The evolution of structural databases

Current Bioinformatics, 2009

Proteins are the molecules of life which are involved in cellular processes. The functional specificity of a protein is linked to its structure. A great section of bioinformatics deals with the prediction, analysis and visualization of protein 3D structures. High-throughput methods for the determination of protein structures provide the information needed to build structure-activity relationships. The accessibility of these structural data together with genomic and clinical data is of crucial importance for the application of bioinformatics in medical research. The experimental methods are supplemented by homology modelling, where new protein structures are predicted by exploiting structural information from known configurations. Computer visualization of protein models provide insights into biological processes which can not be adequately explained otherwise. For the analysis of protein-protein interactions, Voronoi tessellations are used to quantify the macromolecular interfaces. Details at the atomic and electronic levels of the protein molecules, needed for a deeper understanding of properties that remain unrevealed after structural elucidation, are provided by methods based on quantum theoretical calculations. Many proteins are of immediate medical and pharmacological relevance. The structural analysis is therefore of special interest to understand diseases at a molecular level, which is the prerequisite for new developments in diagnosis and therapy.

European Journal of Biochemistry, 1977

The Protein Data Bank is a computer-based archival file for macromolecular structures. The Bank stores in a uniform format atomic co-ordinates and partial bond connectivities, as derived from crystallographic studies. Text included in each data entry gives pertinent information for the structure at hand (e.g. species from which the molecule has been obtained, resolution of diffraction data, literature citations and specifications of secondary structure). In addition to atomic co-ordinates and connectivities, the Protein Data Bank stores structure factors and phases, although these latter data are not placed in any uniform format. Input of data to the Bank and general maintenance functions are carried out at Brookhaven National Laboratory. All data stored in the Bank are available on magnetic tape for public distribution, from Brookhaven (to laboratories in the Americans), Tokyo (Japan), and Cambridge (Europe and worldwide). A master file is maintained at Brookhaven and duplicate copies are stored in Cambridge and Tokyo. In the future, it is hoped to expand the scope of the Protein Data Bank to make available co-ordinates for standard structural types (e.g. α-helix, RNA double-stranded helix) and representative computer programs of utility in the study and interpretation of macromolecular structures.

Acta Crystallographica Section D Biological Crystallography, 1998

Databases containing macromolecular structure data provide a crystallographer with important tools for use in solving, refining and understanding the functional significance of their protein structures. Given this importance, this paper briefly summarizes past progress by outlining the features of the significant number of relevant databases developed to date. One recent database, PDB+, containing all current and obsolete structures deposited with the Protein Data Bank (PDB) is discussed in more detail. PDB+ has been used to analyze the self-consistency of the current (1 January 1998) corpus of over 7000 structures. A summary of those findings is presented (a full discussion will appear elsewhere) in the form of global and temporal trends within the data. These trends indicate that challenges exist if crystallographers are to provide the community with complete and consistent structural results in the future. It is argued that better information management practices are required to ...

RADS Journal of Biological Research & Applied Sciences

Databases are the computerized platform where information is stored and can be retrieved easily by public users. Biological databases are the repositories of biological data. These biological data libraries contain facts and figures related to various disciplines of research including genomics, proteomics, microarray technology, metabolomics and phylogenetics. By using biological databases, a broad collection of essential biological information can be exploited ranging from function, structure and localization of gene, clinical consequences of mutation to similarity index among biological sequences and structures. Nowadays, different kinds of biological databases are available on the web. The present write up focuses on biological databases and bioinformatics tools for protein structure analysis. This review also aims to elaborate the searching schemes, available in different structural databases. The wide variety of different levels and types of information content related to 3D pr...

Acta Crystallographica Section D Biological Crystallography, 1998

The Protein Data Bank (PDB) at Brookhaven National Laboratory, is a database containing experimentally determined three-dimensional structures of proteins, nucleic acids and other biological macromolecules, with approximately 8000 entries. Data are easily submittedviaPDB's WWW-based toolAutoDep, in either mmCIF or PDB format, and are most conveniently examinedviaPDB's WWW-based tool3DB Browser.

Nucleic acids research, 2015

The RCSB Protein Data Bank (RCSB PDB, http://www.rcsb.org) provides access to 3D structures of biological macromolecules and is one of the leading resources in biology and biomedicine worldwide. Our efforts over the past 2 years focused on enabling a deeper understanding of structural biology and providing new structural views of biology that support both basic and applied research and education. Herein, we describe recently introduced data annotations including integration with external biological resources, such as gene and drug databases, new visualization tools and improved support for the mobile web. We also describe access to data files, web services and open access software components to enable software developers to more effectively mine the PDB archive and related annotations. Our efforts are aimed at expanding the role of 3D structure in understanding biology and medicine.

Current medicinal chemistry, 2004

During the last two decades, the number of sequence-known proteins has increased rapidly. In contrast, the corresponding increment for structure-known proteins is much slower. The unbalanced situation has critically limited our ability to understand the molecular mechanism of proteins and conduct structurebased drug design by timely using the updated information of newly found sequences. Therefore, it is highly desired to develop an automated method for fast deriving the 3D (3-dimensional) structure of a protein from its sequence. Under such a circumstance, the structural bioinformatics was emerging naturally as the time required. In this review, three main strategies developed in structural bioinformatics, i.e., pure energetic approach, heuristic approach, and homology modeling approach, as well as their underlying principles, are briefly introduced. Meanwhile, a series of demonstrations are presented to show how the structural bioinformatics has been applied to timely derive the 3D structures of some functionally important proteins, helping to understand their action mechanisms and stimulating the course of drug discovery. Also, the limitation of these approaches and the future challenges of structural bioinformatics are briefly addressed.

Bioinformatics (Oxford, England), 2014

The Chemical Component Dictionary (CCD) is a chemical reference data resource that describes all residue and small molecule components found in Protein Data Bank (PDB) entries. The CCD contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands and solvent molecules. Each chemical definition includes descriptions of chemical properties such as stereochemical assignments, chemical descriptors, systematic chemical names and idealized coordinates. The content, preparation, validation and distribution of this CCD chemical reference dataset are described. Availability and implementation: The CCD is updated regularly in conjunction with the scheduled weekly release of new PDB structure data. The CCD and amino acid variant reference datasets are hosted in the public PDB ftp repository at ftp://ftp.wwpdb.org/pub/pdb/data/monomers/components.cif.gz, ftp://ftp.wwpdb.org/pub/pdb/data/monomers/aa-variants-v1.cif.gz, and its mirror sites, and...

Briefings in functional genomics & proteomics, 2007

The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Lib...