namus

pDynamo3

The pDynamo molecular modeling and simulation program

encodermap

python library for dimensionality reduction

GME_tutorials

Tutorials for non-Markovian dynamic models (qMSM and IGME) to study protein dynamics.

westpa2_tutorials

Advanced tutorials for WESTPA 2.0

tutorials

Landing Page/HUB for all WESTPA Tutorials

westpa_tutorials

Tutorials and additional documentation for the WESTPA suite

pytorchrl

torchmd

End-To-End Molecular Dynamics (MD) Engine using PyTorch

misato-dataset

Pytorch-VAE-tutorial

A simple tutorial of Variational AutoEncoders with Pytorch

Prothon

A local order parameter-based method for efficient comparison of protein ensembles

mdanalysis

MDAnalysis is a Python library to analyze molecular dynamics simulations.

KIN

Repo for the publication titled: "Key Interaction Networks: Identifying Evolutionarily Conserved Non-Covalent Interaction Networks Across Protein Families".

PyTorch-VAE

A Collection of Variational Autoencoders (VAE) in PyTorch.

harmonic-oscillator-pinn

Code accompanying my blog post: So, what is a physics-informed neural network?

harmonic-oscillator-pinn-workshop

Introductory workshop on PINNs using the harmonic oscillator

subpex

SubPEx (Sub-Pocket Explorer) is a tool to enhance ensemble (multiple-receptor/relaxed-complex) virtual screening. It uses weighted ensemble path sampling and molecular dynamics simulations to accelerate binding-pocket sampling.

fast

scientific-python-lectures

Lectures on scientific computing with python, as IPython notebooks.

pandas-ai

Chat with your database (SQL, CSV, pandas, polars, mongodb, noSQL, etc). PandasAI makes data analysis conversational using LLMs (GPT 3.5 / 4, Anthropic, VertexAI) and RAG.

manim

Animation engine for explanatory math videos

ImageMol

alchemlyb

the simple alchemistry library

ohmyzsh

🙃 A delightful community-driven (with 2,300+ contributors) framework for managing your zsh configuration. Includes 300+ optional plugins (rails, git, macOS, hub, docker, homebrew, node, php, python, etc), 140+ themes to spice up your morning, and an auto-update tool so that makes it easy to keep up with the latest updates from the community.

fessa-color-palette

DeepLearningExamples

State-of-the-Art Deep Learning scripts organized by models - easy to train and deploy with reproducible accuracy and performance on enterprise-grade infrastructure.

accelerated_sampling_with_autoencoder

Accelerated sampling framework with autoencoder-based method

yellowbrick

Visual analysis and diagnostic tools to facilitate machine learning model selection.

wepy

Weighted Ensemble simulation framework in Python

seekr2

Simulation-Enabled Estimation of Kinetic Rates - Version 2