, BA Math… - Communications …, 2020 - nature.com
In the last decades, antibodies have emerged as one of the most important and successful
classes of biopharmaceuticals. The highest variability and diversity of an antibody is …

Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2

F Gaudreault, CR Corbeil, T Sulea - Scientific Reports, 2023 - nature.com
Predicting the structure of antibody-antigen complexes has tremendous value in biomedical
research but unfortunately suffers from a poor performance in real-life applications …

Defining and studying B cell receptor and TCR interactions

CG Rappazzo, ML Fernández-Quintero… - The Journal of …, 2023 - academic.oup.com
Abstract BCRs (Abs) and TCRs (or adaptive immune receptors [AIRs]) are the means by
which the adaptive immune system recognizes foreign and self-antigens, playing an integral …

Local and global rigidification upon antibody affinity maturation

ML Fernández-Quintero, JR Loeffler… - Frontiers in molecular …, 2020 - frontiersin.org
During the affinity maturation process the immune system produces antibodies with higher
specificity and activity through various rounds of somatic hypermutations in response to an …