UniLectin exploration platform and database for curated and predicted lectin carbohydrate binding proteins

This endpoint enables to perform queries on UniLectin3D's lectin, ligand and bibliography tables.
It retrieves the content of the specified column(s) (getcolumns) where another column (wherecolumn) has a specific value (isvalue). Results are grouped per lectin entry. The columns marked with superscript 1 aggregate multiple values per lectin into a comma-separated list and can only be used in getcolumns. The columns marked with superscript 2 can only be used for conditional filtering (i.e. wherecolumn). Columns without any superscript can be used in both.

Lectin columns:

• lectin.lectin_id: UniLectin3D's lectin ID, e.g. 1000
• lectin.pdb: PDB ID, e.g. 2CY6
• chain: PDB chain, e.g. A
• fold: Lectin fold, e.g. b-sandwich / ConA-like
• class: Lectin class, e.g. L-type (legume lectin)
• family: Lectin family, e.g. ConA and related
• origin: Lectin origin, e.g. Plant lectins
• species: Lectin species, e.g. Rattus norvegicus
• resolution: Structure resolution in Å, e.g. 2
• uniprot: UniProt ID, e.g. P81460
• protein_name: Common protein name, e.g. Concanavalin-A (Con A)

Ligand columns (from the ligand table):

• glytoucan_id²: Search by ligand's GlyTouCan ID, e.g. G10543DQ
• glytoucan_id_list¹: List the ligand GlyTouCan ID(s), e.g. G10543DQ
• iupac²: Search by ligand's IUPAC, e.g. Glc(a1-1)Glc
• iupac_list¹: List the ligand IUPAC(s), e.g. Glc(a1-1)Glc
• monosac²: Search by monosaccharide composition, e.g. D-Glcp
• monosac_list¹: List the monosaccharide composition(s), e.g. D-Glcp
• glycoct²: Search by ligand's GlycoCT

Bibliography columns (from the bibliography table):

• doi²: Search by DOI, e.g. 10.1016/j.str.2005.12.008
• doi_list¹: List the DOI(s), e.g. 10.1016/j.str.2005.12.008
• pubmed²: Search by PubMed ID, e.g. 16438930
• pubmed_list¹: List the PubMed ID(s), e.g. 16438930
• title²: Search by article title
• title_list¹: List the article title(s)
• authors²: Search by author name(s)
• authors_list¹: List the author name(s)
• year²: Search by publication year, e.g. 2006
• year_list¹: List the publication year(s), e.g. 2006
• journal²: Search by journal name, e.g. Structure
• journal_list¹: List the journal name(s), e.g. Structure

• getcolumns: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are accepted, e.g. "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get all PDB IDs and their UniProt IDs:
  Try this query { "getcolumns": "lectin.pdb,uniprot", "wherecolumn": "lectin.pdb", "isvalue": "%%", "limit": "1000"}
• Get all lectins of a specific species with their ligand IUPACs:
  Try this query { "getcolumns": "lectin.pdb,uniprot,iupac_list", "wherecolumn": "species", "isvalue": "Rattus norvegicus", "limit": "1000"}
• Get all lectins that have a ligand, with their GlyTouCan IDs:
  Try this query { "getcolumns": "lectin.pdb,uniprot,glytoucan_id_list", "wherecolumn": "iupac", "isvalue": "VALUE_NOT_EMPTY", "limit": "1000"}
• Get all lectins with their associated references (DOI and PubMed ID):
  Try this query { "getcolumns": "lectin.pdb,uniprot,doi_list,pubmed_list", "wherecolumn": "lectin.pdb", "isvalue": "%%", "limit": "1000"}
• Get all lectins published in a specific year with their ligands and references:
  Try this query { "getcolumns": "lectin.pdb,uniprot,species,iupac_list,doi_list,year_list", "wherecolumn": "year", "isvalue": "2006", "limit": "1000"}
• Get all lectins referenced by a specific author:
  Try this query { "getcolumns": "lectin.pdb,uniprot,authors_list,title_list", "wherecolumn": "authors", "isvalue": "%Hamelryck%", "limit": "1000"}

