Structure-based drug repurposing: Traditional and advanced AI/ML-aided methods

C Choudhury, NA Murugan, UD Priyakumar - Drug discovery today, 2022 - Elsevier
Highlights•Repurposing existing drugs for new diseases is cost effective and time saving.•In
silico methods are crucial for rapid drug screening in the early stages.•Machine learning …

[HTML][HTML] 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 optimization of antibody humanness and stability by systematic energy-based ranking

A Tennenhouse, L Khmelnitsky, R Khalaila… - Nature biomedical …, 2024 - nature.com
Conventional methods for humanizing animal-derived antibodies involve grafting their
complementarity-determining regions onto homologous human framework regions …

Molecularly imprinted polypyrrole nanotubes based electrochemical sensor for glyphosate detection

S Ding, Z Lyu, S Li, X Ruan, M Fei, Y Zhou, X Niu… - Biosensors and …, 2021 - Elsevier
An electrochemical sensor based on molecularly imprinted polypyrrole nanotubes (MIPNs)
has been developed for the detection of glyphosate (Gly) with high sensitivity and specificity …

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 …

SAbDab: the structural antibody database

J Dunbar, K Krawczyk, J Leem, T Baker… - Nucleic acids …, 2014 - academic.oup.com
Structural antibody database (SAbDab; http://opig. stats. ox. ac. uk/webapps/sabdab) is an
online resource containing all the publicly available antibody structures annotated and …

[HTML][HTML] Performance and its limits in rigid body protein-protein docking

IT Desta, KA Porter, B Xia, D Kozakov, S Vajda - Structure, 2020 - cell.com
The development of fast Fourier transform (FFT) algorithms enabled the sampling of billions
of complex conformations and thus revolutionized protein-protein docking. FFT-based …

[HTML][HTML] A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding

R Akbar, PA Robert, M Pavlović, JR Jeliazkov… - Cell Reports, 2021 - cell.com
Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-
epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo …

A specific antidote for dabigatran: functional and structural characterization

F Schiele, J van Ryn, K Canada… - Blood, The Journal …, 2013 - ashpublications.org
Dabigatran etexilate is a direct thrombin inhibitor and used widely as an anticoagulant for
the prevention of stroke in patients with atrial fibrillation. However, anticoagulation therapy …

Non-specificity as the sticky problem in therapeutic antibody development

H Ausserwöger, MM Schneider, TW Herling… - Nature Reviews …, 2022 - nature.com
Antibodies are highly potent therapeutic scaffolds with more than a hundred different
products approved on the market. Successful development of antibody-based drugs …