CompuCell3D

Provides functionality for producing geometric representations of protein and RNA structures, and biological interaction networks.

OpenChem is a deep learning toolkit for Computational Chemistry with PyTorch backend.

NanoporeDB is an open-access structural database dedicated to the exploration, analysis, and design of protein nanopores, which serve as essential molecular gateways in biological membranes and form the basis of many advanced biosensing and sequencing technologies. This platform integrates large-scale structure-guided mining and deep learning-based modeling using AlphaFold-Multimer and AlphaFold3 to provide about 7,000 high-confidence multimeric nanopore structures. Each entry includes detailed information on membrane embedding, pore geometry annotation, and constriction profiling to support functional and biophysical interpretation. Through an interactive 3D visualization interface and quantitative parameters such as tilt angle, insertion depth, and pore geometry, NanoporeDB enables researchers to explore nanopore diversity, discover novel scaffolds, and accelerate innovation in molecular sensing, precision diagnostics, and synthetic biology.