Short Abstract

Molecular surface areas of proteins are responsible for selective binding of ligands and protein-protein recognition, and are considered the basis for specific interactions between different parts of a protein. All such interfaces from known protein structures were collected in a comprehensive Data bank of Interfaces in Proteins (DIP). The up-to-date DIP contains interface files for 351 selected Protein Data Bank entries with a total of about 160,000 surface elements formed by 12,475 secondary structures. For special purposes the inclusion of additional structures or selection of subgroups of proteins can be performed in an easy and straightforward manner (send a mail). Atomic coordinates of the constituents of molecular surface patches are directly accessible as well as the corresponding contact distances of given atoms to their neighboring secondary structural elements. The existing retrieval system for the DIP allows selection (out of the set of molecular patches) according to different criteria, such as geometric features, atomic composition, type of secondary structure, contacts, etc.. A fast, sequence-independent 3-D superposition procedure was developed for automatic searches for geometrically similar molecular surface patches.
Details were published in J.M.B.. You can look at a PDF-file.

To understand data given by this approach you can read the glossary.
To get data derived from 350 proteins (standard set) or to compare sets of atoms you have to download a program and protein related files.
If you are interested in interface files of further proteins or any kind of collaboration send an email to the authors!