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is a molecular design tool powered by the Boltz model for designing protein-protein interactions and biomolecular complexes. It features an end-to-end pipeline that includes sequence optimization using ProteinMPNN/LigandMPNN, structure validation with AlphaFold3, and support for small molecules, DNA, and RNA targets. The tool provides trajectory visualization capabilities and automated setup for complete molecular design workflows.

a software suite for modeling macromolecular structures and for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.

tools to help design potent and selective bioactive molecules.

a self-supervised framework for cryo-ET reconstruction that integrates equivariance principles from modern imaging theory into a deep-learning architecture.

is a Python package for executing alchemical free energy calculations.

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

is a tool for refining AlphaFold predictions using crystallographic and cryo-EM likelihood targets. It integrates with OpenFold to condition experimental structure determination on pretrained neural networks, requiring both OpenFold and Phenix installations for automatic data preprocessing and post-refinement geometry polishing.

Antibody Numbering and Antigen Receptor ClassIfication

a widely used molecular visualization package developed by Warren DeLano, now maintained by Schödinger, LLC. This installation includes official incentive builds of PyMOL.

CTFMeasure is a software for estimating CTF parameters of cryo-ET tilt series. It features tilt-series-based joint estimation and Thon ring rescaling technique to retrieve power spectrums with higher SNR and more clear Thon rings, leading to higher estimation accuracy.