), and classified and made searchable at the sequence, secondary structure and structure levels. We are witnessing the emergence of a web based "data rich" era on chemical and biological compounds. Knots in the backbone traces of proteins are relatively poorly understood, but important especially regarding the field of protein folding [81]. I acknowledge EMBO for a Long-Term Postdoctoral Fellowship. Both have also pre-built pictures of each PDB entry, those of PDB Europe being more varied in their colors, orientations and rendering of different units and ligands, and of better quality. These numbers will continue to grow rapidly over the coming years. Both RCSB PDB and PDB Europe have extensive search and download facilities, simplified programmatic access, online 3D visualization capabilities and internal tools for performing sequence, motif and structure analysis, structural alignments, etc. PDB entries are available chiefly from three data centers: the Research Collaboratory for Structural Bioinformatics PDB [3], PDB Europe [4] and PDB Japan [5], whose contents are centralized by the worldwide PDB but each having its own series of original ways to search, browse and display data, as well as different associated analysis tools and connections to external databases. Last, each of the sites mentioned in this paragraph contains its own educational resources about protein structures for experts and nonexperts. Another unique feature is that the user can download the sets of aligned protein structures in each cluster. A new version, PDBFINDER II, includes also information about chain breaks, quality indicators, B-factors and much more, also in a single compact text file. PDB ligand gateway (d) is the largest collection of 3-D structures of ligands of interest to technological development and this database … In case the user cannot find an entry of interest, the WHYNOT database (http://www.cmbi.ru.nl/WHY_NOT2) attempts to explain why a given PDB entry is not available in the PDB-derived databases from the Vriend group, PDBREPORT, B-factor Data Bank (BDB), PDB_REDO, PDBFINDER and PDB_SELECT [17]. The output is rich in geometric and chemical data about the interactions between ligands and proteins, and including enticing yet simple 2D diagrams of the binding site besides the usual 3D visualization (example in Figure 5, top part). The new database MemProtMD [45] contains proteins pre-equilibrated into explicit membranes using coarse-grained self-assembly MD simulations. For structural bioinformatics, Hadoop provides a new framework to analyse large fractions of the Protein Data Bank that is key for high-throughput studies of, for example, protein–ligand docking, clustering of protein–ligand complexes and structural alignment. Structural Bioinformatics. Published by Oxford University Press. For a color version of this figure please visit the online article. Interesting effects of some residues on transmembrane secondary structures were unveiled by analyses with these servers [46]. 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. The ArchDB [83] database provides a simple interface to perform complex PDB searches of loops that connect specific secondary structure elements (i.e. •Bioinformatics is the application of information technology to mine, visualize, analyze, integrate, and manage biological and genetic information, which can then be … Thus, they often contain precomputed descriptors, for example, about molecular geometries, that would be cumbersome to calculate for nonexperts. But on the other hand, they are the main human protein targets of current drugs [39]. These databases (Figure 1) simplify the process of finding and analyzing specific sequences, molecules or their interactions, and facilitate browsing and mining PDB entries related by a property, interaction or molecule of interest. A clickable version of this figure is available at http://lucianoabriata.altervista.org/papersdata/bib2016.html. As such, this server is a valuable resource for research involving disordered peptides and proteins too flexible to be found in the PDB. It is annotated by crossing information from Uniprot and GO, includes several classification criteria and chemoinformatic descriptors of the ligands and binding sites. Secure .gov websites use HTTPS While some biological databases are built on data derived from the primary literature, all of the wwPDB's data is directly submitted as a prerequisite to … Other relevant databases specific for RNA combine data from several sources, including the NDB and occasionally directly the PDB sites, to provide more comprehensive annotations, which are in many cases combined with sequence-based predictions [48–52]. These ontological trees facilitate seamless integration, annotation and linking of structural data across the Web. A few webservers directly connected to active databases, and a few databases that have been discontinued but would be important to have