Pinned Repositories
annotated_deep_learning_paper_implementations
🧑🏫 60 Implementations/tutorials of deep learning papers with side-by-side notes 📝; including transformers (original, xl, switch, feedback, vit, ...), optimizers (adam, adabelief, sophia, ...), gans(cyclegan, stylegan2, ...), 🎮 reinforcement learning (ppo, dqn), capsnet, distillation, ... 🧠
AutoDock-Vina
AutoDock Vina
autogluon
AutoGluon: AutoML for Text, Image, and Tabular Data
awesome-robotics-ee-opensource
(CN) 机器人、电子设计、机器学习中文开源项目列表 (by 云飞机器人实验室)
AwsomeCADD
好的CADD教程,资源总结
BAPA
BAPA preprocessing scripts and model
BEPb
Config files for my GitHub profile.
CS_Python_Notes
Some notes about computer sience and Python.
deepmd-kit
A deep learning package for many-body potential energy representation and molecular dynamics
Pymol-script-repo
Collected scripts for Pymol
yqyang733's Repositories
yqyang733/Grokking-Deep-Learning
this repository accompanies the book "Grokking Deep Learning"
yqyang733/ChatPaper
Use ChatGPT to summarize the arXiv papers.
yqyang733/selfies
Robust representation of semantically constrained graphs, in particular for molecules in chemistry
yqyang733/REMD_analysis
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
yqyang733/DRPScore_v1.0
yqyang733/rdkit_blog
RDKit related blog posts, notebooks, and data.
yqyang733/remd-temperature-generator
Temperature generator for Replica Exchange MD simulations
yqyang733/ZJU-Clock-In
探究浙江大学健康打卡的原理与对抗策略
yqyang733/rdkit
The official sources for the RDKit library
yqyang733/mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
yqyang733/mdtraj
An open library for the analysis of molecular dynamics trajectories
yqyang733/LigninBuilder
VMD Plugin and associated scripts to build lignin structures from topological specifications
yqyang733/d2l-en
Interactive deep learning book with multi-framework code, math, and discussions. Adopted at 400 universities from 60 countries including Stanford, MIT, Harvard, and Cambridge.
yqyang733/transformato
Set up relative free energy calculations using a common scaffold
yqyang733/perses
Experiments with expanded ensembles to explore chemical space
yqyang733/TCL_VMD_scripts
Some of useful tcl scripts to analyse data from VMD
yqyang733/NAMD-MD
Prepare a molecular dynamic simulation from scratch without installing local VMD, use LigParGen for topology, it is one of the most reliable MD for a general solution protein-ligand simulation.
yqyang733/ligpargen
yqyang733/vmd-patches
Patches for bugfixes or improvements to the VMD package
yqyang733/PyTorch-VAE
A Collection of Variational Autoencoders (VAE) in PyTorch.
yqyang733/rna-tools
🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
yqyang733/g4rna_screener
yqyang733/NAMD-FEP
You should run this on a computer station or cluster. Calculate the binding free energy difference between two small molecules against the same protein target.
yqyang733/DeepLearning-MuLi-Notes
Notes about courses Dive into Deep Learning by Mu Li
yqyang733/making-it-rain
Cloud-based molecular simulations for everyone
yqyang733/tREMD-GROMACS
Script to run Replica Exchange Molecular Dynamics simulation in GROMACS
yqyang733/fragalysis-api
A python API for fragalysis (fragalysis.diamond.ac.uk)
yqyang733/covid-moonshot
Scripts and input files associated with docking and free energy calculations for the COVID Moonshot
yqyang733/vmd_plumed
Main code repository for the PLUMED-GUI plugin for VMD
yqyang733/EViS
EViS: an Enhanced Virtual Screening Approach based on Pocket Ligand Similarity