AlphaKnot 2.0 API



You can find examples on how to use the AlphaKnot 2.0 API in the Tutorial Application: https://github.com/ilbsm/databases_api_tutorial

AlphaKnot 2.0 search API

AlphaKnot 2.0 has 2 search APIs. The new flexible multi-criteria search API was added in the 2.0 version and is available independently of the previous API based on the "Browse database" page.

Both APIs share the same mechanism - they can be invoked by sending a set of parameters in the URL (HTTP GET or POST method), however, these parameters are different.

Multi-criteria API:

The results page of any search run on AlphaKnot 2.0 has a "raw" button which can be used to open a TSV formatted list of results.

Example: display CSV formatted list of models of Human proteins of any but Unknown topology having a name that starts with "Mucin"

https://alphaknot.cent.uw.edu.pl/browse?field=Organism&val=HUMAN&conj=NOT&field=Knot_type&val=Unknown&conj=AND&field=Protein_name&val=Mucin%25

The query can be specified using a combination of "field" and "val" parameters. Each such pair should be linked using a conjunction (AND, OR, NOT) specified as the "conj" parameter. The sequence is in this case important.

ParameterMandatory/OptionalValues/TypeDescription
fieldMandatory{Knot_Type, Category, pLDDT_chain, pLDDT_knotcore, Knot_probability, Knotcore_range, Knotcore_length, Chain_length, Protein_name, Gene_name, Kingdom, Family, Organism, Uniprot, InterPro, PDB, PFAM, EC} Name of the criteria field (case insensitive).
Each category is explained here.
valMandatoryvalue1;value2;value3
  • Multiple values can be entered using ";" as a separator.
  • You can use wildcards in values: * - replaces any string value, ? - replaces a single character
  • In case of number values (pLDDT_chain, pLDDT_knotcore, Main knot probability, Knotcore_length, Chain_length) you can use >, <, >= or <= expressions. If you don't use any of them an exact match will be performed which may yield a small number of results.
  • In the case of the "Kingdom" field use just the first capitalized letter {A, B, E, U} for {Archae, Bacteria, Eukaryota, Unclassified} respectively.
  • "Category" - refers to the Predicting Model Category: {AF4, ESM1, AF1, AF1-Knot, AF1-Unsure, AF1-Artifact, AF1-Unassigned}. AF1 spans all AF1 subcategories (AF1-Knots, AF1-Unsure etc.).
    		•
    conjOptional{AND, OR, NOT}Conjunction of the neighbouring field and value pairs.
    The "NOT" conjunction is interpreted as AND NOT.
    rawOptional{0, 1, 2, 3}
  • 0 - (default) return results as a browsable web page
  • 1 - returns results as a "raw" text file (TSV) web page
  • 2 - downloads the "raw" results as a text TSV file
  • 2 - downloads the "raw" results as a gzipped text TSV file
    • result_colsOptional";" joined list of
    {Knot_type, Category, Uniprot, Version, Organism, Knot_probability, pLDDT_knotcore, Knotcore_range, Knotcore_length, pLDDT_chain, Protein_name, Chain_length, EC, Kingdom, Family, Gene_name, InterPro, Fingerprint, PDB, PFAM}
  • A list of columns returned in the results.
  • The "Uniprot" is always included to identify a given model of a protein.
  • If this parameter is omitted the following columns are returned by default: [Category, Uniprot, Version, Organism, pLDDT_knotcore, Protein_name]
    •

    Knots API:

    Example: display CSV formatted list of models belonging to the Artifacts category and having a 31 main knot

    /browse/?cats=AF1-Artifact&organisms=HUMAN&knotTypes=3_1&raw=1

    The query can be specified using the following GET parameters

    ParameterValues/TypeDescription
    raw {0, 1, 2, 3} if "1" returns results as a "raw" text file instead of a webpage. "2" - download as TSV file, "3" - download as gzipped TSV file
    cats {AF4, ESM1, AF1, AF1-Knot, AF1-Unsure, AF1-Artifact, AF1-Unassigned} comma separated list of categories to search. AF1 spans all AF1 subcategories (AF1-Knots, AF1-Unsure etc.).
    organisms {HUMAN, ARATH, ...} comma separated list of short names of organisms to filter or search
    knot_len x;y Filter results containing knot core length between x and y
    n_depth x;y Filter results containing knots N-end length between x and y. is_sknot determines if knots or slipknots are taken into account
    c_depth x;y Filter results containing knots C-end length between x and y. is_sknot determines if knots or slipknots are taken into account
    Parameters for knots/slipknots
    knotTypes String Filter results containing only specific knot types
    knot_main_tags String Filter results containing only knot or slipknot fingerprints

    AlphaKnot 2.0 API functions

    /all.txt.gz Return a gzipped list of all AlphaFold models which are deposited in the AlphaKnot database, Format:

    uniprot_id;Entity ID;Predicting Model Version;
    /af4unknotted.tsv.gz Return a list of uniprot accessions of AlphaFold v4 structures that were tested and found unknotted based
    on the probability of the main knot that was lower than 0.42 and/or the probability of an unknot was at least 0.5. Format:

    uniprot_id;
    /af4pLDDTlow.tsv.gz Return a list of uniprot accessions of AlphaFold v4 structures that were not tested for the existence
    of knots due to a low AlphaFold structure prediction score (pLDDT < 70). Format:

    uniprot_id;
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