Protein glycosylation, a vital post-translational modification, is pivotal in various biological processes and disease pathogenesis. Computational approaches, including protein language models and machine learning algorithms, have emerged as valuable...
Journal of chemical information and modeling
40309917
While predicting structure-function relationships from sequence data is fundamental in biophysical chemistry, identifying prospective single-point and collective mutation sites in proteins can help us stay ahead in understanding their potential effec...
Deep machine learning demonstrates a capacity to uncover evolutionary relationships directly from protein sequences, in effect internalising notions inherent to classical phylogenetic tree inference. We connect these two paradigms by assessing the ca...
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence ...
The pursuit of obtaining enzymes with high activity and stability remains a grail in enzyme evolution due to the stability-activity trade-off. Here, we develop an isothermal compressibility-assisted dynamic squeezing index perturbation engineering (i...
A comprehensive, computable representation of the functional repertoire of all macromolecules encoded within the human genome is a foundational resource for biology and biomedical research. The Gene Ontology Consortium has been working towards this g...
In infected individuals, viruses are present as a population consisting of dominant and minor variant genomes. Most databases contain information on the dominant genome sequence. Since the emergence of SARS-CoV-2 in late 2019, variants have been sele...
Journal of chemical theory and computation
40079215
Protein evolution has shaped enzymes that maintain stability and function across diverse thermal environments. While sequence variation, thermal stability and conformational dynamics are known to influence an enzyme's thermal adaptation, how these fa...
Most antibodies for treating COVID-19 rely on binding the receptor-binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). However, Omicron and its sub-lineages, as well as other heavily mutated variants, have rendered m...
Phylogenetic inference aims at reconstructing the tree describing the evolution of a set of sequences descending from a common ancestor. The high computational cost of state-of-the-art maximum likelihood and Bayesian inference methods limits their us...