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 …

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 …

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 …

Exploring the sequence features determining amyloidosis in human antibody light chains

P Rawat, R Prabakaran, S Kumar, MM Gromiha - Scientific Reports, 2021 - nature.com
The light chain (AL) amyloidosis is caused by the aggregation of light chain of antibodies
into amyloid fibrils. There are plenty of computational resources available for the prediction …

[HTML][HTML] Accelerating therapeutic protein design with computational approaches toward the clinical stage

Z Chen, X Wang, X Chen, J Huang, C Wang… - Computational and …, 2023 - Elsevier
Therapeutic protein, represented by antibodies, is of increasing interest in human medicine.
However, clinical translation of therapeutic protein is still largely hindered by different …

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 …

CPAD 2.0: a repository of curated experimental data on aggregating proteins and peptides

P Rawat, R Prabakaran, R Sakthivel… - Amyloid, 2020 - Taylor & Francis
Abstract The Curated Protein Aggregation Database (CPAD) is a manually curated and
open-access database dedicated to providing comprehensive information related to …

Understanding the mutational frequency in SARS-CoV-2 proteome using structural features

P Rawat, D Sharma, M Pandey, R Prabakaran… - Computers in biology …, 2022 - Elsevier
The prolonged transmission of the severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) virus in the human population has led to demographic divergence and the …

Investigating the mechanism of action of aggregation-inducing antimicrobial Pept-ins

G Wu, L Khodaparast, L Khodaparast… - Cell Chemical …, 2021 - cell.com
Aggregation can be selectively induced by aggregation-prone regions (APRs) contained in
the target proteins. Aggregation-inducing antimicrobial peptides (Pept-ins) contain …

NmSEER V2. 0: a prediction tool for 2′-O-methylation sites based on random forest and multi-encoding combination

Y Zhou, Q Cui, Y Zhou - BMC bioinformatics, 2019 - Springer
Abstract Background 2′-O-methylation (2′-O-me or Nm) is a post-transcriptional RNA
methylation modified at 2′-hydroxy, which is common in mRNAs and various non-coding …