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Topic: Protein Data Bank


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In the News (Tue 25 Jun 19)

  
  Protein Data Bank - Wikipedia, the free encyclopedia
The Protein Data Bank (PDB) is a repository for 3-D structural data of proteins and nucleic acids.
This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists and biochemists from around the world, is released into the public domain, and can be accessed for free.
Founded in 1971 by Brookhaven National Laboratory, the Protein Data Bank was transferred in 1998 to the Research Collaboratory for Structural Bioinformatics (RCSB), which is composed of Rutgers University, the University of Wisconsin, Madison, NIST and the San Diego Supercomputer Center.
en.wikipedia.org /wiki/Protein_Data_Bank   (971 words)

  
 Protein Data Bank
This data, typically obtained by X-ray crystallography or NMR spectroscopy, is submitted by biologists from around the world, is released into the public domain, and can be accessed for free.
The structural data can be used to visualize the biomolecules with appropriate software, such as rasmol[?], chime or a VRML plugin.
Founded in 1971 by Brookhaven National Laboratory, the Protein Data Bank was transferred in 1998 to the Research Collaboratoy for Structural Bioinformatics (RCSB), which is composed of Rutgers University, the University of Wisconsin, Madison, NIST and the San Diego Supercomputer Center[?].
www.ebroadcast.com.au /lookup/encyclopedia/pd/PDB.html   (372 words)

  
 [No title]
Over the years, the PDB has observed that one of the most useful reasons for storing structure factors is for the crystallographer who did the experiment to be able to retrieve his/her own data which have been misplaced in their laboratory.
This data is highly structured and most of the crystallographers are used to thinking of a piece of data from a PDB entry as belonging to a particular "record" or "field".
Data for the last quarter are accumulated until the date specified on the graph.
msdlocal.ebi.ac.uk /docs/rcsb/pdb/doc/newsletters/bnl/news83_jan98/newslttr.txt   (10184 words)

  
 Newswise
Showcased as the PDB's January 2004 "Molecule of the Month," it is crucial for photosynthesis in plants and bacteria, the building of coral reefs and many fundamental processes in animals - such as bone formation, breathing and muscle contraction.
As the PDB grows and evolves, one of its central challenges will be the expanded integration of its wealth of information with other biological data, images and research articles.
Along with serving scientists, the PDB also serves as an educational resource for students and educators at all levels, thus another challenge is to meet the needs of an expanding, diverse and global user community.
www.newswise.com /articles/view/502878   (1268 words)

  
 The Protein Data Bank and the challenge of structural genomics - Nature Structural & Molecular Biology   (Site not responding. Last check: 2007-10-21)
During data processing, formats and nomenclatures are standardized and many different checks are made on the structure, agreement of the model with the primary data, and sequence.
PDB staff members are also participating in an analogous project, the Collaborative Computational Project for NMR (CCPN), which is just being initiated with the NMR community (http://www.bio.cam.ac.uk/nmr/ccp/).
Data quality may be evaluated using the currently available validation server (http://pdb.rutgers.edu/validate) as well as new stereochemistry and experimental data checking tools that will be made available on the PDB web sites.
www.nature.com /cgi-taf/DynaPage.taf?file=/nsmb/journal/v7/n11s/full/nsb1100_957.html   (2549 words)

  
 Rutgers Research Highlights: Protein Data Bank   (Site not responding. Last check: 2007-10-21)
The Rutgers-based Protein Data Bank (PDB) began 2004 with the commitment of a record $30 million in federal support for the next five years.
The PDB is an Internet-accessible repository of 3-D models of nearly 24,000 proteins and other macromolecules in its growing inventory.
The PDB is managed by three members of a consortium: the Research Collaboratory for Structural Bioinformatics (RCSB): Rutgers, the San Diego Supercomputer Center at the University of California, San Diego; and the Center for Advanced Research in Biotechnology of the National Institute of Standards and Technology.
ur.rutgers.edu /medrel/science/protein-data.shtml   (321 words)

