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.
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"
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.
Parameter | Mandatory/Optional | Values/Type | Description |
---|---|---|---|
field | Mandatory | {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. |
val | Mandatory | value1;value2;value3 |
|
conj | Optional | {AND, OR, NOT} | Conjunction of the neighbouring field and value pairs. The "NOT" conjunction is interpreted as AND NOT. |
raw | Optional | {0, 1, 2, 3} | |
result_cols | Optional | ";" 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} |
|
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
Parameter | Values/Type | Description |
---|---|---|
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 |
/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; |