Documentation

Definitions


A tutorial usage example (Analysis of the proteasome complex) is available here.


Querying BISC

Basic search

Several options are available to query BISC. On the front page, a browsing option(clustered by interface size) for the template section is offered and keyword search for both, template modellable interactions. Keywords in the template section can be PDB ID, part of the protein name (e.g. 'histone'), part of a SCOP classification or the scientific organism name (e.g. Homo sapiens). Keywords in BISC-MI can be a UniProt accession number (e.g. Q9NSY8), part of the protein name (like 'protease') or the scientific organism name.

Advanced search

In the Advanced Search the user is offered a more refined search where he/she can specify which field is searched. For example Keyword 'proteasome' AND organism 'Saccharomyces cerevisiae' shows all templates where the word 'proteasome' occurs in the title or SCOP name and limits the organism to S. cerevisiae. A BLAST search against the template section is also available. We are working on implementing a service that allows the automated modelling of user sequences.

Template Pages

The next paragraphs describe sections on the template pages.

Example: PROTEASOME FROM THERMOPLASMA ACIDOPHILUM (Template 1pma:I:J)

On the template page, the user can examine the interaction in greater detail.

Modellable Interactions

If interactions from a functional genomics database have been identified as modellable, they are shown as a tabular bar on the top of the page (Taken from template page( 1pma:I:J) :

bar

Jmol Visualisation

Emphasis is put on the interface. Two embedded Jmol applets visualise and allow the user to investigate it. The left applet highlights all residues that are believed to form the interface in wireframe formating, the one on the right uses spacefill.

MolSurfer

Next, the user is offered the opportunity to inverstigate the interface using MolSurfer MolSurfer is a graphical tool that links a 2D projection of a macromolecular interface to a 3D view of the macromolecular structures. The macromolecular interface generated by adsi (the interface module of ads, analytically defined molecular surfaces ), has been pre-computed for all templates. MolSurfer can be used to study protein-protein and protein-DNA/RNA interfaces. The 2D projections of the computed interface aid visualization of complicated interfacial geometries in 3D. Molecular properties, including hydrophobicity and electrostatic potential, can be projected onto the interface. MolSurfer can thereby aid exploration of molecular complementarity, identification of binding "hot spots" and prediction of the effects of mutations. MolSurfer can also facilitate the location of cavities at macromolecular interfaces

Download

The user can download the template itself in PDB format and the sequences of each partner in FASTA-format. The sequences are offered in two version, one based on the PDB SEQRES record and one based on the PDB ATOM records. The ATOM sequence are extracted from Roland Dunbrack's S2C database.

Interface Scores

All interfaces have been scored using PISA. Scores haven calculated using a local standalone version of PISA.

SCOP classifications

Wherever possible, SCOP domain classifications are listed where they have been assigned to each chain.

Request Modellable Interactions

Example: BioGRID Modellable Interactions for 1PMA:I:J

All interactions that have been identified as modellable using the specific template are listed on a separate page. Interactions are separted depending on the underlying database (BioGRID, HPRD, IntAct). A brief overview at the possibility to request a model by entering an email address is given. The next BISC release will replace the UniProt accession numbers with protein descriptions. A detail page offers a few more details about the interaction, together with a link to the source database.
Example: Modellable Interaction P23639-P21243

Usage example: Analysis of a the proteasome complex

Literature references