Pinned Repositories
3DMolMS
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
AlphaPulldown
Auto_AutoDock-GPU
Tools that help high-throughput protein-ligand docking in batch mode using AutoDock-GPU.
blogs
Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/
cryodrgn
Neural networks for cryo-EM reconstruction
CSpred
UCBShift is a program for predicting chemical shifts for backbone atoms and β-carbon of a protein in solution. It utilizes a machine learning module that makes predictions from features extracted from the 3D structures of the proteins.
DD_protocol
Official repository for the Deep Docking protocol
deep_learning_for_biologists_with_keras
tutorials made for biologists to learn deep learning
deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
deeplearning-biology
A list of deep learning implementations in biology
wushaowen1992's Repositories
wushaowen1992/3DMolMS
3DMolMS: prediction of tandem mass spectra from 3D molecular conformations
wushaowen1992/AlphaPulldown
wushaowen1992/blogs
Jupyter notebooks that support my graph data science blog posts at https://bratanic-tomaz.medium.com/
wushaowen1992/cryodrgn
Neural networks for cryo-EM reconstruction
wushaowen1992/deepchem
Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology
wushaowen1992/deeplearning-biology
A list of deep learning implementations in biology
wushaowen1992/dgl-lifesci
Python package for graph neural networks in chemistry and biology
wushaowen1992/FRET_X_fingerprinting_simulation
wushaowen1992/HDXer
HDXer is a package to compute Hydrogen-Deuterium exchange data from biomolecular simulations, compare to experiment, and perform ensemble refinement to fit a structrual ensemble to the experimental data
wushaowen1992/hotspot3d
3D hotspot mutation proximity analysis tool
wushaowen1992/ibm3202
Google Colab Tutorials for IBM3202
wushaowen1992/making-it-rain-MD-simultion
Cloud-based molecular simulations for everyone
wushaowen1992/massformer
Tandem Mass Spectrum Prediction with Graph Transformers
wushaowen1992/MAW
Metabolome Annotation Workflow
wushaowen1992/mdigest
wushaowen1992/MiniCPM-V
MiniCPM-Llama3-V 2.5: A GPT-4V Level MLLM on Your Phone
wushaowen1992/MoBioTools_QM-MM
A simple yet versatile toolkit to setup quantum mechanical/molecular mechanical (QM/MM) calculations from molecular dynamics trajectories.
wushaowen1992/ms-pred
Predicting tandem mass spectra from molecules
wushaowen1992/packmol
Packmol - Initial configurations for molecular dynamics simulations
wushaowen1992/PPI-Miner
A Motif-Based PPI Searching Pipeline for PPI Mining and Protein Design
wushaowen1992/ProLIF
Interaction Fingerprints for protein-ligand complexes and more
wushaowen1992/pyinteraph2
development repository for PyInteraph2
wushaowen1992/PyLipID
A python toolkit for analysing membrane protein-lipid interactions.
wushaowen1992/Pymol-script-repo
Collected scripts for Pymol
wushaowen1992/PySAGES
Python Suite for Advanced General Ensemble Simulations
wushaowen1992/QCxMS
Quantum mechanic mass spectrometry calculation program
wushaowen1992/ring-pymol
This is the public repository for the RING PyMOL plugin developed by the BioComputing UP laboratory at the University of Padua
wushaowen1992/Spec2Mol
wushaowen1992/streamd
Automate MD associated calculations
wushaowen1992/tuning_playbook
A playbook for systematically maximizing the performance of deep learning models.