  
 Press-release: ACD and PDB
Advanced Chemistry Development (ACD) and the Protein Data Bank (PDB) are proud to announce a collaboration in which ACD will provide their naming software product ACD/Name to the PDB for use in its data processing and annotation operations.
Due to the size of the PDB and the complexity of the structures, the Name algorithm will be provided to the PDB in the form of ACD's IUPAC Name Batch software, capable of running on the SGI platform.
The PDB is the authoritative worldwide data repository for the processing and distribution of 3-D biological macromolecular structure data and protein crystal structures, dating back to the very first structures ever solved by x-ray diffraction.
www.nmrsoftware.com /clients/pr_pdb.html   (568 words)

  
 Protein Data Bank input
PDB files may contain explicit coordinates for a potentially tautomeric hydrogen, such as a serine hydroxyl hydrogen for example.
However, a second protein sequence may follow after a TER record, and the N-terminal nitrogen of this second protein will automatically be treated as a terminal amino group; i.e.
The coordinates of a hydrogen atom bonded to a protein backbone nitrogen are determined by the positions of the nitrogen itself, and its bonded C-alpha and carbonyl-carbon neighbours.
www.moldiscovery.com /docs/grid/c33.html   (5213 words)

  
 RCSB Protein Data Bank
The PDB Advisory Notice defines the PDB data terms and conditions.
The RCSB PDB Advisory Committee is made up of a international team of experts in X-ray crystallography, Cryo-EM, NMR, modeling, bioinformatics and education.
The RCSB is a member of the wwPDB (worldwide Protein Data Bank); a collaborative effort with the MSD-EBI (European Bioinformatics Institute - UK) and PDBj (Protein Data Bank Japan) to ensure the PDB archives is global and uniform.
pdbbeta.rcsb.org /pdb/static.do?p=general_information/about_pdb/index.html   (519 words)

  
 Protein Data Bank goes global
"The PDB is an important tool for biomedical and pharmaceutical researchers and a critical asset to 21st century genomic research and drug design," said Rutgers Board of Governors Professor of Chemistry and Chemical Biology Helen M. Berman, director of the Protein Data Bank.
The processed data will be forwarded to the RCSB and entered into a data bank archive by the RCSB — the "archive keeper" with sole direct access to the database and control over its directory structure and contents.
The PDB is supported by funds from the National Science Foundation, the Department of Energy and the National Institutes of Health.
www.eurekalert.org /pub_releases/2003-11/rtsu-pdb112003.php   (353 words)

  
 Protein Data Bank Files and HyperChem
Some software creates "PDB" files that do not follow this format properly; for example, the data entries on a line of the file may be in the wrong columns, or shifted left or right within a section.
Most PDB files contain all the information that is necessary for HyperChem to regenerate the structure.
The Protein Data Bank is operated by the Research Collaboratory for Structural Bioinformatics (RCSB) and is supported by funds from the National Science Foundation, the Department of Energy, and two units of the National Institutes of Health: the National Institute of General Medical Sciences and the National Library of Medicine.
www.cyberchem.com /PDB_Hyperchem.htm   (803 words)

  
 The RCSB Protein Data Bank
The Protein Data Bank is operated by the
One of the goals of the RCSB is to educate the community about the PDB portal and related topics of interest...
Structural Genomics Supplement issue, the PDB has a paper entitled "The Protein Data Bank and the challenge of structural genomics" (Berman et al.
www.mrc-lmb.cam.ac.uk /genomes/madanm/pres/pdb1.htm   (183 words)

  
 Advanced Chemistry Development/Partners: Protein Data Bank (PDB)
Advanced Chemistry Development (ACD/Labs) and the Protein Data Bank (PDB) are proud to announce a collaboration in which ACD/Labs will provide their naming software product ACD/Name to the PDB for use in its data processing and annotation operations.
Due to the size of the PDB and the complexity of the structures, the Name algorithm will be provided to the PDB in the form of ACD/Labs' IUPAC Name Batch software, capable of running on the SGI platform.
In recent years, the Protein Databank has come under the progressive leadership of the Research Collaboratory for Structural Biology, a collaboration between Rutgers University's Department of Chemistry, the San Diego Supercomputer Center, and NIST (National Institute of Standards and Technology).
www.acdlabs.com /partners/pdb.html   (329 words)

