Box3D is a 3D physics engine for games

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

BRIDGE: A Coarse-Grained Architecture to Embed Protein-Protein Interactions for Therapeutic Applications

A community-maintained Python framework for creating mathematical animations.

Designing antibody CDRs with flexible CDR definition, using equivariant graph neural networks. Bioinformatics (2024).

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

Antibody developability prediction using a novel Delaunay tessellation GNN adjacency

Spatial alignment of single cell transcriptomic data.

Fitness landscapes for antibodies

Allostery pocket prediction

overview of datasets for ML in chemistry

Integrative Generalized Master Equation (IGME): A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels

Standardized data set for machine learning of protein structure

Python package built around protein structure and dynamics. OpenBabel-inspired objects.

Clinically reportable structural variant calls

Generate input parameters and coordinates for atomistic and coarse-grained simulations of polymers, ssDNA, and carbohydrates

Google Research

A machine-learning package for navigating combinatorial protein fitness landscapes.

Pure Python cross-platform pyclean. Clean up your Python bytecode.

Tabula is a tool for liberating data tables trapped inside PDF files

Open Babel is a chemical toolbox designed to speak the many languages of chemical data.