MatthewChen's repositories
Attentive-Neural-Protein-Structure-Prediction
Prediction of protein tertiary structure via the “translation” of amino acid sequences into internal torsional angles.
SARS2_RBD_Ab_escape_maps
Interactive visualization of deep mutational scanning maps of mutations to SARS-CoV-2 RBD that escape antibody or sera binding
af2_conformations
A series of scripts that facilitate the prediction of protein structures in multiple conformations using AlphaFold2
af2complex
Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.
AttnPacker
Code and Pre-Trained Models for "AttnPacker: An end-to-end deep learning method for protein side-chain packing"
CollepardoLab_Chromatin_Model
Source code for "Nucleosome plasticity is a critical element of chromatin liquid–liquid phase separation and multivalent nucleosome interactions".
cornell-cs5785-applied-ml
Teaching materials for the applied machine learning course at Cornell Tech
dgl-lifesci
Python package for graph neural networks in chemistry and biology
EvoClustRNA
RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io
genie
De Novo Protein Design by Equivariantly Diffusing Oriented Residue Clouds
gmx_makecyclictop
This script makes a cyclic peptide or cyclic nucleotide topology file for GROMACS out of (specially prepared) linear molecule topology file
GuthrieSolv
Experimental small molecule hydration free energy dataset
manyfold
🧬 ManyFold: An efficient and flexible library for training and validating protein folding models
pensa
PENSA (Protein Ensemble Analysis) - a collection of python methods for exploratory analysis and comparison of protein structural ensembles.
phdthesis
Gaussian Processes and Statistical Decision-making in Non-Euclidean Spaces
pyFrustratometer
Google Colab/Python implementation of AWSEM frustratometer