Aravinda Munasinghe's repositories
bash_files
This repository contains patch files I have made to make bio conjugates
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
arfoundation-samples
Example content for Unity projects based on AR Foundation
ASE_ANI
ANI-1 neural net potential with python interface (ASE)
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
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
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