Just another interface library?

Interfaces of macromolecules are a valuable basis to analyse the process of molecular recognition. JAIL classifies not only the interfaces between domain architectures but also those between protein chains and those between proteins and nucleic acids.

Of course not!

Gt-alpha/Gi-alpha chimera (PDB-ID: 1GOT). Interfaces of 1GOT

Interacting proteins are difficult to crystallize and rarely present within the Protein Data Base. Nevertheless, it is essential to analyse the interacting parts of the proteins to understand the process of protein-protein docking.

To overcome this problem we have built up the JAIL database. Since interacting domains exhibit similiar structural features than proteins, all known interfaces between interacting domains of the SCOP database were extracted and classified in JAIL.

Only a part of all protein structures are included in SCOP. Particularly, new PDB entries are not yet annotated. To overcome this problem additionally all interfaces between protein chains were calculated and included in the database. This type of interface also comprises the interacting parts of the assumed biological units. The last important type of interfaces provided here is composed of the interacting parts between proteins and nucleic acids. Overall the data set consists of about 180,000 interfaces.

JAIL is a comfortable tool to browse through the interface library and to analyze single interfaces. However, more general questions require large-scale analysis. For this purpose, a detailed form enables the compiling of comprehensive non redundant data sets for download.

UPDATED April 2009: Evolutionary conservation, interface definition. Please find detailed information in the FAQs.