The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids. Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information These data, typically obtained by X-ray crystallography or NMR spectroscopy and submitted by biologists and biochemists from around the world, are released into the public domain, and can be accessed for free. X-ray crystallography is a method of determining the arrangement of Atoms within a Crystal, in which a beam of X-rays strikes a crystal and scatters Protein nuclear magnetic resonance spectroscopy (usually abbreviated protein NMR) is a field of Structural biology in which NMR spectroscopy is used A biologist is a Scientist devoted to and producing results in Biology through the study of Organisms Typically biologists study organisms and their relationship Biochemistry is the study of the chemical processes in living Organisms It deals with the Structure and function of cellular components such as The public domain is a range of abstract materials &ndash commonly referred to as Intellectual property &ndash which are not owned or controlled by anyone See also protein structure. Proteins are an important class of biological Macromolecules present in all biological organisms made up of such elements as Carbon, Hydrogen

History

Founded in 1971 by Drs. Edgar Meyer and Walter Hamilton Brookhaven National Laboratory, management of the Protein Data Bank was transferred in 1998 to members of the Research Collaboratory for Structural Bioinformatics (RCSB). Brookhaven National Laboratory ( BNL) is a United States national laboratory located in Upton New York on Long Island, and was formally established Rutgers University is the lead site and is currently under the direction of Helen M. Berman. Rutgers The State University of New Jersey (also known as Rutgers University) is the largest institution for higher education in the state of New Jersey Helen M Berman (born 1943 is the director of the Protein Data Bank, “a repository for 3-D structural data of proteins and nucleic acids” and a professor of chemistry and ^[1]

The Worldwide Protein Data Bank (wwPDB) consists of organizations that act as deposition, data processing and distribution centers for PDB data. The founding members are RCSB PDB (USA), MSD-EBI (Europe) and PDBj (Japan). The BMRB (USA) group joined the wwPDB in 2006. The mission of the wwPDB is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. The term macromolecule by definition implies "large Molecule "

The PDB is a key resource in structural biology and is critical to more recent work in structural genomics. Structural biology is the branch of Molecular biology concerned with the Architecture and shape of biological Macromolecules especially Proteins Structural genomics consists in the determination of the three dimensional structure of all Proteins of a given organism by experimental methods such as X-ray crystallography

Countless derived databases and projects have been developed to integrate and classify the PDB in terms of protein structure, protein function and protein evolution. Proteins are an important class of biological Macromolecules present in all biological organisms made up of such elements as Carbon, Hydrogen

Growth

When the PDB was originally founded it contained just 7 protein structures. Since then it has undergone an approximate exponential growth in the number of structures, which does not show any sign of falling off.

The growth rate of the PDB has been the subject of fairly extensive analysis.

Contents

As of 15 April 2008, the database contained 50,277 released atomic coordinate entries (or "structures"), 46,400 of that proteins, the rest being nucleic acids, nucleic acid-protein complexes, and a few other molecules. Events 1450 - Battle of Formigny: Toward the end of the Hundred Years' War, the French attack and nearly annihilate English 2008 ( MMVIII) is the current year in accordance with the Gregorian calendar, a Leap year that started on Tuesday of the Common About 5,000 new structures are released each year. Data are stored in the mmCIF format specifically developed for the purpose. 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. It is estimated that the size of the PDB archive will triple to 150,000 structures by the year 2014. ^[2]

Note that the database stores information about the exact location of all atoms in a large biomolecule (although, usually without the hydrogen atoms, as their positions are more of a statistical estimate); if one is only interested in sequence data, i. History See also Atomic theory, Atomism The concept that matter is composed of discrete units and cannot be divided into arbitrarily tiny Hydrogen (ˈhaɪdrədʒən is the Chemical element with Atomic number 1 e. , the list of amino acids making up a particular protein or the list of nucleotides making up a particular nucleic acid, the much larger databases from Swiss-Prot and the International Nucleotide Sequence Database Collaboration should be used. In Chemistry, an amino acid is a Molecule containing both Amine and Carboxyl Functional groups In Biochemistry, this Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl Nucleotides are Organic compounds that consist of three joined structures a nitrogenous base a Sugar, and a Phosphate group A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information Swiss-Prot is a manually curated Biological database of Protein sequences The International Nucleotide Sequence Database Collaboration (INSDC http//insdc

