Protein Similarity Local Tools#

Configuration File: protein_similarity_local_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the protein_similarity_local_tools.json configuration file.

Available Tools#

ProteinSimilarity_search_sequence_local (Type: LocalProteinSimilarityTool)#

Search proteins locally with MMseqs2 against caller-managed FASTA/database files. Returns identit…

ProteinSimilarity_search_sequence_local tool specification

Tool Information:

  • Name: ProteinSimilarity_search_sequence_local

  • Type: LocalProteinSimilarityTool

  • Description: Search proteins locally with MMseqs2 against caller-managed FASTA/database files. Returns identities and coverage as fractions. CPU binary required; builtin:1UBQ is a public self-control. No upload or novelty certification.

Parameters:

  • query_path (string) (required) Local protein FASTA with up to 50 unique identifiers, uppercase standard residues/X and no gaps/stops; builtin:1UBQ is bundled public ubiquitin.

  • reference_path (string) (required) Local reference file or prebuilt database prefix (.dbtype must exist); builtin:1UBQ uses bundled public ubiquitin.

  • threads ([‘integer’, ‘null’]) (optional) CPU threads; defaults to 2.

  • timeout_seconds ([‘integer’, ‘null’]) (optional) Bounded process runtime; defaults to 300 seconds.

  • max_hits_per_query ([‘integer’, ‘null’]) (optional) Returned hits per query, defaults to 20; truncation is explicit.

  • minimum_query_coverage ([‘number’, ‘null’]) (optional) Minimum fraction of query residues covered; defaults to 0.

  • sensitivity ([‘number’, ‘null’]) (optional) MMseqs2 search sensitivity; defaults to 7.5.

  • evalue_threshold ([‘number’, ‘null’]) (optional) MMseqs2 reported E-value cutoff; defaults to 0.001. No hit does not certify novelty.

Example Usage:

query = {
    "name": "ProteinSimilarity_search_sequence_local",
    "arguments": {
        "query_path": "example_value",
        "reference_path": "example_value"
    }
}
result = tu.run(query)

ProteinSimilarity_search_structure_local (Type: LocalProteinSimilarityTool)#

Compare single-chain PDB queries locally with Foldseek/TM-align and caller-managed references. Re…

ProteinSimilarity_search_structure_local tool specification

Tool Information:

  • Name: ProteinSimilarity_search_structure_local

  • Type: LocalProteinSimilarityTool

  • Description: Compare single-chain PDB queries locally with Foldseek/TM-align and caller-managed references. Returns query/target-normalized TM-scores and coverage. CPU binary required; builtin:1UBQ is a public control. No upload.

Parameters:

  • query_path (string) (required) Local single-chain one-model .pdb file, or directory of 1–50 such files with standard CA records and no alternate locations; builtin:1UBQ is bundled public ubiquitin.

  • reference_path (string) (required) Local reference PDB file or prebuilt Foldseek database prefix (.dbtype must exist); builtin:1UBQ uses the bundled public control. Clustered prefixes search representatives by default; request expand_cluster_members to align matching members.

  • threads ([‘integer’, ‘null’]) (optional) CPU threads; defaults to 2.

  • timeout_seconds ([‘integer’, ‘null’]) (optional) Bounded process runtime; defaults to 300 seconds.

  • max_hits_per_query ([‘integer’, ‘null’]) (optional) Returned hits per query, defaults to 20; truncation is explicit.

  • minimum_query_coverage ([‘number’, ‘null’]) (optional) Minimum fraction of query residues covered; defaults to 0.

  • expand_cluster_members ([‘boolean’, ‘null’]) (optional) For a prebuilt clustered Foldseek database, align members of matched representative clusters. Defaults to false. Use the representative prefix with _clu.dbtype and _seq.dbtype companions; the member _seq prefix is not a directly searchable reference.

Example Usage:

query = {
    "name": "ProteinSimilarity_search_structure_local",
    "arguments": {
        "query_path": "example_value",
        "reference_path": "example_value"
    }
}
result = tu.run(query)