  
 PDB: RCSB/Protein Data Bank
Release 107F includes the full set of experimentally determined structures (23, 792) and models (709) deposited in the PDB by January 1, 2004, on a six (6) disk set.
New subscribers receive the full data release of the current year and all subsequent updates while supplies last.
The Protein Data Bank is distributed in ISO 9660 format.
www.nist.gov /srd/nist80.htm   (247 words)

  
 Protein Data Bank Format
This is a small portion of a protein data bank file.
The header consists of the protein along with its date of submission to the Data Bank.
The journal the protein structure was first presented in is displayed along with the authors and other references.
www.sju.edu /~sforman/thesis-html/node10.html   (359 words)

  
 Protein Data Bank (PDB)   (Site not responding. Last check: 2007-10-21)
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules, serving a global community of researchers, educators, and students.
PDB Files are found in the directory pointed to by the middle two letters of the four letter PDB entry code.
See also more information on determining the PDB entry code for a molecule.
www.psc.edu /general/software/packages/pdb/pdb.html   (172 words)

  
 PDB - Protein Data Bank
The indexers at the Data Bank devised mnemonics so that the files would be easy to remember.
Although organized, a PBD file, is difficult to understand due to the length and the amount of data included in the file.
PDB therefore offers a Structure Explorer built within the website itself that displays the content in an easily comprehensible manner.
ginto.chem.admu.edu.ph /~nina/rosby/pdbtxt.htm   (846 words)

  
 Search Proteins   (Site not responding. Last check: 2007-10-21)
Several thousand 3-D structures are directly available for public use from the Brookhaven Protein Data Bank.
The first file will only give the information found in the header, it will not give coordinate data, the *.full file gives all data and is needed if you wish to manipulate structures from your own terminal.
The NRL Database is a is a sequence--structure database derived from the 3 dimensional structure of proteins deposited with the Brookhaven National Laboratory's Protein Data Bank.
www.nyu.edu /pages/mathmol/modules/proteins/pdb.html   (493 words)

  
 Protein Data Bank Database
The Protein Data Bank (PDB) is an archive of experimentally determined three-dimensional structures of biological macromolecules.
The database on the helix systems is a mirror of that at the Protein Data Bank.
The PDB entries are also available to helix users directly in /db/pdb/.
helix.nih.gov /apps/bioinfo/pdb.html   (117 words)

  
 SWBIC - Protein Data Bank (PDB)   (Site not responding. Last check: 2007-10-21)
[Protein Data Bank] A quarterly newsletter providing current information on the various activities occurring at the Protein Data Bank.
It is useful for finding sequences in the PDB protein structure database that are homologous to a sequence of unknown structure.
[Research Collaboratory for Structural Bioinformatics] The PDB is the single international repository for the processing and distribution of 3-D macromolecular structure data primarily determined experimentally by X-ray crystallography and NMR.
www.swbic.org /links/1.12.1.php   (355 words)

  
 TECHNICAL MEMORANDUM 418: Protein Data Bank (PDB)  Accession Numbers   (Site not responding. Last check: 2007-10-21)
TM 347 includes PDB (Protein Data Bank, also known as Brookhaven Protein Data Bank) as one of the databanks for which we should be selecting citations and coordinating with MOLECULAR SEQUENCE DATA.
With the conclusion of the gene sequence indexing project in the Index Section, it is now appropriate to pick up all PDB numbers as well.
  As specified in TM 409, the data entry contractors have been directed to pick up PDB accession numbers (also be referred to as "codes" or "files") from the title page or the end of the text of an article.
www.nlm.nih.gov /mesh/indexingmanual/TM_418.htm   (224 words)