Statistics

As of 9 April 2008, the "PDB Holdings List" at RCSB reported the following statistics:

Note that theoretical models are no longer accepted in the PDB. Events 193 - Septimius Severus is proclaimed Roman Emperor by the army in Illyricum (in the Balkans) 2008 ( MMVIII) is the current year in accordance with the Gregorian calendar, a Leap year that started on Tuesday of the Common Proteins are large Organic compounds made of Amino acids arranged in a linear chain and joined together by Peptide bonds between the Carboxyl A nucleic acid is a Macromolecule composed of chains of monomeric Nucleotides In Biochemistry these Molecules carry Genetic information X-ray scattering techniques are a family of non-destructive analytical techniques which reveal information about the crystallographic structure chemical composition Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy, is the name given to a technique which exploits the magnetic properties of certain nuclei An electron microscope is a type of Microscope that uses Electrons to illuminate a specimen and create an enlarged image

22,461 structures in the PDB have a structure factor file. In Physics, in the area of Crystallography, the structure factor of a Crystal is a mathematical description of how the crystal scatters incident radiation 3,138 structures in the PDB have an NMR restraint file.

The current breakdown of holdings is updated weekly.

File format

Through the years the PDB file format has undergone many, many changes and revisions. 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. Its original format was dictated by the width of computer punch cards.

• PDB Format Guide - Prepared by the PDB Staff at BNL The PDB format specification can be found here, and it is vital that you read this before looking at the raw data.
• Recently PDB provides a representation of PDB data in XML format, PDBML format.
• ftp.rcsb.org The raw data can be downloaded from here.
• PDB format files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.pdb.gz
• PDBML (XML) files can be downloaded using HTTP with URLs like this: http://www.pdb.org/pdb/files/4hhb.xml.gz
• ftp.ebi.ac.uk/pub/databases/rcsb/ Alternate download location for the PDB archive.
• www.pdb.org Statistics about the PDB can be found here.

This legacy format has caused many problems with the format, and consequently there are 'clean-up' projects;

• The Molecular Modeling DataBase (MMDB) from NCBI
• wwPDB

The MMDB uses ASN. The National Center for Biotechnology Information ( NCBI) is part of the United States National Library of Medicine (NLM a branch of the National Institutes 1 (and an XML conversion of this format). The wwPDB members RCSB PDB, MSD-EBI, and PDBj are working together to make the data uniform across the archive. Some believe this to be desirable; others argue that, without a universal repository of information (i. e. , a common dictionary), it is not possible to draw comparisons.

Each structure published in PDB receives a four-character alphanumeric identifier, its PDB ID. This should not be used as an identifier for biomolecules, since often several structures for the same molecule (in different environments or conformations) are contained in PDB with different PDB IDs.

If a biologist submits structure data for a protein or nucleic acid, wwPDB staff reviews and annotates the entry. The data are then automatically checked for plausibility. The source code for this validation software has been released for free. In Computer science, source code (commonly just source or code) is any sequence of statements or declarations written in some Human-readable The main data base accepts only experimentally derived structures, and not theoretically predicted ones (see protein structure prediction). Protein structure prediction is one of the most important goals pursued by Bioinformatics and Theoretical chemistry.

Various funding agencies and scientific journals now require scientists to submit their structure data to PDB.

