PTGL - SearchKey Help

SearchKey provides a simple text-based search of information found in the PTGL database and returns one or more topologies, which contain the text that matches the query string.

Contents

Simple Queries
    Attributes
    Complex Queries
    Boolean Expressions
    Additional Information
Examples

Simple Queries

The simplest query is a single keyword, such as:

        kinase

Note that partial word searches are supported, hence

kinas or

inase

would also return kinase (as well as other things).

Such queries can be time consuming and result in too many hits of little consequence.

Queries can be made more meaningful by:

1. using a phrase e.g. tyrosine kinase
2. Distinguishing kinase as the header and a compound attribute which includes the word kinase as follows:

header: kinase

where header is an example of an attribute and kinase is an example of a text string. Simply stated, only header fields are searched for the string kinase, not the complete PTGL database. The text string following an attribute can be a phrase containing multiple words.

The following is a list of attributes and their definitions:
 

Attribute	Definition
header	Text found in a PTGL database that refers to the PDB-HEADER record, which classifies the macromolecule.
compound	Text found in a PTGL COMPND record, which describes the macromolecular components or the experiment or analysis of the macromolecule of the PTGL entry.
het	Text found in the HET records, a 3 letter/number abbreviation for HET groups
hetname	Description of the HET group as found in the HET record.
pdb_id	Text describing the unique PDB identifier as found in the PDB HEADER record and consisting of 4 alphanumeric characters.
molecule	Text found in the PTGL MOLECULE records which describes the name/function of a certain protein chain.
scop	Text found in the PTGL SCOP table records CLASS, FOLD, SUPERFAMILY, FAMILY, DOMAIN, SPECIES, which describe the different hierachy levels, domain name or species name of a certain SCOP domain.
cath	Text found in the PTGL CATH table records CLASS, TOPOLOGY, ARCHITECTURE, HOMOLOGOUS FAMILY, COMM, SOURCE which describe the different hierachy levels, the species and some comments of a certain CATH domain.

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Complex Queries

Boolean Expressions

The above queries can be combined with a Boolean (AND/OR/NOT) operator. Examples:

header: kinase and het: hem

all topologies whose header contains the word kinase and have the HET-group hem.

het: hem or hetname: Zn

all topologies which have a HET group hem or a HETNAME description which contains the word Zn.

kinase not compound: complexed

all topologies containing the phrase kinase AND NOT the phrase complexed in the record COMPOUND.

((header: kinase and het: hem) not molecule: glucose) not compound: alpha-amylase

all topologies whose HEADER contains kinase and which a HET group hem, that has no MOLECULE whose name contains the word glucose and do not contain the COMPOUND alpha-amylase

Additional Information

1. The characters *, & and , are ignored if they are included as part of a keyword.
2. It is necessary to use ( )'s to maintain the logic of a query that uses more than one "not" clause, or use the Refine Your Query option at the top of the Query Results page.
3. Operators should only be used individually (for example, the syntax 'and not' should not be used).
4. Search strings should not begin with the 'not' operator.

Examples

Example 1

molecule: hemoglobin and header: oxygenase

All topologies of oygenases from hemoglobin chains.

Example 2

header: kinase and compound: complexed glucose

Protein kinases complexed with glucose
 

Example 3

compound: lysozyme and compound: native

Find native lysozyme topologies.

Example 4

hetname: FE.

Find all topologies whose FE in the HET group.