SitEx


Main Search Statistics Exon BLAST Search 3D Exon Search

Documentation

Main page

On the main page the several examples of the usage of SitEx database and its services could be found.

Search page

Although on the main page the quick general search through all fields of the database is available, it is possible to use additional search parameters on this page.
PDB Site ID - it is 7 letter code, the first 4 letters presents the PDB general identifier, the other 3 is the code for the functional site in PDB database, for example 1JPAAC1;
PDB ID - general PDB 4-letter identifier;
Organism - the name of the organism which proteins are presented in the database. Could be asked for binomial name (for example, Mus musculus) or common or any synonymous names (for example, mouse);
Keyword - it is possible to ask the word that could be presented in the description of the protein (in PDB or Ensembl);
Ligand - the name of the ligand which is bound to any functional site. Could be written in short form of the code from PDB or molecule name;
Ensembl ID - standard Ensembl identifier for genes, transcripts or proteins;
SCOP - SCOP identifier, eg. b.7.1.2;
Pfam - Pfam identifier, for example PF00459, or the keyword from Pfam domain description;
Also exons could be found by Exon Length, that is measured in base pairs (BP) or translated in amino acids (AA). The minimal exon length in SitEx database is equal to 1 bp.
Due to different encoding function peculiarities it could be useful to search for exons in definite position that is why it is possible to specify the Exon Order from 1 to any.
It is possible to use one, several or all fields to specify the request and then press the button "Send query". Using the buton "Reset" one could clear all fields of the request.
On the result one could see the list of the functional sites and the list of exons that take part in coding of it for each of them. Functional site is named like in description of PDB Site ID field. In the bottom of the page it is shown the number of pages of results. If nothing was found for the request the string "No results" returns.

Statistics

This page presents the statistics of the content of SitEx database. The amount of entries is shown for each category and is clickable. The results of this are shown the same way the results of the search are.

Exon BLAST Search

Exon BLAST Search was created to make available the search of similar sequences through nucleotide sequences dataset as well is through polypeptides encoded by single exons. The input sequence should be in FASTA format and the option for protein or nucleotide should be placed. In the output one could find the list of exons which description include Ensembl identifier of the gene and PDB identifier and PDB Chain which is encoded by it and protein description. If the exon or the encoded polypeptide contains functional site amino acids in the result of BLAST alignment they are coloured and linked to site's page.

3DExonScan Search

3DExonScan could be used for search for tertiary analogue. It is possible to insert PDB identifier or upload the structure in pdb format. On the next step one could choose the chain from PDB structure or the file. The result page contains the Ensembl gene identifier, PDB identifier, protein description and Z-score and RMSD as the measure of the superimposition. Column "Aligned" demonstrates how much residues take part in superimposition while the column "Size" shows number of the residues in found polypeptide. The superimposition of chosen structure could be visualized in Jmol using general functions and downloaded in PDB format. Under the picture the alignment of the sequences presents using positions in the structures and positions of the functional site amino acids coloured in different colours in the case they are from different functional sites.

Institute of Cytology and Genetics, Computer Proteomics Group (c), 2009-2016