yang yanqing's repositories
ChatPaper
Use ChatGPT to summarize the arXiv papers.
covid-moonshot
Scripts and input files associated with docking and free energy calculations for the COVID Moonshot
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.
DeepLearning-MuLi-Notes
Notes about courses Dive into Deep Learning by Mu Li
EViS
EViS: an Enhanced Virtual Screening Approach based on Pocket Ligand Similarity
fragalysis-api
A python API for fragalysis (fragalysis.diamond.ac.uk)
Grokking-Deep-Learning
this repository accompanies the book "Grokking Deep Learning"
LigninBuilder
VMD Plugin and associated scripts to build lignin structures from topological specifications
making-it-rain
Cloud-based molecular simulations for everyone
mdanalysis
MDAnalysis is a Python library to analyze molecular dynamics simulations.
mdtraj
An open library for the analysis of molecular dynamics trajectories
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.
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.
perses
Experiments with expanded ensembles to explore chemical space
PyTorch-VAE
A Collection of Variational Autoencoders (VAE) in PyTorch.
rdkit
The official sources for the RDKit library
rdkit_blog
RDKit related blog posts, notebooks, and data.
remd-temperature-generator
Temperature generator for Replica Exchange MD simulations
REMD_analysis
A repository for the development of data analysis tools for replica exchange molecular dynamics (REMD) simulations
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
selfies
Robust representation of semantically constrained graphs, in particular for molecules in chemistry
TCL_VMD_scripts
Some of useful tcl scripts to analyse data from VMD
transformato
Set up relative free energy calculations using a common scaffold
tREMD-GROMACS
Script to run Replica Exchange Molecular Dynamics simulation in GROMACS
vmd-patches
Patches for bugfixes or improvements to the VMD package
vmd_plumed
Main code repository for the PLUMED-GUI plugin for VMD
ZJU-Clock-In
探究浙江大学健康打卡的原理与对抗策略