Functional site information for molecules

A simple XML file is defined in jV3 in order to describe functional sites of a molecule. If an external database server that returns this type of XML file is prepared, you can let jV3 read the file through the network and obtain the functional site information. An example of the XML file is as follows.

             

The XML schema file that defines the document type of the above XML file is published at http://ef-site.hgc.jp/eF-site/schema/sitelist10.xsd. When a text file ‘properties.txt’ exists in the same directory as the application jar file, jV3 reads the file as a configuration file for the application. The current configuration file, which is attached to the binary distribution, contains a set of URL necessary to connect to the PDBMLplus and eF-site system as follows.

pdbml_noatom=ftp://ftp.pdbj.org/XML/all-noatom/ pdbml_extatom=ftp://ftp.pdbj.org/XML/all-extatom/ pdbml_plus=ftp://ftp.pdbj.org/XML/pdbmlplus/pdbml_xp_gz/ efsite=http://ef-site.hgc.jp/eF-site/
 * 1) PDBML files are retrieved from the following site.
 * 1) eF-site data are retrieved from the following site.

If a database server that returns the functional site file is prepared, its URL should be appended to the configuration file. Because one functional site file is assumed to exist for one PDB ID, the URL written in the configuration file depends on the PDB ID. Therefore, the URL is represented with the use of substitute characters {0}, {1}, {2} and {3} that are substituted by each column of the PDB ID sequentially. An example is as follows.

mydb=http://myhost.jp/mydb/jv3/{0}{1}{2}{3}_jv.xml
 * 1) works with my database.

Here, the property name, ‘mydb’ in the above example, is arbitrary. Note that a PDB ID {0}{1}{2}{3} is substituted as lowercases and available protocols are http:, ftp: and file:. For simplicity, it is assumed that only one molecule file that corresponds to the above example XML file is opened in the application. Then functional site information can be displayed by the ‘show’ command as follows.

jV3> show site mydb File 1: db          category --- CATRES       catalytic pdb_hetatom binding godata      biological_process godata      molcular_function jV3> show site mydb:CATRES File 1: id=CATRES1 category=catalytic  region=A:100-100,A:46-46,A:116-116 description=a catalytic site defined by CATRES, Medline 98100076 jV3> show site mydb:pdb_hetatom:binding File 1: id=ASN category=binding  region=A:48-48,A:72-74 description=ASPARAGINE binding site jV3> show site mydb:godata File 1: id=0006529 category=biological_process  region=A description=asparagine biosynthesis id=0016874 category=molecular_function  region=A description=ligase activity jV3> show site mydb:godata:molecular_function File 1: id=0016874 category=molecular_function  region=A description=ligase activity jV3>

With a similar syntax, the ‘select’ command can be used to select the relevant set of atoms. To demonstrate the operations described in this section, let us add a following line to the configuration file ‘properties.txt’.

ex=http://ef-site.hgc.jp/jv3site/servlet/Site?pdb={0}{1}{2}{3}

The above URL provides functional site information whose contents are equivalent to those of PDBMLplus for all PDB. To reload the configuration file, quit the application (if it runs) and restart it. Then open the molecule ‘1yec’ as an example. To do this, you can use [File] – [Open – Remote] – [PDB ID] menu item as in the 'Displaying molecules' section, or equivalently execute ‘load ftp 1yec’ in the command line. Subsequently, execute ‘show site ex’ and the following keywords will be listed (the contents may change in the future).

jV3> show site ex File 1: db          category - prosite      prosite pdb_hetatom binding

Detail site information can be shown as follows.

jV3> show site ex:prosite File 1: id=PS00290 db=prosite  category=prosite  region=L:192-198 description=Immunoglobulins and major histocompatibility complex proteins signature. [FY]-{L}-C-x-[VA]-{LC}-H

Atoms in the region ‘L:192-198’ can be selected with a similar syntax.

jV3> select ex:prosite 56 Atoms Selected.

In the same way, the following atom selections are possible.

jV3> select ex:pdb_hetatom 298 Atoms Selected. jV3> select ex: 354 Atoms Selected.

Here the last command selects both regions specified by ‘prosite’ and ‘pdb_hetatom’ keywords, respectively.