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426ml

ndcg opt

a-sample-lipid-simulation

A lipid assembly for MD simulation produced by CHARMM-GUI website

alchemy

alphazero_connect4

PyTorch implementation of AlphaZero Connect from scratch (with results)

alphazero_ultimate_tictactoe

andreidbr.github.io

My resume

autodock-vina-example

A simple tutorial for using Autodock Vina to find the ligand binding pose

awesome-bio-ml-pku

awesome-mol-gen-comp-chem

Awesome papers related to generative molecular modeling and design from computational chemistry perspective

chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

chatgpt-on-wechat

cryo-em-processing

Script and operations for processing EM data

data_science_projects

This folder contains most of my independent data science projects.

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

dockerfile-charmm

A Dockerfile repository for using CHARMM in Docker container

dockerfile-openmm-cuda

Dockerfile for GPU-supported OpenMM in Docker containers

ed

A jekyll theme for minimal editions

for-sharing

For sharing my jupyter notebook materials and scripts

github-pages-with-jekyll

gnn_molecules

The code of a graph neural network (GNN) for molecules, which is based on learning representations of r-radius subgraphs (i.e., fingerprints) in molecules.

gremlin_cpp

GREMLIN - learn MRF/potts model from input multiple sequence alignment! Implementation now available in C++ and Tensorflow/Python!

hello-world

install_pytorch

Install PyTorch with GPU support on HPC

lanczosnetwork

Lanczos Network, Graph Neural Networks, Deep Graph Convolutional Networks, Deep Learning on Graph Structured Data, QM8 Quantum Chemistry Benchmark, ICLR 2019

md-traj-lipid-residence

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics trajectories.

mk8-isoprenoid-arch-memb

Repository that contains parameter files for MK-8 head group and isoprenoid tails

mldl-md-dynamics

A repository of update in molecular dynamics field by recent progress in machine learning and deep learning.

model-long-missing-loop

This repository contains code and examples to model multiple missing loops in tetrameric protein.

mpnn

Open source implementation of "Neural Message Passing for Quantum Chemistry"