back, are also briefly commented on. It attempts to model and discover the basic principles underlying biological machinery at the molecular level. It is a vast repository and a public database of nucleic acid sequences, literature and genome specific resources. Aiming to facilitate browsing and structure visualization online through a picture-rich interface, PDBsum [10] lists brief descriptions of all PDB entries including precomputed views of most molecular components, easy-to-browse displays of structure resolution and R-factors, protein sequences with annotated PFAM and CATH domains, wire diagrams and Ramachandran plots for protein components, varied information about ligands and metal sites, and summaries of interactions between molecular components. Moreover, new tools were introduced in 2014 to analyze RNA sequences, align RNA and DNA molecules and calculate and visualize RNA structural geometries and base-pairing patterns, which are more complex and varied than those for 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. Importantly, most PDB-derived databases have the added value that they are built, maintained and updated by experts in a specific field of structural biology, therefore they perform analyses and calculations on the coordinates that would be cumbersome for a nonexpert user to carry out. A related important database, of less structural content but with more annotations, is MobiDB [32]. Entries with NMR structural restraints are interconnected to the corresponding PDB entries; indeed submission of new NMR structures to the PDB is entangled with submission of NMR data to the BMRB [34]. The work leading to the development of NPIDB yielded unprecedented classification of protein-nucleic acid interactions defined by the contacts established between different structural elements of the intervening proteins and nucleic acids, a classification that the server performs. This is owing to the complex 3D structure as observed in the online 3D visualization or in the simple circular representation at the RNA 3D hub. Bioinformatics databases and applications Eitan Rubin, December 2002. The first database of nucleic acid structures, NDB [47], has been around since the early 1990s and is today the main reference in the field. An example based on part of a real-world investigation of the molecular features of β-lactam-binding sites. Orientations are optimized by minimizing protein transfer energies from water to membrane as computed with an implicit solvent model [43]; and usefully, a related Web server allows orientation of user-uploaded structures. PDB Europe and RCSB also quickly display information about the experimental conditions, structure quality (with direct reports from PROCHECK and WHATIF coming from PDBsum) and refinement statistics (which in this case can be slightly improved according to PDB_REDO). The scripts can be obtained at http://lucianoabriata.altervista.org/papersdata/bib2016.html. Another novel server that is not a database but is related to database building and could revolutionize data mining studies is PatternQuery, a web scripting-based application to extract structure patterns from PDB files [91]. Bioinformatics data derived from structure determination experiments enables life-science researchers to address a wide variety of questions. Last in this section, PDB_SELECT [12] compiles minimal lists of representative X-ray structures at a sequence identity cutoff of 30%, of the highest available quality (measured as a combination of resolution and R-factor). 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. But B-factors are affected by variables other than true dynamics, hence caution must be taken for their interpretation. Besides, it provides several biocomputational tools for sequence analysis and FTPs for sequence retreival. In the highly dynamic extreme of the flexibility spectrum, intrinsically disordered proteins and peptides simply lack structures that can be captured neither by crystallography nor by NMR, and are therefore poorly represented in the PDB. Specialized databases built down from the PDB through mining methodologies, curation (sometimes even manual) and connections to other data repositories, facilitate browsing and finding specific kinds of molecules and molecular features as well as connecting structures to sequence, dynamics, interactions and function. • Information contained in biological databases includes gene function, structure, … In recent years, the large number of PDB entries for some proteins has allowed protein-specific databases to appear, like the ones for kinases or antibody–antigen pairs reviewed above. Part of the rich connectivity among the databases covered up to this point is schematized through an example in Figure 2A. Another example is UbSRD [87], which compiles structures of ubiquitin, ubiquitin-like folds and their interaction partners, browsable in different ways. It crosses information from the