Can protein complexes (multi-chain) structures be clustered? [not bug]

[minirose2021]

Expected Behavior

Thanks for your amazing tool! I want to obtain clustering results for a set of protein complex structures, not the clustering results of each chain within the protein complexes.

Current Behavior

The CMD is:
foldseek easy-cluster ./pdb/ res tmp -c 0.9
where ./pdb/ contains the protein complexes structures to be clustered.

The picture shows part of the result file res_cluster.tsv, with protein IDs suffixed by ABCD, etc., representing different chains of the protein complexes. Can I obtain clustering results that consider the entire structure of the protein complexes without these suffixes? I look forward to your response.

[sooyoung-cha]

Hi!

We are currently developing multimer clustering, and it is in another fork: https://github.com/rachelse/foldseek.
The parameters and outputs are described in the README under the MultimerCluster section of that fork.
You can run it with the command below.

wget https://github.com/rachelse/foldseek.git
cd foldseek
mkdir build && cd build
cmake ../ -DCMAKE_BUILD_TYPE=Release && make 
./src/foldseek easy-multimercluster /your/examples clu tmp --multimer-tm-threshold 0.65 --chain-tm-threshold 0.5 --interface-lddt-threshold 0.65 --cluster-mode 1

Please feel free to ask if you have any questions or suggestions, or encounter any bugs.

[minirose2021]

Hi!

We are currently developing multimer clustering, and it is in another fork: https://github.com/rachelse/foldseek. The parameters and outputs are described in the README under the MultimerCluster section of that fork. You can run it with the command below.

wget https://github.com/rachelse/foldseek.git
cd foldseek
mkdir build && cd build
cmake ../ -DCMAKE_BUILD_TYPE=Release && make 
./src/foldseek easy-multimercluster /your/examples clu tmp --multimer-tm-threshold 0.65 --chain-tm-threshold 0.5 --interface-lddt-threshold 0.65 --cluster-mode 1

Please feel free to ask if you have any questions or suggestions, or encounter any bugs.

Please forgive me for coming to thank you now. It's a great function. You are simply my God. Thank you all.