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ai-paper-references

References for read papers + relevant links

ailearning

AiLearning: 机器学习 - MachineLearning - ML、深度学习 - DeepLearning - DL、自然语言处理 NLP

alphafold2

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

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

amberutils

Utilities to assist with Amber Molecular Dynamics structure preparation and MMPBSA.py energy methods

analysismdnotebooks

Personal repository for storing notebooks used for MD Analysis.

awesome-protein-representation-learning

Awesome Protein Representation Learning

chroma-pytorch

Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch

colabfold

Making Protein folding accessible to all!

computationalphysics300

computational physics class taught at UNLV (Phys300)

confgf

Implementation of Learning Gradient Fields for Molecular Conformation Generation (ICML 2021).

deep-drug-coder

A tensorflow.keras generative neural network for de novo drug design, first-authored in Nature Machine Intelligence while working at AstraZeneca.

deep-learning-for-image-processing

deep learning for image processing including classification and object-detection etc.

deeppurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

deeptime

Deep learning meets molecular dynamics.

diffusion

Denoising Diffusion Probabilistic Models

doing_the_phd

dpdata

Manipulating DeePMD-kit, VASP, LAMMPS data formats.

drfold

duivy

some scripts for analysis of MD and CADD. And some tutorials.

eat_pytorch_in_20_days

Pytorch🍊🍉 is delicious, just eat it! 😋😋

en-transformer

Implementation of E(n)-Transformer, which extends the ideas of Welling's E(n)-Equivariant Graph Neural Network to attention

fucking-algorithm

刷算法全靠套路，认准 labuladong 就够了！English version supported! Crack LeetCode, not only how, but also why.

getcontacts

Library for computing dynamic non-covalent contact networks in proteins throughout MD Simulation

gmx_mmpbsa

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.

gmxtool

tools for GROMACS

gromacs-cluster

gromit

Auxiliary tools for automated atomistic and coarse-grained molecular dynamics simulations using gromacs

hello-world

this is first rpository

hotspots

A knowledge-based method for determining small molecule binding "hotspots".