The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations. The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB.
Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.
BioJava is an open-source software project dedicated to provide Java tools to process biological data. BioJava is a set of library functions written in the programming language Java for manipulating sequences, protein structures, file parsers, Common Object Request Broker Architecture (CORBA) interoperability, Distributed Annotation System (DAS), access to AceDB, dynamic programming, and simple statistical routines. BioJava supports a huge range of data, starting from DNA and protein sequences to the level of 3D protein structures. The BioJava libraries are useful for automating many daily and mundane bioinformatics tasks such as to parsing a Protein Data Bank (PDB) file, interacting with Jmol and many more. This application programming interface (API) provides various file parsers, data models and algorithms to facilitate working with the standard data formats and enables rapid application development and analysis.
A chemical file format is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the chemical table file format, which is similar to Structure Data Format (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another.
RasMol is a computer program written for molecular graphics visualization intended and used mainly to depict and explore biological macromolecule structures, such as those found in the Protein Data Bank. It was originally developed by Roger Sayle in the early 1990s.
The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Wellcome Genome Campus in Hinxton near Cambridge, and employs over 600 full-time equivalent (FTE) staff. Institute leaders such as Rolf Apweiler, Alex Bateman, Ewan Birney, and Guy Cochrane, an adviser on the National Genomics Data Center Scientific Advisory Board, serve as part of the international research network of the BIG Data Center at the Beijing Institute of Genomics.
The Protein Data Bank (PDB) file format is a textual file format describing the three-dimensional structures of molecules held in the Protein Data Bank. The PDB format accordingly provides for description and annotation of protein and nucleic acid structures including atomic coordinates, secondary structure assignments, as well as atomic connectivity. In addition experimental metadata are stored. The PDB format is the legacy file format for the Protein Data Bank which now keeps data on biological macromolecules in the newer mmCIF file format.
The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the MSD/PDBe group of the European Bioinformatics Institute (EBI), where the European site of the EMDataBank.org consortium is located. As of 2015, the resource contained over 2,600 entries with a mean resolution of 15Å.
Helen Miriam Berman is a Board of Governors Professor of Chemistry and Chemical Biology at Rutgers University and a former director of the RCSB Protein Data Bank. A structural biologist, her work includes structural analysis of protein-nucleic acid complexes, and the role of water in molecular interactions. She is also the founder and director of the Nucleic Acid Database, and led the Protein Structure Initiative Structural Genomics Knowledgebase.
In biology, a protein structure database is a database that is modeled around the various experimentally determined protein structures. The aim of most protein structure databases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in protein structure databases often includes three-dimensional coordinates as well as experimental information, such as unit cell dimensions and angles for x-ray crystallography determined structures. Though most instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas sequence databases focus on sequence information, and contain no structural information for the majority of entries. Protein structure databases are critical for many efforts in computational biology such as structure based drug design, both in developing the computational methods used and in providing a large experimental dataset used by some methods to provide insights about the function of a protein.
David S. Goodsell, is an associate professor at the Scripps Research Institute and research professor at Rutgers University, New Jersey. He is especially known for his watercolor paintings of cell interiors.
The Re-referenced Protein Chemical shift Database (RefDB) is an NMR spectroscopy database of carefully corrected or re-referenced chemical shifts, derived from the BioMagResBank (BMRB). The database was assembled by using a structure-based chemical shift calculation program to calculate expected protein (1)H, (13)C and (15)N chemical shifts from X-ray or NMR coordinate data of previously assigned proteins reported in the BMRB. The comparison is automatically performed by a program called SHIFTCOR. The RefDB database currently provides reference-corrected chemical shift data on more than 2000 assigned peptides and proteins. Data from the database indicates that nearly 25% of BMRB entries with (13)C protein assignments and 27% of BMRB entries with (15)N protein assignments require significant chemical shift reference readjustments. Additionally, nearly 40% of protein entries deposited in the BioMagResBank appear to have at least one assignment error. Users may download, search or browse the database through a number of methods available through the RefDB website. RefDB provides a standard chemical shift resource for biomolecular NMR spectroscopists, wishing to derive or compute chemical shift trends in peptides and proteins.
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule, come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties.
Protein Structure Evaluation Suite & Server (PROSESS) is a freely available web server for protein structure validation. It has been designed at the University of Alberta to assist with the process of evaluating and validating protein structures solved by NMR spectroscopy.
Nuclear magnetic resonance chemical shift re-referencing is a chemical analysis method for chemical shift referencing in biomolecular nuclear magnetic resonance (NMR). It has been estimated that up to 20% of 13C and up to 35% of 15N shift assignments are improperly referenced. Given that the structural and dynamic information contained within chemical shifts is often quite subtle, it is critical that protein chemical shifts be properly referenced so that these subtle differences can be detected. Fundamentally, the problem with chemical shift referencing comes from the fact that chemical shifts are relative frequency measurements rather than absolute frequency measurements. Because of the historic problems with chemical shift referencing, chemical shifts are perhaps the most precisely measurable but the least accurately measured parameters in all of NMR spectroscopy.
Protein chemical shift re-referencing is a post-assignment process of adjusting the assigned NMR chemical shifts to match IUPAC and BMRB recommended standards in protein chemical shift referencing. In NMR chemical shifts are normally referenced to an internal standard that is dissolved in the NMR sample. These internal standards include tetramethylsilane (TMS), 4,4-dimethyl-4-silapentane-1-sulfonic acid (DSS) and trimethylsilyl propionate (TSP). For protein NMR spectroscopy the recommended standard is DSS, which is insensitive to pH variations. Furthermore, the DSS 1H signal may be used to indirectly reference 13C and 15N shifts using a simple ratio calculation [1]. Unfortunately, many biomolecular NMR spectroscopy labs use non-standard methods for determining the 1H, 13C or 15N “zero-point” chemical shift position. This lack of standardization makes it difficult to compare chemical shifts for the same protein between different laboratories. It also makes it difficult to use chemical shifts to properly identify or assign secondary structures or to improve their 3D structures via chemical shift refinement. Chemical shift re-referencing offers a means to correct these referencing errors and to standardize the reporting of protein chemical shifts across laboratories.
The Biological Magnetic Resonance Data Bank is an open access repository of nuclear magnetic resonance (NMR) spectroscopic data from peptides, proteins, nucleic acids and other biologically relevant molecules. The database is operated by the University of Wisconsin–Madison and is supported by the National Library of Medicine. The BMRB is part of the Research Collaboratory for Structural Bioinformatics and, since 2006, it is a partner in the Worldwide Protein Data Bank (wwPDB). The repository accepts NMR spectral data from laboratories around the world and, once the data is validated, it is available online at the BMRB website. The database has also an ftp site, where data can be downloaded in the bulk. The BMRB has two mirror sites, one at the Protein Database Japan (PDBj) at Osaka University and one at the Magnetic Resonance Research Center (CERM) at the University of Florence in Italy. The site at Japan accepts and processes data depositions.
Gaetano T. Montelione is an American biophysical chemist, Professor of Chemistry and Chemical Biology, and Constellation Endowed Chair in Structural Bioinformatics at Rensselaer Polytechnic Institute in Troy, NY.
