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alphafold

Open source code for AlphaFold.

amino_acid_encoding_deep_learning_applications

The repository contains all the code for the paper amino acid encoding using deep learning application

antibody-2019

arfoundation-samples

Example content for Unity projects based on AR Foundation

ase_ani

ANI-1 neural net potential with python interface (ASE)

bash_files

This repository contains patch files I have made to make bio conjugates

bioinfo-tools

Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.

blueprint_builder_demo

This repository contains the demonstrations prepared for report 'De novo protein design using the blueprint builder in Rosetta'.

deepsequence

A generative latent variable model for biological sequence families.

dl_binder_design

for RFDesign

dms_opt

graphbar

gtc2017-numba

Numba tutorial for GTC 2017 conference

hcv-e2

Software for in silico identification of immunologically-vulnerable regions of the HCV E2 glycoprotein and broadly neutralizing antibodies that target them

logomaker

Software for the visualization of sequence-function relationships

machine-learning-projects

Machine Learning Experiments and Work

mpf-bml

Fast and efficient code to solve the inverse Ising/Potts (aka maximum entropy) problem

mpf-bml-gui

Minimum Probability Flow-Boltzmann Machine Learning (MPF-BML) standalone GUI-based application for the inference of maximum entropy distribution parameters

nnp-mm

Scripts to interface TorchANI NNP with NAMD

potential-neutralizing-antibodies-discovered-for-novel-corona-virus-using-machine-learning

Potential Neutralizing Antibodies Discovered for Novel Corona Virus Using Machine Learning

ppdx

Build protein-protein complexes and compute binding descriptors

protac-rl

pyro

Pyro models of SARS-CoV-2 variants

pyrosetta_help

Some scripts that I keep using over and over.

rfdiffusion

Code for running RFdiffusion

vibfold

python setup for AF2 analysis

viral-mutation

Language modeling of viral evolution