Here's how to predict binding of tens or hundreds of small molecules to protein assemblies using Boltz 2 in ChimeraX.
Accuracy depends on how similar the ligands and binding pockets are to existing experimental structures.
www.rbvi.ucsf.edu/chimerax/dat...

ChimeraX 1.10.1 is available now, incorporating critical bugfixes since last month's release.

www.cgl.ucsf.edu/chimerax/dow...

ChimeraX daily builds can predict binding affinity of small molecules using Boltz 2 on your Mac, Windows or Linux computer. www.rbvi.ucsf.edu/chimerax/dat...

UCSF ChimeraX version 1.10 has been released!

www.rbvi.ucsf.edu/chimerax/dow...

LocScale-SURFER is a ChimeraX extension that shows cryoEM density maps after removing detergent micelles based on output from command-line program Locscale-2.0. Install it using ChimeraX menu Tools / More Tools.... More details at cxtoolshed.rbvi.ucsf.edu/apps/chimera...

When ChimeraX runs Boltz it uses the boltz --use_msa_server flag which uses the Colabfold MSA server api.colabfold.com. ChimeraX remembers the MSA results in ~/Downloads/ChimeraX/Boltz so if you run predictions with the same sequences it uses the cached MSA.

ChimeraX can predict protein, nucleic acid and ligand atomic models on your Mac, Windows or Linux computer using Boltz. This table shows how long it takes in minutes using different computers. www.rbvi.ucsf.edu/chimerax/dat...

Due to a mismatched version of SciPy targeting fewer macOS versions than we support, users with ARM macs running macOS below 14 should use the 1.10 release candidate or 1.11 daily builds. Since we are close to a release, a 1.9.1 is not planned at this time.

The first release candidate for ChimeraX 1.10 is available now.

www.cgl.ucsf.edu/chimerax/dow...

ChimeraX daily builds can predict small complexes of proteins, nucleic acids and small molecules using Boltz on your Mac, Windows or Linux computer without Nvidia graphics. www.rbvi.ucsf.edu/chimerax/dat...

ChimeraX AlphaFold prediction is working again. It was broken the past couple days because Google Colab updated from Python library numpy from version 1 to 2. Thanks to ColabFold developer Milot Mirdita for making Colabfold work with numpy 2.

We've just been notified that our previous article in Protein Science (2023) is among the 10 most cited papers for that year! You can find 'UCSF ChimeraX: Tools for structure building and analysis' at doi.org/10.1002/pro....

ChimeraX can be used to find pockets and cavities in protein structures using the Find Cavities tool or kvfinder command. This feature is available in daily builds from 10 March 2025 or later.

ChimeraX can cluster different backbone conformations of distantly related proteins found with Foldseek, here clustering similar structures to CRAF kinase. www.rbvi.ucsf.edu/chimerax/dat...

ChimeraX can run Foldseek to find similar structures, such as distantly related homologs, and analyze the results, for example, mapping all ligands onto your query structure. Here are ligands mapped onto Nipah virus G protein. www.rbvi.ucsf.edu/chimerax/dat...

ChimeraX can display deep mutational scan data where all possible single mutations of a protein are assayed using high-throughput experiments. www.rbvi.ucsf.edu/chimerax/dat...

Sony Spatial Reality 3D display shows molecular structures and electron microscopy data at HD resolutions with no glasses. www.rbvi.ucsf.edu/chimerax/dat...

Anisotropic B-factors can now be shown as ellipsoids in ChimeraX daily builds, shown here for the heme in myoglobin. www.rbvi.ucsf.edu/chimerax/fea...

ChimeraX 1.9 has been released and is available now on our website

Thanks for the tip!