This endpoint enables to perform queries on the predicted lectin table.
It retrieves the content of the specified column(s) (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• uniprot: Uniprot ID, e.g. P36307
• protein.protein_id: e.g. 6
• protein.name: e.g. Outer capsid protein VP4
• alt_ac: NCBI ID, e.g. NP_187120
• protein_ac: Accession ID selected for LectomeXplore, usually (1) UniProt or (2) NCBI ID
• fold: e.g. b-sandwich ConA-like
• domains.domains_id: e.g. 787209
• length: e.g. 772
• genus: e.g. Rotavirus
• gene: e.g. PYEQ01000096.1
• gene_begin: e.g. 6118
• gene_end: e.g. 11124
• cluster: e.g. P35746
• strain: e.g. CCP5
• species: e.g. Rotavirus A
• superkingdom: e.g. Viruses
• kingdom e.g. Orthornavirae
• phylum: e.g. Duplornaviricota
• domain: Lectin class, e.g. Rotavirus spike protein
• score: Score of prediction similarity to the reference, from 0 to 1, e.g. 0.539
• ref_seq: Reference protein sequence
• match_seq: Protein sequence of the predicted lectin

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted such as "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get the predicted lectome from all the proteins of the bacteria superkingdom:
  Try this query { "getcolumns": "fold,domain,uniprot,superkingdom", "wherecolumn": "superkingdom", "isvalue": "Bacteria%" , "limit": "2000"}
• Get all predicted lectins:
  Try this query { "getcolumns": "uniprot,domain", "wherecolumn": "uniprot", "isvalue": "%%", "limit": "2000"}

This endpoint enables to perform queries on the ligand table.
It retrieves the content of the specified columns (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• ligand_id
• iupac
• glycoct
• glytoucan_id

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted such as "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get ALL the columns and rows of the ligand table:
  Try this query { "getcolumns": "ligand_id,iupac,glycoct,glytoucan_id", "wherecolumn": "ligand_id", "isvalue": "%%" , "limit": "-1"}
• Get the ligands whose iupac contain a NAc:
  Try this query { "getcolumns": "iupac", "wherecolumn": "iupac", "isvalue": "%NAc%", "limit": "1000"}

This endpoint enables to perform queries on the Human Lectome table.
It retrieves the content of the specified columns (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• id: HumanLectome's lectin ID, e.g. 2
• UniProt_ID: UniProt ID, e.g. Q13438
• RefSeqID: NCBI ID, e.g. NP_006803
• GeneID: e.g. 10956
• lectomeXplore_score: Score of prediction similarity to the reference, from 0 to 1, e.g. 1.0
• infer_class: Lectin class, e.g. P-type lectin-like
• infer_fold: Lectin fold, e.g. b-barrel
• PDB_ID: e.g. 3AIH
• family: Protein family, e.g. MRH
• common_protein_name e.g. MRH - mannose-6-phosphate receptor homology domain
• lectinStatus: Curated, Low evidence or Very low evidence
• glycanStatus: Specific or Uncharacterised
• Chromosome: e.g. 12
• iupac: IUPAC of the ligand(s) that bind(s) the concerned lectin, e.g. Man(a1-6)Man(a1-6)Man
• lectomexplore_id: Lectin ID in LectomeXplore (if any), e.g. 553088
• pubmed_NCBI_inTxt_NCBIdata: PubMed identifier(s) of publications associated with the protein entry as retrieved from NCBI, e.g. 11389730
• pubmed_NCBI_inTxt_NCBIdata_title: Title(s) of the publications associated with the protein entry as retrieved from NCBI
• PubMed_ID_UniProtCanonical: PubMed identifier(s) of publications associated with the canonical UniProt entry of the protein, e.g. 11389730
• PubMed_ID_UniProtCanonical_title: Title(s) of the publications associated with the canonical UniProt entry of the protein

• getcolumn: string of the column to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted as e.g. "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get all the human lectins with a curated status:
  Try this query { "getcolumns": "RefSeqID,UniProt_ID", "wherecolumn": "lectinStatus", "isvalue": "Curated" , "limit": "1000"}
• Get all the SIGLEC lectins:
  Try this query { "getcolumns": "RefSeqID,UniProt_ID", "wherecolumn": "common_protein_name", "isvalue": "%SIGLEC%" , "limit": "1000"}

This endpoint enables to perform queries in BiotechLec's dataset.
It retrieves the content of the specified columns (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this dataset are:

• Lectin: Commercial name of the lectin, e.g. MPA
• Organism: Species name, e.g. Maclura pomifera
• Preferred glycan: IUPAC of the lectin's preferred glycan, e.g. Gal(b1-3)GalNAc
• Origin: e.g. Plant
• uniprot: UniProt ID, e.g. P18674
• protein name: Common protein name, e.g. Agglutinin alpha chain
• Length: Protein sequence length, e.g. 133
• PDB: PDB ID, e.g. 3LLZ
• Fold Lectin fold, e.g. b-prism I
• Class Lectin class, e.g. Jacalin-like
• InterPro family InterPro family ID, e.g. IPR001229

