An example on how to use PDBsum as a hub to structural information of the protein aquaporin-0 in this database and in related PDB-derived databases (A), with the goal of learning about the protein before setting up a molecular dynamics simulation of the protein embedded in a membrane based on the orientation stored in the OPM database (B). These are databases of the macromolecular structures. Notice that this protocol does not require downloading any files other than the single ASCII PDBFINDER II file (ftp://ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder2/PDBFIND2.TXT.gz, under 450 MB by April 2016); and that it does not require any kind of secondary structure calculations to be performed because they are already included from DSSP analysis on PDBFINDER II update. A .gov website belongs to an official government organization in the United States. One can then search for each of the PDB entries retrieved by scPDB at Pocketome, which will return structural and chemical information about the conserved and variable features of similar sites in other PDB entries. The article presents the databases in groups such as those aimed to facilitate browsing through PDB entries, their molecules and their general information, those built to link protein structure with sequence and dynamics, those specific for transmembrane proteins, nucleic acids, interactions of biomacromolecules with each other and with small molecules or metal ions, and those concerning specific structural features or specific protein families. It is a vast repository and a public database of nucleic acid sequences, literature and genome specific resources. From these coarse-grained models it is straightforward to inspect the lipid environment of a membrane protein and to setup more complicated simulations, even of atomistic level. Moreover, they differ from secondary structures in that they do not adopt regular conformations, and therefore, they are not easy to model even though they are accurately predicted from sequences. The NCBI has cross-linked structural data to bibliographic information, to the sequence databases, and to the NCBI taxonomy. PDBTM [40] was the first comprehensive database of transmembrane proteins from the PDB, with currently >2600 entries. The scripts can be obtained at http://lucianoabriata.altervista.org/papersdata/bib2016.html. Primary and secondary database. [2]). Last in this section, the now discontinued database ProDDO [30] was particularly interesting because it was built by text mining the PDB files for keywords related to protein dynamics, such as ‘disorder’, ‘gap’ (referring to unresolved residues), ‘unfolded’, etc. In addition, extraction of mechanistic information from the structures is another key task. E-mail: Search for other works by this author on: Announcing the worldwide protein data bank, The RCSB Protein Data Bank: views of structural biology for basic and applied research and education, PDBe: improved accessibility of macromolecular structure data from PDB and EMDB, Protein Data Bank Japan (PDBj): maintaining a structural data archive and resource description framework format, Inference of macromolecular assemblies from crystalline state, A dimerization interface mediated by functionally critical residues creates interfacial disulfide bonds and copper sites in CueP, eF-site and PDBjViewer: database and viewer for protein functional sites, eF-seek: prediction of the functional sites of proteins by searching for similar electrostatic potential and molecular surface shape, PDB-Explorer: a web-based interactive map of the protein data bank in shape space, Enlarged representative set of protein structures, PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003, The PDB_REDO server for macromolecular structure model optimization, Detection of trans-cis flips and peptide-plane flips in protein structures, A series of PDB-related databanks for everyday needs, The PDBFINDER database: a summary of PDB, DSSP and HSSP information with added value, PCDB: a database of protein conformational diversity, CoDNaS: a database of conformational diversity in the native state of proteins, PDBFlex: exploring flexibility in protein structures, The use of experimental structures to model protein dynamics, Protein conformational diversity modulates sequence divergence, Comparison of tertiary structures of proteins in protein-protein complexes with unbound forms suggests prevalence of allostery in signalling proteins, The interplay of structure and dynamics: insights from a survey of HIV-1 reverse transcriptase crystal structures, Dissecting the effects of concentrated carbohydrate solutions on protein diffusion, hydration, and internal dynamics, On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions, BDB: databank of PDB files with consistent B-factors, ProDDO: a database of disordered proteins from the Protein Data Bank (PDB), ComSin: database of protein structures in bound (complex) and unbound (single) states in relation to their intrinsic disorder, MobiDB: a comprehensive database of intrinsic protein disorder annotations, BioMagResBank (BMRB) as a partner in the Worldwide Protein Data Bank (wwPDB): new policies affecting biomolecular NMR depositions, PACSY, a relational database management system for protein structure and chemical shift analysis, pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins, Prediction of the human membrane proteome, Properties and identification of human protein drug targets, PDBTM: Protein Data Bank of transmembrane proteins after 8 years, Expediting topology data gathering for the TOPDB database, OPM database and PPM web server: resources for positioning of proteins in membranes, Anisotropic solvent model of the lipid bilayer. Structural macro-analysis (folds, classification, similarity, sequence alignments) CATH (classification database; UCL) CATH PFDB (protein family database; UCL) SCOP (classification database; MRC-LMB) FSSP (Fold classification based on Structure-Structure alignment of Proteins; EBI) Interesting statistics emerged from building and updates of SATPdb; for example, showing that most peptides in the database have more than one therapeutic activity. I acknowledge EMBO for a Long-Term Postdoctoral Fellowship. B-factors are additional atom-specific outputs from the process of structure refinement from X-ray diffraction data, often interpreted in terms of internal atomic motions to extrapolate information about protein dynamics. Biological Databases- Types and Importance. GFDB allows users to search for specific glycan sequences in a set precompiled from the PDB, to retrieve structural information. Part of the rich connectivity among the databases covered up to this point is schematized through an example in Figure 2A. sequences that adopt radically different conformations across PDB entries [19]. The worldwide PDB is a large and complex database, and each of its entries contains large amounts of data besides the already rich information of its atomic coordinates. nonintegral) membrane proteins. Published by Oxford University Press. This database is particularly useful for mining studies as it reduces the number of PDB entries to analyze, minimizing redundancy as well as noise and errors on the mined values. 7 Oct 2016 16 Classification of biological databases Primary: hold experimentally derived data experimental data repositories sequence databases structure databases. As an example of its importance beyond the curation of specific errors in PDB structures, high-throughput analyses based on PDB_REDO led to a large compilation of peptide planes predicted to be flipped and peptide bonds predicted to be swapped between trans and cis conformations in the PDB [16]. Its construction and updates filter out solvent molecules, detergents, ions and other common additives used for protein crystallization, thus enriching relevant binding sites. Because of this, making the most out of existent structures by mining the PDB, and using this information for simulations, modeling and driving experiments, is of utmost importance. But other resourceful databases are available, widely used for point applications and also for mining and thus better understanding protein metal sites [67–70], a knowledge that in turn helps to better refine the metal sites of newly solved metalloprotein structures [68, 71, 72]. Finally, a few comments on Web services that do not contain structures of biological macromolecules but are extremely relevant to computational and experimental research in biochemistry and structural biology. While most databases and Web servers about posttranslational modifications are dedicated to their compilation and prediction, PTM-SD is probably the only one that focuses globally on the structures of protein amino acid modifications as retrieved from the PDB [78]. Metal Interactions in Protein Structures (MIPS [73]) allows to easily find, download and visualize all PDB entries that contain a given metal ion (also monoatomic anions), filtering them by the types of molecules interacting with the ion and by structure quality and degree of redundancy. The structural bioinformatics research group was created in March 2001. Related (derived) Structural Databases; Jena Library: The database aim to integrate information regarding structural models in the PDB with an emphasis on visualization and analysis. One is EMDataBank [89], the main repository for primary electron microscopy data, important as cryo-EM structures rapidly populate the PDB providing unprecedented structural data for large macromolecular assemblies. The search interface is complex, but this allows detailed queries specifying which bases to allow in the inner and outer coordination spheres, restraints on their distances to the metal ion, restraints on the relative positions of different bases bound to the metal ion and more. Now discontinued, Scripp’s Metalloprotein database and Browser was structural database in bioinformatics first comprehensive database of representative chains. Often contain precomputed descriptors, for example, about molecular geometries, that would be cumbersome to calculate nonexperts... 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