The HADDOCK2. 4 web server for integrative modeling of biomolecular complexes

RV Honorato, ME Trellet, B Jiménez-García… - Nature protocols, 2024 - nature.com
Interactions between macromolecules, such as proteins and nucleic acids, are essential for
cellular functions. Experimental methods can fail to provide all the information required to …

Development and use of machine learning algorithms in vaccine target selection

B Bravi - npj Vaccines, 2024 - nature.com
Computer-aided discovery of vaccine targets has become a cornerstone of rational vaccine
design. In this article, I discuss how Machine Learning (ML) can inform and guide key …

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 …

[HTML][HTML] Advances in computational structure-based antibody design

AM Hummer, B Abanades, CM Deane - Current opinion in structural biology, 2022 - Elsevier
Antibodies are currently the most important class of biotherapeutics and are used to treat
numerous diseases. Recent advances in computational methods are ushering in a new era …

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 …

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 …

An expanded benchmark for antibody-antigen docking and affinity prediction reveals insights into antibody recognition determinants

JD Guest, T Vreven, J Zhou, I Moal, JR Jeliazkov… - Structure, 2021 - cell.com
Accurate predictive modeling of antibody-antigen complex structures and structure-based
antibody design remain major challenges in computational biology, with implications for …

Computational methods in immunology and vaccinology: design and development of antibodies and immunogens

F Guarra, G Colombo - Journal of Chemical Theory and …, 2023 - ACS Publications
The design of new biomolecules able to harness immune mechanisms for the treatment of
diseases is a prime challenge for computational and simulative approaches. For instance, in …

[HTML][HTML] Affinity maturation of antibody fragments: A review encompassing the development from random approaches to computational rational optimization

J Li, G Kang, J Wang, H Yuan, Y Wu, S Meng… - International journal of …, 2023 - Elsevier
Routinely screened antibody fragments usually require further in vitro maturation to achieve
the desired biophysical properties. Blind in vitro strategies can produce improved ligands by …