Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

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 …

AggreProt: a web server for predicting and engineering aggregation prone regions in proteins

J Planas-Iglesias, S Borko, J Swiatkowski… - Nucleic Acids …, 2024 - academic.oup.com
Recombinant proteins play pivotal roles in numerous applications including industrial
biocatalysts or therapeutics. Despite the recent progress in computational protein structure …

AMYPred-FRL is a novel approach for accurate prediction of amyloid proteins by using feature representation learning

P Charoenkwan, S Ahmed, C Nantasenamat… - Scientific reports, 2022 - nature.com
Amyloid proteins have the ability to form insoluble fibril aggregates that have important
pathogenic effects in many tissues. Such amyloidoses are prominently associated with …

Machine learning prediction of antibody aggregation and viscosity for high concentration formulation development of protein therapeutics

PK Lai, A Gallegos, N Mody, HA Sathish, BL Trout - MAbs, 2022 - Taylor & Francis
Machine learning has been recently used to predict therapeutic antibody aggregation rates
and viscosity at high concentrations (150 mg/ml). These works focused on commercially …

Are fibrinaloid microclots a cause of autoimmunity in Long Covid and other post-infection diseases?

DB Kell, E Pretorius - Biochemical Journal, 2023 - portlandpress.com
It is now well established that the blood-clotting protein fibrinogen can polymerise into an
anomalous form of fibrin that is amyloid in character; the resultant clots and microclots entrap …

Protein aggregation: in silico algorithms and applications

R Prabakaran, P Rawat, AM Thangakani, S Kumar… - Biophysical …, 2021 - Springer
Protein aggregation is a topic of immense interest to the scientific community due to its role
in several neurodegenerative diseases/disorders and industrial importance. Several in silico …

Machine learning approaches in diagnosis, prognosis and treatment selection of cardiac amyloidosis

A Allegra, G Mirabile, A Tonacci, S Genovese… - International Journal of …, 2023 - mdpi.com
Cardiac amyloidosis is an uncommon restrictive cardiomyopathy featuring an unregulated
amyloid protein deposition that impairs organic function. Early cardiac amyloidosis …

CORDAX web server: an online platform for the prediction and 3D visualization of aggregation motifs in protein sequences

N Louros, F Rousseau, J Schymkowitz - Bioinformatics, 2024 - academic.oup.com
Motivation Proteins, the molecular workhorses of biological systems, execute a multitude of
critical functions dictated by their precise three-dimensional structures. In a complex and …

ANuPP: a versatile tool to predict aggregation nucleating regions in peptides and proteins

R Prabakaran, P Rawat, S Kumar… - Journal of molecular …, 2021 - Elsevier
Short aggregation prone sequence motifs can trigger aggregation in peptide and protein
sequences. Most algorithms developed so far to identify potential aggregation prone regions …