Menu
SkillsMP has collected 6 skills from GCS-ZHN/protools. Open a skill to review its source and details.
Showing 6 of 6 collected skills.
Cluster or deduplicate sequences with CD-HIT and MMseqs2 through the protools library (`protools4py`): redundancy removal within one FASTA, 2D cross-dataset clustering, parsing .clstr cluster files into DataFrames, and MMseqs2 clustering with…
Fetch and parse protein data from UniProt and WIPO patent sequence listings with the protools library (`protools4py`): download SwissProt records by accession, extract feature tables and extracellular chains, fetch features to TSV, and parse WIPO ST.26-style…
Work with protein ML datasets in the protools library (`protools4py`)'s `protools.dataset` package: reproducible train/validation/test splits (`random_split` with explicit seeds, `grouped_split` that keeps sequence families/clusters intact with partial-random…
Run protein-protein docking and scoring with the protools library (`protools4py`): HDock docking between receptor and ligand PDBs with optional active-site restraints (rsite/lsite), building docked complex PDBs via createpl, and DockQ scoring of models…
Work with protein, DNA, and RNA sequences in the protools library (`protools4py`): read/write FASTA and A3M, translate, reverse-translate and codon-optimize DNA, deduplicate and split FASTA files, filter sequences, number antibody/TCR sequences…
Work with protein 3D structures (PDB/mmCIF) in the protools library (`protools4py`): parse and save structures, download from RCSB, convert PDB to FASTA/DataFrame, extract or delete residue ranges by selection string, split chains at linkers, translate/rotate…