| /chains/<pdbid>/<chain>/chain.xyz.txt | For every knotted chain in the KnotProt database it is possible to download a file containing the 3D coordinates of resiudes in the chain. |
| /sequence/<pdbid>/<chain>/ | For every knotted chain in the KnotProt database it is possible to retrieve its sequence. If it is not found this function returns "N/A" |
| /cysteine.txt | List all cysteine chains in KnotProt. |
| /knotoided.txt | List all chains with knotoids in KnotProt. |
| /knotted.txt | List all chains with a knot in KnotProt. Lists only published ones |
| /knotted_types.txt | List all knotted types in KnotProt- only for published knots. |
| /unknotoided.txt.gz | Generate a gzipped list of all chains without a knotoid. |
| /unknotted.txt.gz | Generate a gzipped list of all unknotted chains. |
| /_all_knotted_chains_sequence | Generate a list containing all knotted chains with PDB code, chain and sequence. |
| /_all | List all pdbids for all proteins in KnotProt - includes published, artifacts and not yet published. |
| /_allChains | List all chains for knotted proteins in KnotProt- includes published and artifacts. |
| /_all_chains_knotted | List all chains with knot_type and pfam accession for knotted proteins in KnotProt- includes published (Y) and artifacts (A) and not yet published (T). |
| /_all_chains_knotted_N_C | List all chains with knot_type and N_cut and C_cut for knotted proteins in KnotProt- includes published (Y) and artifacts (A) and not yet published (T). |
| /_all_chains_knotted_N_C_sequence | List all chains with knot_type and N_cut and C_cut for knotted proteins in KnotProt- includes published (Y) and artifacts (A) and not yet published (T). |
| /_all_chains_with_knot | List all pdbids and chain for all knotted proteins in KnotProt- includes published and artifacts. |
| /_chains_knotted_pfam | List all chains with knot_type and PFAM classifier and family for knotted proteins in KnotProt - includes published (Y) and not yet published (T), It does not include artifacts. |
| /_nr_chains_knotted_N_C | List all Non-Redundant chains with knot_type and N_cut and C_cut for knotted proteins in KnotProt- includes published (Y) and artifacts (A) and not yet published (T). |
| /_red_chains_knotted_N_C | List all Redundant chains with knot_type and N_cut and C_cut for knotted proteins in KnotProt- includes published (Y) and artifacts (A) and not yet published (T). |
The results page of any search run on KnotProt has a "raw" button which can be used to open a CSV formatted list of results
Example - display CSV formatted list of Non-redundant protein chains with knots type +3.1 found using probabilistic or Cysteine/ion probabilistic methods
https://knotprot.cent.uw.edu.pl/browse/?raw=1&set=False&bridgeType=probab%2Ccov_ion&knotTypes=%2B31
The query can be specified using the following GET parameters
| Parameter | Values/Type | Description |
|---|---|---|
| Parameters for both knots and knotoids (is_knotoids decides which ones to show) | ||
| raw | {1, 0} | if "1" returns results as a "raw" text file instead of a webpage |
| is_knotoids | {1, 0} | Show results for knotoids or knots |
| other | {1, 0} | If set to 1 - show results for artifacts |
| set | {True, False} | if True returns full list of results, if False or empty only for Non-Redundant chains |
| bridgeType | [probab,cov_ion,deterministic] | Combination of those parameters filters knots found using the following methods: Probabilistic, Cysteine/ion probabilistic or Cysteine/ion deterministic |
| knot_len | x;y | Filter results containing knot core length between x and y |
| Ndepth | x;y | Filter results containing knots N-end length between x and y. is_sknot determines if knots or slipknots are taken into account |
| Cdepth | x;y | Filter results containing knots C-end length between x and y. is_sknot determines if knots or slipknots are taken into account |
| is_sknot | {K, S} | Filter only for Knots (K) or Slipknots (S). This filter is used together with Ndepthand Cdepth |
| molkey | String | return results for the given Molecule Keyword |
| moltag | String | return results for the given Molecule Tags |
| pfam | String | return results for the given PFAM descriptor |
| ec | String | return results for the given EC code |
| cath | String | return results for the given CATH topology |
| catha | String | return results for the given CATH architecture |
| cathc | String | return results for the given CATH class |
| tag | String | return results for the given Tag keyword |
| Parameters for knots/slipknots | ||
| knotTypes | String | Filter results containing only specific knot types |
| slipknotTypes | String | Filter results containing only specific slipknot types |
| knot_main_tags | String | Filter results containing only knot or slipknot fingerprints |
| knot_main_tagsA | String | Filter results of artifacts containing only knot or slipknot fingerprints |
| knottags | String | Filter results for fingerprints of the topological notation (Main chain + Knotted loops) |
| knottagsA | String | Filter results of artifacts for fingerprints of the topological notation (Main chain + Knotted loops) |
| Parameters for knotoids/slipknotoids | ||
| knotoidTypes | String | Filter results containing only specific knotoid types |
| slipknotoidTypes | String | Filter results containing only specific slipknotoid types |
| knotoidtags | String | Filter results for fingerprints of the topological notation (Main chain + Knotted loops) |
| knotoidtagsA | String | Filter results of artifacts for fingerprints of the topological notation (Main chain + Knotted loops) |
