SNPeffect 5.0: large-scale structural phenotyping of protein coding variants extracted from next-generation sequencing data using AlphaFold models.

Kobe JanssenRamon Duran-RomañaGuy BottuMainak GuharoyAlexander BotzkiFrederic RousseauJoost Schymkowitz

Published in: BMC bioinformatics (2023)

We provide a bioinformatics pipeline that allows structural phenotyping from sequencing data using established stability and aggregation predictors including FoldX, TANGO, and WALTZ; and structural proteome coverage provided by the AlphaFold database. The pipeline and installation guide are freely available for academic users on https://github.com/vibbits/snpeffect and requires a computer cluster.

Keyphrases

electronic health record
high throughput
copy number
big data
single cell
deep learning
healthcare
gene expression
machine learning
protein protein
data analysis
binding protein
amino acid
small molecule
circulating tumor cells
cell free