This simplicity stems from the canonical B conformation adopted by this piece of DNA. The most interesting aspect of iPFAM is that a user can query a PFAM identifier for all the interactions established by proteins of that family with proteins of all PFAM families as seen at the structural level. Interactions between biomolecules are the cornerstone of cellular structure, signal transduction and biochemistry. Of the many links (6,7), shown are those to PDB Europe and RCSB PDB, which provide a picture of the asymmetric unit like PDBsum but also precomputed biological assemblies, in this case an homooctamer that consists of two layers of tetramers. Many proteins and peptides that do not crystallize and/or characterized by extensive flexibility are still represented in the PDB, mostly solved by solution-state NMR. There are a growing number of databases with structural information for protein interactions at varying levels of coverage and resolution. How PDB-derived databases for nucleic acids help highlight the structural complexity of RNA over that of DNA. Finally, from annotation and wiki-based databases like Proteopedia one can quickly learn that aquaporin-0 mediates cell-cell contacts by establishing membrane junctions permeable to water. MPID-T2 help page lists database usability details, definitions for interaction parameters and other useful resources. Searches can be done by PDB ID, SCOP family of the intervening proteins or interaction type, among others, and the output can be filtered by number of intermolecular contacts. Primary and secondary database. The Glycan Fragment Database (GFDB ) focuses on protein-bound oligosaccharides, a special kind of posttranslational modification especially ubiquitous in the extracellular domains of membrane proteins where it is often involved in molecular recognition. A more dynamical classification of loops based on the predicted timescales of their fluctuations can be obtained through a Web server developed from extensive MD simulations . 7 Oct 2016 16 Classification of biological databases Primary: hold experimentally derived data experimental data repositories sequence databases structure databases. By building this database the authors could provide a draft structure-based classification of repeats including coiled coils, β-solenoids and β-propellers as some of the most represented examples, and proposed a large number … Similarly, PDB-REPRDB is a database of representative protein chains . Laboratory for Biomolecular Modeling, School of Life Sciences, Ãcole Polytechnique FÃ©dÃ©rale de Lausanne, and Swiss Institute of Bioinformatics, Switzerland AAB014 Station 19 - 1015 Lausanne, Switzerland. It is hoped that this Briefing would recapitulate most of the currently up-to-date (as of April 2016) databases derived from the PDB, which researchers should have in mind and profit from to better and more easily analyze their structures and mine PDB data. A colour version of this figure is available at BIB online: https://academic.oup.com/bib. The ArchDB  database provides a simple interface to perform complex PDB searches of loops that connect specific secondary structure elements (i.e. But B-factors are affected by variables other than true dynamics, hence caution must be taken for their interpretation. But on top of that, the databank as a whole is a reservoir of broad rich information about biomolecular structure, dynamics and conformational variability, interactions, hydration, etc., and somehow also reflects the state of the art of structure determination methods and programs. 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