TL;DR
This chapter serves as a user-friendly practical tutorial for conducting structural phylogenetic analyses using accessible and computationally efficient tools, using synaptotagmins-calcium-sensing proteins essential for synaptic vesicle fusion-as a running example.
Understanding how positive selection shapes molecular evolution at the protein level remains a major challenge, particularly in non-model species. Here, we integrated phylogenetic evidence from candidate genes evolving under lineage-specific positive selection with comparative structural and biophysical analyses to inv...
Abstract For more than 50 years, the linear sequence and the multiple sequence alignment have been the foundational data structures of protein science, and they remain central to homology search, phylogenetic inference, covariance-based contact prediction, and modern protein language models. However, relational and gra...
Advances in bioinformatics resources and tools have greatly enhanced the capabilities of protein structure prediction, molecular dynamics simulations, pathway analysis, and genomic variant annotation. These tools are essential for figuring out drug targets, comprehending disease mechanisms, and assisting with customize...
This work proves that ancient proteins can be reliably recovered from highly degraded palaeogenomic material, establishing a new computational avenue for evolutionary and biochemical research.
The application of AlphaFold provides significant opportunities for accelerating research in alternative proteins by enabling rapid structural characterization, enzyme engineering, and functional optimization of novel protein sources and its potential applications in alternative protein discovery, design, and processin...
Accurately identifying the host of a virus from its genome sequence is a task with important applications in zoonotic disease surveillance and filling data gaps for metagenomic sampling. Machine learning approaches have seen broad application in making host predictions directly from viral genome sequences. However, mos...
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