• getcolumn: string of the column to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted as e.g. "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get all BiotechLec's lectins from plants:
  Try this query { "getcolumns": "Lectin,Preferred glycan,uniprot,protein name,Length,PDB", "wherecolumn": "Origin", "isvalue": "Plant", "exactmatch": "True"}
• Get all the lectins of a class that contains the word Jacalin:
  Try this query { "getcolumns": "Lectin,Preferred glycan,uniprot,protein name,Length,PDB", "wherecolumn": "Class", "isvalue": "Jacalin", "exactmatch": "False"}

This endpoint enables to perform queries on the predicted propeller lectin table.
It retrieves the content of the specified column(s) (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• ncbi: RefSeq ID, e.g. ABB17278
• uniprot: UniProt ID, e.g. Q309D1
• protein.protein_id: PropLec lectin ID, e.g. 17491
• protein.name: e.g. Lectin PVL (Fragment)
• domain: Lectin family, e.g. PropLec7B_PVL
• domains.domains_id: PropLec domain ID, e.g. 31702
• length: Lectin length, e.g. 395
• genus: e.g. Lacrymaria
• gene: e.g. DQ232759.1
• gene_begin: e.g. 1
• gene_end: e.g. 1188
• cluster: e.g. Q309D1
• species: e.g. Lacrymaria velutina
• superkingdom: e.g. Eukaryota
• kingdom: e.g. Fungi
• phylum: e.g. Basidiomycota
• score: Score of prediction similarity to the reference, from 0 to 1, e.g. 0.871
• nbdomain: Number of lectin domains, e.g. 8

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted such as "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get the propeller lectome from all the proteins of the bacteria superkingdom:
  Try this query { "getcolumns": "domain,uniprot,superkingdom", "wherecolumn": "superkingdom", "isvalue": "Bacteria%" , "limit": "2000"}
• Get all predicted propeller lectins:
  Try this query { "getcolumns": "uniprot,domain", "wherecolumn": "uniprot", "isvalue": "%%", "limit": "2000"}

This endpoint enables to perform queries on the predicted fungal lectin table.
It retrieves the content of the specified column(s) (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• protein_id: MycoLec lectin ID, e.g. 14183377
• protein: e.g. %SS1G_09838T0%
• fold: Lectin fold, e.g. b-trefoil
• domain: Lectin class, e.g. Sclerotinia lectin-like
• domains.domains_id: MycoLec domain ID, e.g. 30121
• length: Lectin length, e.g. 153
• genus: e.g. Sclerotinia
• ref_seq: Reference protein sequence, e.g. MGFKGVGTYEIVPYQ%
• match_seq: Protein sequence of the predicted lectin, e.g. MGFKGVGTYEIVPYQ%
• species: e.g. Sclerotinia sclerotiorum
• phylum: e.g. Ascomycota
• class: e.g. Leotiomycetes
• family: e.g. Sclerotiniaceae
• score: Score of prediction similarity to the reference, from 0 to 1, e.g. 1

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted such as "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get the lectome from all the proteins of the species Sclerotinia sclerotiorum:
  Try this query { "getcolumns": "fold,domain,species", "wherecolumn": "species", "isvalue": "Sclerotinia sclerotiorum" , "limit": "2000"}
• Get all predicted fungal lectins:
  Try this query { "getcolumns": "protein,fold,domain", "wherecolumn": "protein", "isvalue": "%%", "limit": "2000"}

This endpoint enables to perform queries on the predicted trefoil lectin table.
It retrieves the content of the specified column(s) (getcolumns) where another column (wherecolumn) has a specific value (isvalue).

The available columns for this table are:

• ncbi: RefSeq ID, e.g. QBM06340
• uniprot: UniProt ID, e.g. A0A646QV53
• protein.protein_id: TrefLec lectin ID, e.g. 25617
• protein.name: e.g. R-type lectin 1
• domain: Lectin family, e.g. Sevil-like
• domains.domains_id: TrefLec domain ID, e.g. 18336
• length: Lectin length, e.g. 129
• genus: e.g. Mytilisepta
• gene: e.g. MK434191.1
• gene_begin: e.g. 130
• gene_end: e.g. 519
• cluster: e.g. Q309D1
• species: e.g. Mytilisepta virgata
• superkingdom: e.g. Eukaryota
• kingdom: e.g. Metazoa
• phylum: e.g. Mollusca
• score: Score of prediction similarity to the reference, from 0 to 1, e.g. 0.685
• nbdomain: Number of lectin domains, e.g. 3

