AlphaLasso API



AlphaLasso search API

AlphaLasso has 2 search APIs. The flexible multi-criteria search API and a less flexible but easier to use 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 AlphaLasso has a "raw" button which can be used to open a TSV formatted list of results.

Example: display CSV formatted list of models of Aeromonas punctata proteins with LS2N lassos having a N-end Gaussian Linking Number (GLN) > 0.8 and a lasso loop area < 700 Å

https://alphalasso.cent.uw.edu.pl/browse?field=Lasso_type&val=LS2N&conj=AND&field=Lasso_GLN_N&val=>0.8&conj=AND&field=Loop_area&val=<700&conj=AND&field=Organism&val=Aeromonas+punctata&raw=1

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{Lasso_type, Fingerprint, Category, pLDDT_chain, Chain_length, Loop_length, Loop_area, Loop_perimeter, Loop_gyradius, Lasso_pLDDT_deep, Lasso_pLDDT_shallow, Lasso_GLN_N, Lasso_GLN_C, 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, Chain_length, Loop_length, Loop_area, Loop_perimeter, Loop_gyradius, Lasso_pLDDT_deep, Lasso_pLDDT_shallow, Lasso_GLN_N, Lasso_GLN_C) 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 Reviewed, AF4 Unreviewed, AF4, ESM1}. AF4 encompasses both AF4 subcategories (AF4 Reviewed, AF4 Unreviewed).
    		•
    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
    {Lasso_type, Fingerprint, Category, Uniprot, Version, Organism, pLDDT_chain, Protein_name, Chain_length, EC, Kingdom, Family, Gene_name, InterPro, 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: [Fingerprint, Category, Uniprot, Organism, pLDDT_chain, Protein_name]
    •

    Lassos API:

    Example: display CSV formatted list of models belonging to the AlphaFold 4 (AF4) category having a Lasso Type L2 and being part of organisms who's name starts with "Human"

    /browse/?cats=AF4&bridges=&v=&adv=Human&organisms=&lassoType=L2&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 Reviewed, AF4 Unreviewed, AF4, ESM1} comma separated list of categories to search. AF4 encompasses both AF4 subcategories (AF4 Reviewed, AF4 Unreviewed).
    organisms {HUMAN, ARATH, ...} comma separated list of short names of organisms to filter or search
    loop_len x;y Filter results containing lasso loop length between x and y
    n_depth x;y Filter results containing N-end lasso loop length between x and y.
    c_depth x;y Filter results containing C-end lasso loop length between x and y.
    Parameters for lasso types
    lassoTypes String Filter results containing only specific lasso types and their subtypes
    fingerprint String Filter results containing only certain fingerprints

    AlphaLasso API functions

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

    uniprot_id;Entity ID;Predicting Model Version;
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