PDB, UniProt, PTMCuration [79] (which curates modifications on-the-fly on Swiss-Prot updates) and dbPTM [80] (a complete repository of posttranslational modifications but lacking structural information), facilitating sequence-structure-function analyses. Energetics of insertion of small molecules, peptides, and proteins in membranes, CHARMM-GUI Membrane Builder for mixed bilayers and its application to yeast membranes, MemProtMD: automated insertion of membrane protein structures into explicit lipid membranes, TMalphaDB and TMbetaDB: web servers to study the structural role of sequence motifs in α-helix and β-barrel domains of membrane proteins, The nucleic acid database: new features and capabilities, RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures, InterRNA: a database of base interactions in RNA structures, COGNAC: a web server for searching and annotating hydrogen-bonded base interactions in RNA three-dimensional structures, Identifying novel sequence variants of RNA 3D motifs, RNA Bricks–a database of RNA 3D motifs and their interactions, The importance of dynamics in integrative modeling of supramolecular assemblies, Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding, An updated version of NPIDB includes new classifications of DNA-protein complexes and their families, DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions, iPfam: a database of protein family and domain interactions found in the Protein Data Bank, sc-PDB: a 3D-database of ligandable binding sites–10 years on, Pocketome: an encyclopedia of small-molecule binding sites in 4D, PeptiSite: a structural database of peptide binding sites in 4D, PDTD: a web-accessible protein database for drug target identification, TarFisDock: a web server for identifying drug targets with docking approach, KLIFS: a structural kinase-ligand interaction database, Antigen-Antibody Interaction Database (AgAbDb): a compendium of antigen-antibody interactions, Metalloproteomes: a bioinformatic approach, MDB: the metalloprotein database and browser at the Scripps Research Institute, Structural biology of the lanthanides-mining rare earths in the Protein Data Bank, Analysis of copper-ligand bond lengths in X-ray structures of different types of copper sites in proteins, A less-biased analysis of metalloproteins reveals novel zinc coordination geometries, Investigation of non-corrin cobalt(II)-containing sites in protein structures of the Protein Data Bank, Acta Crystallogr B Struct Sci Cryst Eng Mater, Small revisions to predicted distances around metal sites in proteins, Automated identification of elemental ions in macromolecular crystal structures, MIPS: metal interactions in protein structures, MetalPDB: a database of metal sites in biological macromolecular structures, MetalS(3), a database-mining tool for the identification of structurally similar metal sites, MINAS–a database of metal ions in nucleic acids, Validation of metal-binding sites in macromolecular structures with the CheckMyMetal web server, PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins, Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database, dbPTM 2016: 10-year anniversary of a resource for post-translational modification of proteins, RepeatsDB: a database of tandem repeat protein structures, ArchDB 2014: structural classification of loops in proteins, Decoding the mobility and time scales of protein loops, Glycan fragment database: a database of PDB-based glycan 3D structures, Molecular dynamics simulations of glycoproteins using CHARMM, UbSRD: the ubiquitin structural relational database, SATPdb: a database of structurally annotated therapeutic peptides, EMDataBank unified data resource for 3DEM, PatternQuery: web application for fast detection of biomacromolecular structural patterns in the entire Protein Data Bank, ChEBI in 2016: Improved services and an expanding collection of metabolites, ChEMBL web services: streamlining access to drug discovery data and utilities, HMDB 3.0–the human metabolome database in 2013, ZINC–a free database of commercially available compounds for virtual screening, JSmol and the next-generation web-based representation of 3D molecular structure as applied to proteopedia, © The Author 2016. 