  
 MidasPlus -- Protein Data Bank Format   (Site not responding. Last check: 2007-10-21)
The Protein Data Bank at Brookhaven National Laboratory (BNL) is a clearing house for macromolecular coordinate data, and distribution tapes are written in a standardized format specified by BNL.
A complete and concise description of the format is given in the document ``Protein Data Bank Atomic Coordinate Entry Format Description,'' which is published and distributed by Brookhaven National Laboratory.
Since the entire Protein Data Bank entry contains much more information on a macromolecule than is needed for model building, knowledge of a subset of the format is sufficient for MIDAS users.
www.cmpharm.ucsf.edu /~troyer/troff2html/midas/Midas-sh-3.4.html   (223 words)

  
 3.4.7 Protein Data Bank Format   (Site not responding. Last check: 2007-10-21)
Protein geometries are usually defined using the Brookhaven Protein Data Bank format.
There are several ways of converting a PDB file into a form suitable for use by MOPAC.
For most systems in the PDB the hydrogen atoms are missing.
home.att.net /~mopacmanual/node357.html   (177 words)

  
 WPDB - The Protein Data Bank through Microsoft Windows
The PDB through Microsoft Windows, or WPDB for short, is a Microsoft Windows 3.1 Windows95 and Windows NT (client and server) based program to interrogate the 3-dimensional structure of biological macromolecules as found in the Protein Data Bank (PDB) using query and display tools like those shown above.
Further details of the data model used by WPDB can be found in I.N.Shindyalov and P.E. Bourne CABIOS 1997, Submitted.
Protein Data Representation and Query Using Optimized Data Decomposition.
www.sdsc.edu /pb/wpdb/wpdb.htm   (686 words)

  
 Membrane Protein Structure Data Bank   (Site not responding. Last check: 2007-10-21)
Methods used to purify protein from membrane: whole cell lysed in a French pressure cell (150kPa), supernatant separated by sucrose gradient centrifugation.
Add any other comments you think might be relevant as we try to generalize the crystallization and structure determination of membrane proteins.
Native protein was seen to have the same structure as the selenomethionine derivatives
www.lipidat.chemistry.ohio-state.edu /course/99001/TolC.htm   (374 words)

  
 Protein Data Bank at RCSB   (Site not responding. Last check: 2007-10-21)
Protein Data Bank at Research Collaboratory for Structural Bioinformatics (RCSB)
Protein Data Bank (PDB) is a public collection of three-dimensional structures of macromolecular complexes experimentally determined by X-ray crystallographers and NMR spectroscopists.
The characters in the code might be numbers 0-9, and the uppercase letters from A to Z. The PDB ID codes are often reported in the articles as a reference to the structure of a biomolecule.
carrot.mcb.uconn.edu /mcb396_41/pdb.html   (174 words)

  
 Five year funding will significantly extend Protein Data Bank's capabilities
The very first origins of the Protein Data Bank date back to 1971, when it was still maintained at Brookhaven National Laboratory as a huge repository of data.
The PDB upgrading is led by three principal investigators of Rutgers, UCSD and NIST.
At NIST, Gary L. Gilliland, who is Chief of the Biotechnology Division in the Chemical Science and Technology Laboratory, supervises the establishment of data uniformity in the old and new PDB structures.
www.hoise.com /vmw/articles/LV-VM-12-98-4.html   (742 words)

  
 The distribution and query systems of the RCSB Protein Data Bank -- Bourne et al. 32 (Supplement 1): D223 -- Nucleic ...
The Protein Data Bank (PDB; http://www.pdb.org) is the primary
The Protein Data Bank (PDB) (1,2) is the single worldwide repository
Westbrook,J., Feng,Z., Chen,L., Yang,H. and Berman,H.M. (2003) The Protein Data Bank and structural genomics.
nar.oxfordjournals.org /cgi/content/full/32/suppl_1/D223   (1953 words)

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