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steineggerlab / foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.
https://foldseek.com
GNU General Public License v3.0
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Can protein complexes (multi-chain) structures be clustered? [not bug] #349

Open minirose2021 opened 2 months ago

minirose2021 commented 2 months ago

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.

eae9605482792fbfaad7d89e39a070e

sooyoung-cha commented 2 months ago

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 commented 2 months ago

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.