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. MPID-T2 aims to facilitate mining of fundamental relationships and structural descriptors hidden within TR/pMHC and pMHC interactions for in-depth characterization. EBI European Bioinformatics Institute SIB Swiss Institute of Bioinformatics NCBI National Center for Biotechnology Information DDBJ DNA Databank of Japan. The wwPDB partners are the RCSB PDB in the United States, the Molecular Structure Database—European Bioinformatics Institute (MSD–EBI) in Hinxton, United Kingdom, and the Protein Data Bank—Japan (PDBj) in Osaka, Japan. Luciano Abriata is a postdoctoral researcher at the Laboratory for Biomolecular Modeling at École Polytechnique Fédérale de Lausanne and the Swiss Institute of Bioinformatics. Biofuels database (c) is a structural resource for biofuels research. Now discontinued, Scripp’s Metalloprotein Database and Browser was the first PDB-derived database of protein metal sites [66]. This task could be achieved through a number of alternatives, but the fastest is possibly by just scanning PDBFINDER II using this set of Linux scripts and small Python program. This book provides a basic understanding of the theories, associated algorithms, resources, and tools used in structural bioinformatics. For full access to this pdf, sign in to an existing account, or purchase an annual subscription. Introduction to bioinformatics databases. For a color version of this figure please visit the online article. It is dominated by enzymes as targets, but includes also receptors, transport proteins and many others; and it homogeneously covers targets related to varied diseases. Structural databases have increased massively over recent years. Protein Data Bank, PDB provides a primary archive of all . Characterisation of potentially prospective biological macromolecules and other small molecules of therapeutic interest against various diseases, … 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. For example, KLIFS [63] is specialized on kinases, currently containing around 250 different proteins and almost 2000 unique ligands taken from over 3000 PDB entries, including also sequence and structure alignments and annotations of the pockets targeted by the ligands, the conformations of key structural elements of kinases like the DFG loop and more. These databases contain visualization and analysis tools tailored to specific kinds of molecules and interactions, often including also complex metrics precomputed by experts or external programs, and connections to sequence and functional annotation databases. 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]. Most of these servers allow searches from RNA sequences and secondary structures; some offer the possibility of searching and analyzing RNA coordinates from an uploaded PDB file or filter results based on geometries, neither of which is supported by the NDB at the moment. Besides interactions between macromolecules, PDB entries also often contain small molecules bound to proteins, such as additives for crystallization, substrates, substrate analogs, regulators, lipids for proteins purified from membranes, and drugs or drug candidates added to proteins before crystallization or soaked into crystals. Still related to targeting protein function with small molecules, the Pocketome [59] is an automatically updated database of small-molecule binding sites that includes in most cases more than one PDB entry per site, allowing the user to inspect the structural variability of each binding site (example following from scPDB in Figure 5, bottom part). Structural bioinformatics is the subset of bioinformatic efforts related to the archival/retrieval, comparison, and prediction of biological structures. For each retrieved PDB, this webservice shows structural and chemical properties of both the binding pocket and bound ligand, plus a detailed list of protein-ligand interactions and 2D representation of it. Naturally, each PDB entry brings important insights into the structural and functional biochemistry related to the original subject that motivated the study. The NDB server also contains statistics about ideal geometries for bases and sugars as well as for different hydrogen bonding pairing patterns, including a new catalog of base pairing in RNA, an educational section, and software for further offline analyses. It furthers the University's objective of excellence in research, scholarship, and education by publishing worldwide, This PDF is available to Subscribers Only. OPM provides PDB coordinates of integral membrane proteins, some peripheral proteins and membrane-active peptides, pre-oriented relative to the membrane normal for membranes of variable thickness. Webmaster | Contact Us | Our Other Offices, Created March 31, 2009, Updated September 21, 2016, Manufacturing Extension Partnership (MEP), http://bioinfo.nist.gov/SemanticWeb_pr2d/chemblast.do, http://xpdb.nist.gov/image/cell_image.html, http://xpdb.nist.gov/enzyme_thermodynamics/enzyme_thermodynamics_data.html, http://xpdb.nist.gov/enzyme_thermodynamics, http://esw.w3.org/topic/HCLS/ChemicalTaxonomiesUseCase, http://xpdb.nist.gov/hiv2_d/download.html. PDB: Protein Data Bank; Molecular Modelling Database(MMDB) Structural classification of protein at Cambridge University(SCOP) Biomolecular structure and modelling group at the University college ,London; Europian Bioinformatics institute Hinxton,Cambridge; Swiss Institute of Bioinformatics 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. This Briefing describes the most used databases derived from the PDB, which are currently active, curated and updated, giving database-specific remarks and general