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 developing 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 …

Modeling and docking of antibody structures with Rosetta

BD Weitzner, JR Jeliazkov, S Lyskov, N Marze… - Nature protocols, 2017 - nature.com
We describe Rosetta-based computational protocols for predicting the 3D structure of an
antibody from sequence (RosettaAntibody) and then docking the antibody to protein …

ABodyBuilder: Automated antibody structure prediction with data–driven accuracy estimation

J Leem, J Dunbar, G Georges, J Shi, CM Deane - MAbs, 2016 - Taylor & Francis
Computational modeling of antibody structures plays a critical role in therapeutic antibody
design. Several antibody modeling pipelines exist, but no freely available methods currently …

SAbPred: a structure-based antibody prediction server

J Dunbar, K Krawczyk, J Leem, C Marks… - Nucleic acids …, 2016 - academic.oup.com
SAbPred is a server that makes predictions of the properties of antibodies focusing on their
structures. Antibody informatics tools can help improve our understanding of immune …

DLAB: deep learning methods for structure-based virtual screening of antibodies

C Schneider, A Buchanan, B Taddese… - …, 2022 - academic.oup.com
Motivation Antibodies are one of the most important classes of pharmaceuticals, with over 80
approved molecules currently in use against a wide variety of diseases. The drug discovery …

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 …

Modeling antibody-antigen complexes by information-driven docking

F Ambrosetti, B Jiménez-García, J Roel-Touris… - Structure, 2020 - cell.com
Antibodies are Y-shaped proteins essential for immune response. Their capability to
recognize antigens with high specificity makes them excellent therapeutic targets …

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 …

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 …