Jeff Law's repositories
upper-bound-energy-gnn
GNN for predicting an upper bound of the relaxed energy for a given unrelaxed structure
prot_stability_engineering
Using ML to engineer proteins to be more stable
chemview
The new generation molecular viewer for IPython notebook
chomper
Internet blocker for the Linux desktop.
crystal-gnn
Work in progress on graph neural networks for crystal energy prediction
CyGraphSpace
A GraphSpace app for Cytoscape
deepNF
Deep Network Fusion (deepNF)
ensemble_integration
Integration of diverse datasets for building heterogeneous ensembles.
fairseq
Facebook AI Research Sequence-to-Sequence Toolkit written in Python.
fairseq-uniparc
Fairseq modeling for protein function prediction from primary sequence
gapn-engineering
Using language models to engineer the gapn enzyme to switch from the cofactor NADPH to NADH.
geneontology.github.io
Repository for storing GO documentation, directly available through the general GO site
gpdPerm
improved permutation p-value estimates, python port from originally published matlab code
graph-env
Reinforcement learning for combinatorial optimization over directed graphs
ProteinMPNN
Code for the ProteinMPNN paper
rWikiPathways
R package for WikiPathways API
SARS-CoV-2-network-analysis
Software framework for analysis of SARS-CoV-2 molecular networks
spin_gnn
Code for building a graph neural network to predict atom spin
ubiquitous-broccoli
Repository for trying things like subtrees and submodules out
ubiquitous-broccoli-2
Repo for trying out subtree, submodule, and git-subrepo
volume_only_relaxations
Find the volume with the lowest energy using single-point scf calculations
ysi_prediction_flask
A flask app to support ysi prediction online