Third generation antibody discovery methods: in silico rational design

P Sormanni, FA Aprile, M Vendruscolo - Chemical Society Reviews, 2018 - pubs.rsc.org
Owing to their outstanding performances in molecular recognition, antibodies are
extensively used in research and applications in molecular biology, biotechnology and …

Structural aspects of the allergen-antibody interaction

A Pomés, GA Mueller, M Chruszcz - Frontiers in immunology, 2020 - frontiersin.org
The development of allergic disease involves the production of IgE antibodies upon allergen
exposure in a process called sensitization. IgE binds to receptors on the surface of mast …

In-silico evidence for a two receptor based strategy of SARS-CoV-2

E Milanetti, M Miotto, L Di Rienzo, M Nagaraj… - Frontiers in molecular …, 2021 - frontiersin.org
We propose a computational investigation on the interaction mechanisms between SARS-
CoV-2 spike protein and possible human cell receptors. In particular, we make use of our …

Antibody specific B-cell epitope predictions: leveraging information from antibody-antigen protein complexes

MC Jespersen, S Mahajan, B Peters… - Frontiers in …, 2019 - frontiersin.org
B-cells can neutralize pathogenic molecules by targeting them with extreme specificity using
receptors secreted or expressed on their surface (antibodies). This is achieved via molecular …

Rapid and accurate in silico solubility screening of a monoclonal antibody library

P Sormanni, L Amery, S Ekizoglou, M Vendruscolo… - Scientific reports, 2017 - nature.com
Antibodies represent essential tools in research and diagnostics and are rapidly growing in
importance as therapeutics. Commonly used methods to obtain novel antibodies typically …

Molecular mechanisms behind anti SARS-CoV-2 action of lactoferrin

M Miotto, L Di Rienzo, L Bò, A Boffi… - Frontiers in Molecular …, 2021 - frontiersin.org
Despite the huge effort to contain the infection, the novel SARS-CoV-2 coronavirus has
rapidly become pandemic, mainly due to its extremely high human-to-human transmission …

Assessment of therapeutic antibody developability by combinations of in vitro and in silico methods

AM Wolf Pérez, N Lorenzen, M Vendruscolo… - … Antibodies: Methods and …, 2022 - Springer
Although antibodies have become the fastest-growing class of therapeutics on the market, it
is still challenging to develop them for therapeutic applications, which often require these …

Real time structural search of the Protein Data Bank

D Guzenko, SK Burley, JM Duarte - PLoS computational biology, 2020 - journals.plos.org
Detection of protein structure similarity is a central challenge in structural bioinformatics.
Comparisons are usually performed at the polypeptide chain level, however the functional …

A computational method for immune repertoire mining that identifies novel binders from different clonotypes, demonstrated by identifying anti-pertussis toxoid …

E Richardson, JD Galson, P Kellam, DF Kelly, SE Smith… - MAbs, 2021 - Taylor & Francis
Due to their shared genetic history, antibodies from the same clonotype often bind to the
same epitope. This knowledge is used in immune repertoire mining, where known binders …

[HTML][HTML] 2D Zernike polynomial expansion: Finding the protein-protein binding regions

E Milanetti, M Miotto, L Di Rienzo, M Monti… - Computational and …, 2021 - Elsevier
We present a method for efficiently and effectively assessing whether and where two
proteins can interact with each other to form a complex. This is still largely an open problem …