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allosteric-networks-w-networkx

How I mapped protein allostery with NetworkX

alphafold

Install alphafold on the local machine, get out of docker.

cats

CATS clustering algorithm source codes and how to guide

cs7054_example1

cs7054_project2

diamondback

DiAMoNDBack: Diffusion-denoising Autoregressive Model for Non-Deterministic Backmapping of Cα Protein Traces

egnn

egnn-pytorch

Implementation of E(n)-Equivariant Graph Neural Networks, in Pytorch

homemade-machine-learning

🤖 Python examples of popular machine learning algorithms with interactive Jupyter demos and math being explained

ising_model-cp2

Ising model implementation in Python. Metropolis and Swendsen Wang algorithm.

next

Web-interface for nextPYP

pc-based-fel

How I generated free energy landscapes in PC space and visualized them with Python

potts-model-clustering

Super-Paramagnetic Clustering, Maximum entropy, Maximum Likelihood Methods.

pydca

Direct coupling analysis software for protein and RNA sequences

stela-protein-structure-clustering-algorithm

Forked from DimaUCLab 03/01/24 This algorithm is a clustering based algorithm used to characterize local regions of proteins found to be particularly flexible in MD simulation

strobprobe-sensor-design-algorithm

StrobProbe Catalytic Homogenous DNA SERS Sensor Design Algorithm

torchmd-net

Training neural network potentials

torchmd-protein-thermodynamics

Tutorials and data necessary to reproduce the results of publication Machine Learning Coarse-Grained Potentials of Protein Thermodynamics