Tool Updates

Collaboration across the biomolecular modeling and design community continues to drive scientific advancements and discoveries. One way those collaborations shine is through improvements to the accuracy and computational efficiency of AI-based protein design models. In turn, those improvements expand what is possible across medicine, biotechnology, and beyond. The development of RDF4-Proteina, which was released earlier…

Protein design workflows bring together multiple tools for generating protein structures, designing sequences, predicting structures, and evaluating candidate designs. Connecting these tools into a coherent pipeline can require substantial work: managing inputs and outputs, configuring individual tools, coordinating computational jobs, and tracking results across multiple stages. Chaperone, a new tool in the Rosetta Commons GitHub…

Key Takeaways makeshift is an open-source Python package that streamlines retrieving, curating, and analyzing biomolecular Nuclear Magnetic Resonance (NMR) data from the Biological Magnetic Resonance Data Bank (BMRB). It unifies scattered, standalone algorithms, including chemical shift re-referencing, backbone flexibility estimation, and relaxation dynamics, into standard Python workflows. Benchmarking confirms that makeshift’s Python re-implementations closely match…

Key Takeaways OpenBind-0 (OB0) is a fully open-source co-folding model built on OpenFold3, trained on Protein Data Bank (PDB) data, and optimized for predicting protein–small-molecule complexes. Alongside the model, a discovery-relevant benchmark dataset of 717 new ligand-bound structures capturing fragment-to-hit progression across FatA and RdRp targets was released. Evaluation across targets shows wide performance variability,…