Software for automated analysis of molecular dynamics trajectories

Introduction to Machine Learning Systems

KERMT is a pretrained graph neural network model for molecular property prediction.

GatorAffinity: Boosting Protein-Ligand Binding Affinity Prediction with Large-Scale Synthetic Structural Data

Sequence data and code for Shen et al (2025), applying ML to understand membrane protein expression (unpublished)

A curated list of 120+ LLM libraries category wise.

Codebase for Germinal, a broadly enabling generative pipeline for efficient generation of epitope-targeted de novo antibodies.

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

A Streamlit-based app for post-MD analyses and visualization of GROMACS simulation trajectories.

A Model Context Protocol (MCP) server that provides comprehensive access to the NCBI Datasets API

A simple tool for creating and running MD simulations, using Jupyter and OpenMM

FAIR Chemistry's library of machine learning methods for chemistry

A comprehensive Model Context Protocol (MCP) server providing advanced access to the ChEMBL chemical database.

📽️ Game-changing scripts for molecular visualization — produce Hollywood-quality visuals with scientific accuracy and cinematic impact

Physics-Guided All-Atom Diffusion Model for Accurate Protein-Ligand Complex Prediction

The art of using t-SNE for single-cell transcriptomics

Official code repo for the O'Reilly Book - "Hands-On Large Language Models"

Open source code for AlphaFold 2.

This package contains deep learning models and related scripts for RoseTTAFold

CReM-dock: generation of chemically reasonable molecules guided by molecular docking

Code from OMGenomics YouTube Channel videos

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

LAnguage Model Analysis

Official inference framework for 1-bit LLMs

12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

Automated scripts to calculate the free solvation energy using Amber MD