PDBSite 2014 | PDBSite Help

1. Introduction

2. Search fields description

3. PDBSite search

3.1. PDBSite standard search

3.2. PDBSite extended search

4. Search results


1. Introduction


The PDBSite database provides versatile structural and functional information about various protein sites (post-translational modification, catalytic active, organic and inorganic ligand binding in protein-protein, protein-DNA, protein-RNA binding) in the Protein Databank. The database is composed of annotated sites from records of the protein spatial structures and also of calculated spatial, physicochemical, and mutational characteristics of sites and their spatial environment. Furthermore, it contains the structural template of the site, i.e. spatial coordinates of the N, CA, C atoms of the main chain of the residues that form a site. Each entry in the database contains information about a particular site that was described in the PDB structure. The latest PDBSite version (by June 2014) contained information about 370,000 of such sites. The database stores information for PTMSs of the following types: myristylation, phosphorylation, acetylation, cleavage, glycosylation, lipoylation.

2. Search field description


PDBSite database contains the fields of two types: those that could be queried and searched or not. The fields that could not be queried contain additional information on the site structure and their surroundings.

Below is given the description of fields that could be queried:

PDBSite id - Entry identifier. This identifier is unique within PDBSite.
PDB id - PDB ID code. This identifier is unique within PDB.
Site title - contains the title for experiment or analysis described in the entry. The field content corresponds to that in PDB.
Site type - contains type of the site.
Site header - contains PDB classification for the entry. The field content corresponds to that in PDB.
Site description - contains description of the site.
Residue Not AA - contains the names of residues that are not amino acids but contained in the site.
Keywords - contains keywords describing the macromolecule. The content corresponds to that of KEYWDS of PDB.
Molecule - contains names of macromolecules from the COMPND of PDB and is designed to search for entries by the names of macromolecules.
Ligand - contains names of ligands.
Cellular location - contains name of section of cell where site is located.
Tissue - contains name of tissue where site is located.
Organ - contains name of organ where site is located.
Organism name - contains common (scientific) name of organism where site is located.
Gene Ontology id - Gene Ontology identifier.
GO compound, GO function, GO process - contains Gene Ontology terms related to a protein.
External database - contains identifiers of various external databases presented in the dropdown list.
Number of site chains - contains number of different chains to which belong the residues of the site.
Site exposure - contains average exposure of residues of the site.
Surround exposure - contains average exposure of residues of the site environment.
LenSite - contains number of residues in the site.
LenSurround - contains number of residues in the site environment.

3. PDBSite search


In case if you use a direct link to PDBSITE 2014 - go to the step 3, otherwise:
1. Open the 'Protein' page of the GeneNetWorks web portal.
2. Click the hyperlink 'PDBSITE 2014'.

3. The PDBSite 2014 web-interface provides two types of search features: standard search (1.) and extended search (2.). In the left side of the menu select the appropriate search method.


3.1. PDBSite standard search


1. The standard search interface allows to create a complex queries from different terms in different fields. The user can choose a logical operation to combine the query parts from the drop-down list (3.).
2. The specific search fields can be selected from the dropdown list (1.), after the selection a textbox for the input of a search term will appear (2.). Each textbox corresponds to a PDBSite database field.
3. The information from the specific fields of the PDBSite database can be displayed on the Search Results page by selecting the required field names from the list (4.). The multiple fields can be selected by holding down the ctrl key (for the windows and unix OS) or cmd key (for the MAC OS).
4. Pressing the Submit button (5.) will perform a query while the Reset button (6.) will clear all typed information

3.2. PDBSite extended search


1. At the standard query form page click the ADVANCED link of the side menu to be forwarded to the extended search of PDBSite 2014.
2. Each field on this page corresponds to a PDBSite 2014 database field. The strict search checkbox (1.), enables search of records in the corresponding field strictly simular to the input string, while by default an asterisk search will be performed. The text icon (2.) near the name of the field signals that autocomplete feature for this field is enabled.
3. The limiting area for the numerical fields can be set by moving left and right slider limiters (3.). If only one numerical value is required the slider limiters can be joined together. An advanced specification of the limiting area can be made by using the corresponding checkboxes (4.), (5.).
4. To perform query, press the Submit button (6.), the Reset button (7.) will clear all typed information. To return to the standard query form, press the Search link in the side menu (8.) (Fig. 25.2e).

4. Search results


1. The results are displayed in the form of a list of records meeting the query criterion. The first line of each record is a hyperlink (1.), by clicking on it a new window containing the extended information from the PDBSite database on a corresponding site will appear. The search interface allows to obtain data from several records, by clicking the checkboxes that correspond to required records (2.).
2. To save selected information on the local disc press the SAVE RESULTSM button (3.). Pressing the SAVE RESULTS button without any records checked will save all the data from the PDBSite database corresponding to the query results on the local disk of your computer.