Mingchenchen

Attentive-Neural-Protein-Structure-Prediction

Prediction of protein tertiary structure via the “translation” of amino acid sequences into internal torsional angles.

deepdist

Deep learning prediction of protein residue-residue distances

DIPS

Database of Interacting Protein Structures (DIPS)

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

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

EvoClustRNA

RNA 3D structure prediction using multiple sequence alignment information docs @ http://EvoClustRNA.rtfd.io

ExpandedBenchmark

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

ibm3202

Google Colab Tutorials for IBM3202

manyfold

🧬 ManyFold: An efficient and flexible library for training and validating protein folding models

MCMG

MCMG_V1

p2rank

P2Rank: Protein-ligand binding site prediction tool based on machine learning. Stand-alone command line program / Java library for predicting ligand binding pockets from protein structure.

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

plddt2csv

Extract the plddt value of Alphafold2 from .pkl to .csv file

pyFrustratometer

Google Colab/Python implementation of AWSEM frustratometer

qligfep

qml

Introductions to key concepts in quantum machine learning, as well as tutorials and implementations from cutting-edge QML research.

ref-Alphafold-Code

SAGERank

SAGERank: Inductive Learning of Protein-Protein Interaction from Antibody-Antigen Recognition using Graph Sample and Aggregate Networks Framework

SNfold

The protein structure prediction software SNfold

TankBind

Open source code for TankBind. Galixir Tenchnologies