Structural fold space for AF2 predicted models across 21 proteomes

Topic modelling of structural shape-mers to explore differences between the AlphaFold DB and the PDB

Requirements

• numpy
• scipy
• scikit-learn
• geometricus (https://github.com/TurtleTools/geometricus)
• portein (https://github.com/TurtleTools/portein)
• kneed (https://github.com/arvkevi/kneed)

Publications

Akdel, M., Pires, D.E., Pardo, E.P., Jänes, J., Zalevsky, A.O., Mészáros, B., Bryant, P., Good, L.L., Laskowski, R.A., Pozzati, G. and Shenoy, A., 2021. A structural biology community assessment of AlphaFold 2 applications. bioRxiv.