Viewing the data

The structural data can be used to visualize the biomolecules with appropriate software, such as VMD, RasMol, PyMOL, Jmol, MDL Chime, QuteMol, web browser VRML plugin or any web-based software designed to visualize and analyse the protein structures such as STING. A biomolecule is any organic Molecule that is produced by living Organisms including large Polymeric molecules such as Proteins Visual molecular dynamics ( VMD) is a Molecular modelling and Visualization Computer program. RasMol is a computer program written for Molecular graphics visualization intended and used primarily for the PyMOL is an open-source user-sponsored molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC which is a private Jmol is a Molecule viewer for use in Chemistry and Biochemistry. MDL Chime is a free Plugin used by Web browsers to display the three dimensional structures of Molecules. QuteMol is an Open source, interactive high quality molecular visualization system A web browser is a software application which enables a user to display and interact with text images videos music games and other information typically located on a VRML ( Virtual Reality Modeling Language, pronounced vermal or by its initials originally — before 1995 — known as the Virtual Reality Markup Language STING ( S equence T o and with' IN' G raphics is a free Web-based suite of programs for a comprehensive analysis of the relationship between protein sequence A recent desktop software addition is Sirius. Sirius is a molecular modeling and analysis system developed at San Diego Supercomputer Center. The RCSB PDB website also contains resources for education, structural genomics, and related software.

References

1. ^ Helen M. Berman - Rutgers Chemistry and Chemical Biology Department
2. ^ PDB Archive Contains More Than 50,000 Structures. Retrieved on 2008-04-12. 2008 ( MMVIII) is the current year in accordance with the Gregorian calendar, a Leap year that started on Tuesday of the Common Events 467 - Anthemius is elevated to Emperor of the Western Roman Empire.

Printed

• H. M. Berman, K. Henrick, H. Nakamura (2003): Announcing the worldwide Protein Data Bank. Nature Structural Biology 10 (12), p. 980 PMID 14634627.
• H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne: The Protein Data Bank. Nucleic Acids Research, 28 pp. 235-242 (2000). PMID 10592235
• Bernstein FC, Koetzle TF, Williams GJ, Meyer Jr EF, Brice MD, Rodgers JR, Kennard O, Shimanouchi T, Tasumi M. The Protein Data Bank: a computer-based archival file for macromolecular structures. J Mol Biol 1977;112:535-542. PMID 875032.
• E. F. Meyer “The First Years of the Protein Data Bank“, Protein Science 6:1591-1597 (1997)
• Sussman, JL, Lin, D, Jiang, J, Manning, NO, Prilusky, J, Ritter, O & Abola, EE. Protein data bank (PDB): a database of 3D structural information of biological macromolecules. Acta Cryst 1998; D54:1078-1084. PMID 10089483.

External links

• The Worldwide Protein Data Bank (wwPDB) — parent site to regional hosts (below)
• RCSB Protein Data Bank - home page
• MSD-EBI - home page
• Protein Data Bank Japan - home page
• The PDB FAQ - frequently asked questions about the PDB and working with structural models.

Related (derived) resources

Main article: Protein structure databases

• Macromolecular Structure Database — MSD Home Page - project for data about macromolecular structures from the PDB. In Biology, a protein structure database is a Database that is modeled around the various experimentally determined Protein structures The European Bioinformatics Institute (EBI is a centre for research and services in Bioinformatics, and is part of European Molecular Biology Laboratory (EMBL
• PDBWiki — PDBWiki Home Page - a website for community annotation of PDB structures. PDBWiki is a user contributed Database of Protein structure Annotations listing all the protein structures currently available in the Protein Data
• PDBsum — PDBsum Home Page - an overview of macromolecular structures in the PDB.
• Proteopedia The collaborative, 3D encyclopedia of proteins and other molecules

Enzyme database data

• EBI. Proteopedia is a collaborative Wiki 3D encyclopedia of Proteins and other Molecules Proteopedia contains a page for every entry in the Protein Data The best mapping is provided by Kim Henrick's group at EBI as part of the MSD SIFTS initiative.
• PDB provide a mapping on their beta site, but it is at the whole PDB level not chain level.
• Search at BRENDA enzyme database portal.
• PDBSProtEC

Molecular graphic visualisation tools

• PyMOL — PyMol Home Page
• Sirius — Sirius Home Page
• STING — STING Home Page
• RasMol — RasMol Home Page
• Garlic
• Swiss-PDB Viewer
• Jmol Viewer — Jmol Home Page Open Source, Java based interactive molecular viewer
• QuteMol — QuteMol Home Page Open Source, Win & Mac, high quality interactive molecular viewer
• StarBiochem Java based interactive molecular viewer with integrated search of protein databank