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted such as "Rattus%" to match everything starting with "Rattus")
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get the trefoil lectome from all the proteins of the bacteria superkingdom:
  Try this query { "getcolumns": "domain,uniprot,superkingdom", "wherecolumn": "superkingdom", "isvalue": "Bacteria%" , "limit": "2000"}
• Get all predicted trefoil lectins:
  Try this query { "getcolumns": "uniprot,domain", "wherecolumn": "uniprot", "isvalue": "%%", "limit": "2000"}

This endpoint enables to perform queries on the PathoLec lectin, ligand, annotation and article tables.
It retrieves the content of the specified column(s) (getcolumns) where a column (wherecolumn) has a specific value (isvalue). Results are grouped per lectin entry. The columns marked with superscript 1 aggregate multiple values per lectin into a comma-separated list and can only be used in getcolumns. The columns marked with superscript 2 can only be used for conditional filtering (i.e. wherecolumn). Columns without any superscript can be used in both.

Lectin columns:

• pl.lectin_id: Pathogen lectin ID, e.g. 11
• lectin_name: Lectin name, e.g. Botulinum neurotoxin type G
• uniprot: UniProt ID, e.g. Q60393
• refseq: RefSeq ID, e.g. NP_056821
• gene_name: Gene name, e.g. HA
• fold: Lectin fold, e.g. b-sandwich / Ig-like
• class: Lectin class, e.g. Siglec-like adhesin
• family: Lectin family, e.g. GspB

Structure columns:

• pdb²: Search by PDB ID, e.g. 2VXR
• pdb_list¹: List the PDB ID(s), e.g. 2VXR

Annotation columns:

• agent_name²: Search by pathogen agent name, e.g. Clostridium botulinum
• agent_name_list¹: List the pathogen agent name(s), e.g. Clostridium botulinum
• disease_name²: Search by disease name, e.g. Botulism
• disease_name_list¹: List the disease name(s), e.g. Botulism
• area_name²: Search by affected tissue name, e.g. Intestine
• area_name_list¹: List the affected tissue name(s), e.g. Intestine
• organism_name²: Search by host organism name, e.g. Human
• organism_name_list¹: List the host organism name(s), e.g. Human

Ligand columns:

• glytoucan_id²: Search by glycan GlyTouCan ID, e.g. G51331BY
• glytoucan_id_list¹: List the glycan GlyTouCan ID(s), e.g. G51331BY
• iupac²: Search by ligand IUPAC, e.g. Glc(a1-1)Glc
• glycoct²: Search by ligand GlycoCT

Article columns:

• pmid²: Search by PubMed ID, e.g. 16438930
• pmid_list¹: List the PubMed ID(s), e.g. 16438930
• title²: Search by article title
• title_list¹: List the article title(s)
• citation²: Search by citation string
• citation_list¹: List the citation string(s)
• pub_year²: Search by publication year, e.g. 2006
• pub_year_list¹: List the publication year(s), e.g. 2006

• getcolumn: string of the column(s) to be fetched (one or multiple columns, separated by comma)
• wherecolumn: string of the conditional column
• isvalue: string of the value to be matched in wherecolumn (wildcards are also accepted, e.g. "Rattus%" to match everything that starts with "Rattus",)
• limit: (optional) integer of the number of results to be returned (default: 1000, -1 for all)

• Get all the lectin names and the associated pathogen agents:
  Try this query { "getcolumns": "lectin_name,agent_name_list", "wherecolumn": "agent_name", "isvalue": "%%"}
• Get all the lectin names and the associated host organisms:
  Try this query { "getcolumns": "lectin_name,organism_name_list", "wherecolumn": "organism_name", "isvalue": "%%"}
• Get all the lectin names and their ligands' GlyTouCan IDs:
  Try this query { "getcolumns": "lectin_name,glytoucan_id_list", "wherecolumn": "glytoucan_id", "isvalue": "%%"}
• Get all the lectin names and the associated disease names:
  Try this query { "getcolumns": "lectin_name,disease_name_list", "wherecolumn": "disease_name", "isvalue": "%%"}
• Get all the lectin names and the associated affected tissues:
  Try this query { "getcolumns": "lectin_name,area_name_list", "wherecolumn": "area_name", "isvalue": "%%"}
• Get all lectin names with their associated articles (PubMed ID and citation):
  Try this query { "getcolumns": "lectin_name,pmid_list,citation_list", "wherecolumn": "pmid", "isvalue": "%%"}
• Get all lectins published in a specific year with agents and ligands:
  Try this query { "getcolumns": "lectin_name,uniprot,agent_name_list,glytoucan_id_list,pub_year_list", "wherecolumn": "pub_year", "isvalue": "2006"}