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See detailJAIL: a structure-based interface library for macromolecules.
Gunther, Stefan; von Eichborn, Joachim; May, Patrick UL et al

in Nucleic Acids Research (2009), 37(Database issue), 338-41

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular ... [more ▼]

The increasing number of solved macromolecules provides a solid number of 3D interfaces, if all types of molecular contacts are being considered. JAIL annotates three different kinds of macromolecular interfaces, those between interacting protein domains, interfaces of different protein chains and interfaces between proteins and nucleic acids. This results in a total number of about 184,000 database entries. All the interfaces can easily be identified by a detailed search form or by a hierarchical tree that describes the protein domain architectures classified by the SCOP database. Visual inspection of the interfaces is possible via an interactive protein viewer. Furthermore, large scale analyses are supported by an implemented sequential and by a structural clustering. Similar interfaces as well as non-redundant interfaces can be easily picked out. Additionally, the sequential conservation of binding sites was also included in the database and is retrievable via Jmol. A comprehensive download section allows the composition of representative data sets with user defined parameters. The huge data set in combination with various search options allow a comprehensive view on all interfaces between macromolecules included in the Protein Data Bank (PDB). The download of the data sets supports numerous further investigations in macromolecular recognition. JAIL is publicly available at http://bioinformatics.charite.de/jail. [less ▲]

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Peer Reviewed
See detailDocking without docking: ISEARCH--prediction of interactions using known interfaces.
Gunther, Stefan; May, Patrick UL; Hoppe, Andreas et al

in Proteins (2007), 69(4), 839-44

The increasing number of solved protein structures provides a solid number of interfaces, if protein-protein interactions, domain-domain contacts, and contacts between biological units are taken into ... [more ▼]

The increasing number of solved protein structures provides a solid number of interfaces, if protein-protein interactions, domain-domain contacts, and contacts between biological units are taken into account. An interface library gives us the opportunity to identify surface regions on a target molecule that are similar by local structure and residue composition. If both unbound components of a possible protein complex exhibit structural similarities to a known interface, the unbound structures can be superposed onto the known interfaces. The approach is accompanied by two mathematical problems. Protein surfaces have to be quickly screened by thousands of patches, and similarity has to be evaluated by a suitable scoring scheme. The used algorithm (NeedleHaystack) identifies similar patches within minutes. Structurally related sites are recognized even if only parts of the template patches are structurally related to the interface region. A successful prediction of the protein complex depends on a suitable template of the library. However, the performed tests indicate that interaction sites are identified even if the similarity is very low. The approach complements existing ab initio methods and provides valuable results on standard benchmark sets. [less ▲]

Detailed reference viewed: 145 (2 UL)