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 …

An introduction to B‐cell epitope mapping and in silico epitope prediction

L Potocnakova, M Bhide… - Journal of immunology …, 2016 - Wiley Online Library
Identification of B‐cell epitopes is a fundamental step for development of epitope‐based
vaccines, therapeutic antibodies, and diagnostic tools. Epitope‐based antibodies are …

The structural basis of antibody-antigen recognition

I Sela-Culang, V Kunik, Y Ofran - Frontiers in immunology, 2013 - frontiersin.org
The function of antibodies (Abs) involves specific binding to antigens (Ags) and activation of
other components of the immune system to fight pathogens. The six hypervariable loops …

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 …

Reliable B cell epitope predictions: impacts of method development and improved benchmarking

JV Kringelum, C Lundegaard, O Lund… - PLoS computational …, 2012 - journals.plos.org
The interaction between antibodies and antigens is one of the most important immune
system mechanisms for clearing infectious organisms from the host. Antibodies bind to …

Structural analysis of B-cell epitopes in antibody: protein complexes

JV Kringelum, M Nielsen, SB Padkjær, O Lund - Molecular immunology, 2013 - Elsevier
The binding of antigens to antibodies is one of the key events in an immune response
against foreign molecules and is a critical element of several biomedical applications …

Improving B-cell epitope prediction and its application to global antibody-antigen docking

K Krawczyk, X Liu, T Baker, J Shi, CM Deane - Bioinformatics, 2014 - academic.oup.com
Motivation: Antibodies are currently the most important class of biopharmaceuticals.
Development of such antibody-based drugs depends on costly and time-consuming …

Progress and challenges in predicting protein interfaces

R Esmaielbeiki, K Krawczyk, B Knapp… - Briefings in …, 2016 - academic.oup.com
The majority of biological processes are mediated via protein–protein interactions.
Determination of residues participating in such interactions improves our understanding of …

How repertoire data are changing antibody science

C Marks, CM Deane - Journal of Biological Chemistry, 2020 - ASBMB
Antibodies are vital proteins of the immune system that recognize potentially harmful
molecules and initiate their removal. Mammals can efficiently create vast numbers of …

Antigen–antibody complexes

AB Kapingidza, K Kowal, M Chruszcz - Vertebrate and Invertebrate …, 2020 - Springer
Abstract In vertebrates, immunoglobulins (Igs), commonly known as antibodies, play an
integral role in the armamentarium of immune defense against various pathogens. After an …