EngqvistLab

Tome

A machine learning model for the prediction of optimal growth temperature of microorganisms and enzyme catalytic optima

fetch_microbial_growth_temperatures

Code to go with the https://doi.org/10.1101/271569 publication. Downloads html pages from culture-collection centers and mines these for growth temperature data.

UniRep50

A slighlty modified version of the UniRep model

DeepET_reps

An installable library to get DeepET representations.

cheminformatics

orgtools

A library to get information on organisms and UniProt identifiers. This includes growth temperature, growth ph, pfam domains, taxonomic lineage.

Supplemetenary_scripts_datasets_R2LG

This repo contains the supplementary scripts and datasets for Li G, et al, 2019 (https://arxiv.org/abs/1912.08141).

analyze_1.1.3.15

Code to analyze the 1.1.3.15 experimental data

brenparse

A library for parsing out data from the BRENDA database html files

tome_cool

Improve the prediction OGT of psychrophiles

reproducible-reports-init

A template library for use in making research reports/grant proposals follow standard guidelines

yeast_xylanase

A bioinformatic analysis was carried out with the goal of identifying carbohydrate-active enzymes in 332 published yeast genomes.

biomark_assays

Enzyme kinetic assays in the Fluidigm Biomark HD instrument

DeepET

Summary of scripts and results for the manuscript

Supplementary_scripts_Tome1.0