Computational approaches to therapeutic antibody design: established methods and emerging trends

RA Norman, F Ambrosetti, AMJJ Bonvin… - Briefings in …, 2020 - academic.oup.com
Antibodies are proteins that recognize the molecular surfaces of potentially noxious
molecules to mount an adaptive immune response or, in the case of autoimmune diseases …

Vaccination induces HIV broadly neutralizing antibody precursors in humans

DJ Leggat, KW Cohen, JR Willis, WJ Fulp, AC Decamp… - Science, 2022 - science.org
Broadly neutralizing antibodies (bnAbs) can protect against HIV infection but have not been
induced by human vaccination. A key barrier to bnAb induction is vaccine priming of rare …

Protein design with guided discrete diffusion

N Gruver, S Stanton, N Frey… - Advances in neural …, 2023 - proceedings.neurips.cc
A popular approach to protein design is to combine a generative model with a discriminative
model for conditional sampling. The generative model samples plausible sequences while …

[HTML][HTML] Progen2: exploring the boundaries of protein language models

E Nijkamp, JA Ruffolo, EN Weinstein, N Naik, A Madani - Cell systems, 2023 - cell.com
Attention-based models trained on protein sequences have demonstrated incredible
success at classification and generation tasks relevant for artificial-intelligence-driven …

IgLM: Infilling language modeling for antibody sequence design

RW Shuai, JA Ruffolo, JJ Gray - Cell Systems, 2023 - cell.com
Discovery and optimization of monoclonal antibodies for therapeutic applications relies on
large sequence libraries but is hindered by developability issues such as low solubility, high …

Observed Antibody Space: A diverse database of cleaned, annotated, and translated unpaired and paired antibody sequences

TH Olsen, F Boyles, CM Deane - Protein Science, 2022 - Wiley Online Library
The antibody repertoires of individuals and groups have been used to explore disease
states, understand vaccine responses, and drive therapeutic development. The arrival of B …

Enhancing stability of camelid and shark single domain antibodies: an overview

ER Goldman, JL Liu, D Zabetakis… - Frontiers in …, 2017 - frontiersin.org
Single domain antibodies (sdAbs) are gaining a reputation as superior recognition elements
as they combine the advantages of the specificity and affinity found in conventional …

Versatile and multivalent nanobodies efficiently neutralize SARS-CoV-2

Y **ang, S Nambulli, Z **ao, H Liu, Z Sang, WP Duprex… - Science, 2020 - science.org
Cost-effective, efficacious therapeutics are urgently needed to combat the COVID-19
pandemic. In this study, we used camelid immunization and proteomics to identify a large …

CoV-AbDab: the coronavirus antibody database

MIJ Raybould, A Kovaltsuk, C Marks… - Bioinformatics, 2021 - academic.oup.com
Motivation The emergence of a novel strain of betacoronavirus, SARS-CoV-2, has led to a
pandemic that has been associated with over 700 000 deaths as of August 5, 2020 …

ImmuneBuilder: Deep-Learning models for predicting the structures of immune proteins

B Abanades, WK Wong, F Boyles, G Georges… - Communications …, 2023 - nature.com
Immune receptor proteins play a key role in the immune system and have shown great
promise as biotherapeutics. The structure of these proteins is critical for understanding their …