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💠 A streamlined worfklow for Principal Component Analysis of molecular dynamics in PyMOL
A Model Context Protocol (MCP) server that exposes PyMOL as a typed tool surface to your agent (Claude Code/Desktop, Codex, or any MCP-compatible client)
Claude AI plugin for PyMOL to control PyMOL with plain English
MPID protein force field parameters and example OpenMM simulation scripts
Generative model for protein binder design for protein and small molecule targets. Combines a pretrained flow-based generative model (built on La-Proteina) with inference-time optimization.
Clustering and visualization of billions of molecules (or other high-dimensional data). 1 billion, 100K clusters, less than 3 hours, one GPU.
ChemScreener is an active learning pipeline for small-molecule screening. In each cycle, it trains an ensemble of multi-task Chemprop models, scores an unlabeled library, and selects compounds to a…
Latents-based conformational control in OpenFold3.
A Python toolkit for scalable molecular dynamics trajectory analysis, combining modular workflows, memory-efficient processing and interpretable machine learning via decision trees to identify key …
Sample-efficient Generative Molecular Design using Memory Manipulation
Official code repository for the paper Drug Discovery with Dynamic Goal-aware Fragments (ICML 2024)
Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
AI-powered MD trajectory analysis IDE with cpptraj, RAG, and 3D viewer
Codebase for SigmaDock: Untwisting Molecular Docking with SE(3) Fragmented Diffusion
YuelPocket: Protein-ligand binding site prediction with graph neural network
CosolvKit is a versatile tool for cosolvent MD preparation and analysis
QUICK: A GPU-enabled ab intio quantum chemistry software package
Terminal protein structure viewer — interactive 3D visualization of PDB/mmCIF structures with cartoon ribbons, braille rendering, and Sixel/Kitty graphics
Improving Structure-Based Virtual Screening with Ensemble Docking and Machine Learning
ChemAudit helps researchers validate, standardize, and assess the quality of chemical structures before using them in machine learning models or chemical databases. Upload individual molecules or b…
Toolbox for molecular animations in Blender, powered by Geometry Nodes.