comments. A considerable part of all the above bioinformatics efforts is on new tools and technology development with particular emphasis to Semantic web technology (http://esw.w3.org/topic/HCLS/ChemicalTaxonomiesUseCase), data interoperability and data standards across multiple Web pages. A related server from the same group, MetalS(3) [75], allows to search metal sites structurally similar to the metal site of a given structure (from the PDB or user-uploaded) throughout the whole PDB. The process of building the MemProtMD database illuminated new structural aspects about how proteins stay embedded in membranes, how membranes respond with deformations, amino acid–lipid interactions and lipid-binding protein sites, different distributions of amino acids along the membrane normal, and more; even a protocol for the identification of novel membrane proteins from new structures emerged from that work [45]. It currently contains >8000 experimental structures of DNA and RNA molecules (including DNA–RNA pairs) extracted and curated from the PDB. Using this reoriented structure one can easily set up an MD simulation of the system using Lipidbuilder or CHARMM-GUI. nonintegral) membrane proteins. 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. PDBREPORT [14] is a database that describes structural problems in PDB entries. Primary and secondary database. Thus, despite the PDB servers having powerful querying interfaces, it turns out that for several goals it is often easier, faster and even more informative to resort to the specialized databases derived from the PDB. Among many other informations, the ‘Top page’ tab for this entry has a precomputed Ramachandran plot (globe labeled 1), references listed in the PDB file (2, clicking shows relevant text and figures from the publication), species the protein sequence belongs to (3, in this case Ovis aries, sheep), a direct link to its UniProt entry (4), gene ontologies (5, indicating this is a membrane protein with transport activity), several external links (6,7, a few extended in the bottom part of the panel), two precomputed views (8,9) and a link to online 3D visualization (10). One of the latest servers dedicated to protein variability in the context of flexibility, PDBFlex [22], provides several unique visualization capabilities that clearly highlight dynamics from structures. Although not derived from the PDB, the Protein Ensemble Database [36] gathers these structural ensembles in the same format as normal PDB files, together with the experimental restraints and algorithms used to generate the ensembles. 7 Oct 2016 17 Classification of biological databases Secondary: … It is therefore important to get most out of the biomolecular interactions observed in the PDB. 4 DISCUSSION. Luciano A Abriata, Structural database resources for biological macromolecules, Briefings in Bioinformatics, Volume 18, Issue 4, July 2017, Pages 659–669, https://doi.org/10.1093/bib/bbw049. In this regard, an interesting database, ComSin [31], compares structures of protein complexes with structures of the isolated proteins focusing on order–disorder transitions, with the outcome that the unbound proteins tend to, but not always, have more disordered residues. Christine Orengo, in Encyclopedia of Bioinformatics and Computational Biology, 2019. two helices, a helix and a β-strand, etc.) For Permissions, please email: journals.permissions@oup.com, This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (, Classification and characterization of multigene family proteins of African swine fever viruses, Gene expression profiling of SARS-CoV-2 infections reveal distinct primary lung cell and systemic immune infection responses that identify pathways relevant in COVID-19 disease, idenPC-CAP: Identify protein complexes from weighted RNA-protein heterogeneous interaction networks using co-assemble partner relation, Automation in signal management in pharmacovigilance—an insight, Computational methods for annotation of plant regulatory non-coding RNAs using RNA-seq, PDB data centers and PDB-derived databases that facilitate browsing through PDB entries at a global level, Detecting errors and rebuilding PDB structures, PDB-derived databases that connect protein sequence, structure and dynamics, Protein flexibility and disorder from X-ray and NMR structures, Structural databases of intermolecular interactions, Metal sites in proteins and nucleic acids, Databases of specific structural features of proteins, Other relevant databases of biological macromolecules, http://lucianoabriata.altervista.org/papersdata/bib2016.html, ftp://ftp.cmbi.ru.nl/pub/molbio/data/pdbfinder2/PDBFIND2.TXT.gz, https://academic.oup.com/journals/pages/about_us/legal/notices, Receive exclusive offers and updates from Oxford Academic. 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The study if necessary they may be refined manually and/or through coarse-grained MD simulations user can download the of.