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2023-1st-ai-assisted-drug-discovery-snu

Lecture materials for AI-assissted-drug-discovery

adan-pytorch

Implementation of the Adan (ADAptive Nesterov momentum algorithm) Optimizer in Pytorch

adaptiveumbrella

Adaptive umbrella sampling in Python

alignn

Atomistic Line Graph Neural Network

alphafold

Install alphafold on the local machine, get out of docker.

alphafold2

To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released

alphafold2-multiprocessing

Use AlphaFold by Deep Mind in Batch Mode + Multiprocessing

alphafold_non_docker

AlphaFold2 non-docker setup

amber-umbrella_com_restraint_tutorial

Tutorial to run AMBER umbrella COM restraint code and derive free energy of transfer profile for methanol through DMPC membrane

amber20mpi_plumed

Input files and output for attempts at getting pmemd.cuda.MPI working with PLUMED's MPI multiple walkers

amber_reus

Replica Exchange Umbrella Sampling on GPUs using AMBER

apr

Attach-release-pull: A free energy calculation workflow

ase-plumed_tutorial

atom-openmm

OpenMM-based framework for absolute and relative binding free energy calculations with the Alchemical Transfer Method

aucol

Automatic representation based CVs

awesome-equivariant-network

Paper list for equivariant neural network

awesome-graph-generation

awesome-masked-autoencoders

A collection of literature after or concurrent with Masked Autoencoder (MAE) (Kaiming He el al.).

awesome-pytorch-list

A comprehensive list of pytorch related content on github,such as different models,implementations,helper libraries,tutorials etc.

awesome-turstworthy-graph-neural-networks

bat.py

The Binding Affinity Tool (BAT.py) is a fully automated tool for absolute binding free energy calculations on protein-ligand systems.

bgflow

Boltzmann Generators and Normalizing Flows in PyTorch

biobb

Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools.

biosimspacetutorials

bkit

blues

Applications of nonequilibrium candidate Monte Carlo (NCMC) to ligand binding mode sampling

boltzmanngenerator

An implementation of Boltzmann generators using pytorch.

colabfold

Making Protein folding accessible to all!

combinemols

Easy to combine two molecules

comp_chem