mengqvist

DNApy

Code for DNA plasmid editing.

data_analysis_mbml

Pyro code for reproducing examples from John Winns MBML book.

ANT

Ambiguous Nucleotide Tool (ANT), software for generating and evaluating degenerate codons for natural and expanded genetic codes.

Machine-learning-for-proteins

Listing of papers about machine learning for proteins.

AGADIR

A biophysical model of alpha-helical stability based on statistical mechanics.

cobrapy

COBRApy is a package for constraint-based modeling of metabolic networks.

colcol

A script for color conversions and generating color scales

data_analysis_sivia

Pyro code for reproducing some of the examples from the Data Analysis book by D. S. Sivia.

enzymemap

Python package to atom map, correct and suggest enzymatic reactions

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

mengqvist

resreg

Resampling strategies for regression

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

wsvg

A light wrapper around the svg (scalable vector graphics) format, for scripting svg files.