KnotProt 2.0 API

/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.
/knotted_types.txt List all knotted types in KnotProt- only for published knots.
/knotted.txt List all chains with a knot in KnotProt. Lists only published ones
/_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).
/_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_with_knot List all pdbids and chain for all knotted proteins in KnotProt- includes published and artifacts.
/unknotted.txt.gz Generate a gzipped list of all unknotted chains.
/_all List all pdbids for all proteins in KnotProt - includes published, artifacts and not yet published.
/unknotoided.txt.gz Generate a gzipped list of all chains without a knotoid.
/_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).
/_allChains List all chains for knotted proteins in KnotProt- includes published and 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).
/cysteine.txt List all cysteine chains in KnotProt.
/knotoided.txt List all chains with knotoids in KnotProt.

KnotProt 2.0 Search API

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

ParameterValues/TypeDescription
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)

KnotProt | Interdisciplinary Laboratory of Biological Systems Modelling