Tom Goddard

I am not running MMseqs2 under Docker. I use the distributed binary mmseqs-linux-gpu.tar.gz from the MMseqs2 github https://github.com/soedinglab/MMseqs2/releases/download/18-8cc5c/mmseqs-linux-gpu.tar.gz I also frequently run Boltz structure prediction using CUDA on this same...

I said in the previous comment that Boltz structure prediction using CUDA on the same machine works consistently. But I have a vague recollection that a few times it has...

I'll try compiling MMseqs release 18 for GPU on the machine where I get the errors and see if that helps. It may take a week because I am busy...

I compiled MMseqs2 release 18 on my Ubuntu 24.04 system with Nvidia 4090, CUDA 12.9, driver version 575.64.03, using -DCMAKE_CUDA_ARCHITECTURES="native" and ran a colabfold_search test. It crashed with the libmarv...

I've run both Boltz and AlphaFold 3 predictions of 1500 FDA approved compounds to single virus protein targets. It can run pretty fast, 4 hours total on an Nvidia 4090...

I think this preprint gives a good perspective. It says that ligand binding predictions are good if the training data contained similar ligands in similar pockets but bad otherwise. In...

It is not a serious problem. Duplicate results propagate through subsequent processing of the search results and wastes time when a human ends up looking at them and needs to...

Here are some timings of Boltz with Mac ARM GPUs compared to Windows and Linux Nvidia GPU. https://www.rbvi.ucsf.edu/chimerax/data/boltz-apr2025/boltz_help.html#runtimes Macs with more GPU cores like the M2 Ultra shown on that...

This looks like the same issue as #246. That issue says it has been fixed in the github source code, but I believe the PyPi boltz 1.0.0 is older and...

Could a boltz 1.0.1 release be made on PyPi so that boltz will run on systems without Nvidia graphics? I made a ChimeraX user interface to run Boltz on Mac,...