L&S's repositories
Paulie-ai
Config files for my GitHub profile.
papers_for_protein_design_using_DL
List of papers about Proteins Design using Deep Learning
awesome-protein-representation-learning
Awesome Protein Representation Learning
training-collection
Collection of bioinformatics training materials
chroma-pytorch
Implementation of Chroma, generative models of protein using DDPM and GNNs, in Pytorch
diffusion
Denoising Diffusion Probabilistic Models
alphafold2
To eventually become an unofficial Pytorch implementation / replication of Alphafold2, as details of the architecture get released
ColabFold
Making Protein folding accessible to all!
teachopencadd
TeachOpenCADD: a teaching platform for computer-aided drug design (CADD) using open source packages and data
Machine-learning-for-proteins
Listing of papers about machine learning for proteins.
ComputationalPhysics300
computational physics class taught at UNLV (Phys300)
torchmd-net
Neural network potentials based on graph neural networks and equivariant transformers
deep-learning-for-image-processing
deep learning for image processing including classification and object-detection etc.
python_for_data_analysis_2nd_chinese_version
《利用Python进行数据分析·第2版》
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
pymbar
Python implementation of the multistate Bennett acceptance ratio (MBAR)
SPDBUE
Jupyter-notebook for scraping protein structures from the Uniprot database.
PyAutoFEP
PyAutoFEP: an automated FEP workflow for GROMACS integrating enhanced sampling methods
Reservoir-REMD
This variant of GROMACS 4.6.7 is patched with Reservoir REMD.
vermouth-martinize
Describe and apply transformation on molecular structures and topologies
paper-reading
深度学习经典、新论文逐段精读
ml-template
A single template to solve various Machine Learning tasks on Tabular Data.
NRI-MD
Neural relational inference for molecular dynamics simulations
PyRosetta.notebooks
Jupyter Notebooks for learning the PyRosetta platform for biomolecular structure prediction and design
pdbfixer
PDBFixer fixes problems in PDB files
tutorial_dcTMD
Tutorial for the usage of the dcTMD approach and Langevin simulations employing the trypsin-benzamidine complex as example.
ML-For-Beginners
12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all
En-transformer
Implementation of E(n)-Transformer, which extends the ideas of Welling's E(n)-Equivariant Graph Neural Network to attention