YFeriel

Different outputs between mmseqs2 API and colabfold_search

1

I wanted to run the MSA calculation of a set of proteins to do structure prediction. I used the script that calls the mmseqs2 API that colabfold uses for the...

Different outputs between mmseqs2 API and colabfold_search

1

Hello ! I wanted to run the MSA calculation of a set of proteins to do structure prediction. I used the script that calls the mmseqs2 API that colabfold uses...

Hello Foldseek Team, I hope this message finds you well. I am currently working on a project that involves clustering proteins from another database. To optimize my workflow, I am...

How to "rescue" sequences excluded from the provided AlphaFold/UniProt50 database

1

Hi @martin-steinegger @milot-mirdita , I am using the AlphaFold/UniProt50 database that you provide (~53M representatives). I understand that this database was generated by pre-clustering the full AlphaFold DB using MMseqs2....

Is MMseqs2 required before Foldseek clustering?

2

Hello Foldseek team @milot-mirdita @martin-steinegger Thank you for the great tool and the very insightful Nature 2023 paper. I have a few questions regarding the clustering workflow used on the...

Discrepancy in Foldseek clustering results compared to AFDB clusters

2

Hello, I concatenated my database containing approximately 600k protein structures with the AlphaFold database I downloaded using foldseek databases. I then performed clustering on the concatenated database using default parameters,...

Foldseek clustering stuck for days with errors

1

Hello, I am using a protein structure database with Foldseek for clustering, but I encountered an issue with the following command: foldseek cluster /data/foldseek/concat_db /data/db_clusters /data/cluster_tmp_dir I received this error:...

Clustering performance issue: Foldseek exceeds expected runtime

2

Hello Foldseek team, @martin-steinegger @milot-mirdita I am currently using Foldseek to perform a clusterization, and I am facing some issues with runtime duration. Here is the setup and process I...