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Fast, structure-based, alignment-free protein embedding

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PyPI version DOI

Geometricus Represents Protein Structures as Shape-mers derived from Moment Invariants

A structure-based, alignment-free embedding approach for proteins. Can be used as input to machine learning algorithms.

See the documentation.


Geometricus is a Python (3.7+) package with NumPy, SciPy, Numba and ProDy as dependencies.

Install with pip install geometricus


See the Getting Started page for example usage.


Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D J van Dijk, Geometricus represents protein structures as shape-mers derived from moment invariants, Bioinformatics, Volume 36, Issue Supplement_2, December 2020, Pages i718–i725,

Janani Durairaj, Mehmet Akdel, Dick de Ridder, Aalt D.J. van Dijk, Fast and adaptive protein structure representations for machine learning, bioRxiv 2021.04.07.438777; doi:

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