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The Protein Data Bank and structural genomics

J. Westbrook
2003 Nucleic Acids Research  
The Protein Data Bank (PDB; http://www.pdb.org/) continues to be actively involved in various aspects of the informatics of structural genomics projectsdeveloping and maintaining the Target Registration  ...  Database (TargetDB), organizing data dictionaries that will define the specification for the exchange and deposition of data with the structural genomics centers and creating software tools to capture  ...  and Technology-three members of the Research Collaboratory for Structural Bioinformatics (RCSB).  ... 
doi:10.1093/nar/gkg068 pmid:12520059 pmcid:PMC165515 fatcat:rebyolzynvfqhpxdcb7fwnrl5q

The Protein Data Bank [chapter]

J. L. Sussman, E. E. Abola, D. Lin, J. Jiang, N. O. Manning, J. Prilusky
1999 Structural Biology and Functional Genomics  
The protein data bank (PDB), at Brookhaven National Laboratory, is a database containing information on experimentally determined three-dimensional structures of proteins, nucleic acids, and other biological  ...  The PDB has a 27-year history of service to a global community of researchers, educators, and students in a wide variety of scientific disciplines.  ...  Funding The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S.  ... 
doi:10.1007/978-94-011-4631-9_16 fatcat:tvvl4seswrbgxdxmqou7is3qjq

Integrating genomic information with protein sequence and 3D atomic level structure at the RCSB protein data bank

Andreas Prlić, Tara Kalro, Roshni Bhattacharya, Cole Christie, Stephen K. Burley, Peter W. Rose
2016 Bioinformatics  
The Protein Data Bank (PDB) now contains more than 120,000 three-dimensional (3D) structures of biological macromolecules.  ...  This integration bridges from the human genome across protein sequence to 3D structure space.  ...  The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is the US regional data center for the Worldwide PDB (wwPDB; wwpdb.org), which manages the global PDB archive.  ... 
doi:10.1093/bioinformatics/btw547 pmid:27551105 pmcid:PMC5167066 fatcat:l4rrzkjyafgyhlx45uzgrexd5y

1P481 Real-time Structure Based Queries at the Protein Data Bank japan(23. Bioinformatics, genomics and proteomics (I),Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)

Daron M. Standley, Hiroyuki Toh, Haruki Nakamura
2006 Seibutsu Butsuri  
liadiLioi]aT]y, Lhe Pn}tetin DaLa Bu]k Jupan (PDB.i) has efftiT=d gueties based en keywords such as the PDB ID. compound name,  ...  Moreover. since the arni-o acid sequence and 3D strucn]re arc "analogii data, an exact match is not nccessary.  ...  The details of the approach of dassification and the resulrs of structural analysis are given in the posteT.  ... 
doi:10.2142/biophys.46.s267_1 fatcat:wx43vzayzzdxrplzkic7jfcivq

The European Bioinformatics Institute's data resources

C. Brooksbank
2003 Nucleic Acids Research  
The European Bioinformatics Institute (EBI) hosts six core databases, which store information on DNA sequences (EMBL-Bank), protein sequences (SWISS-PROT and TrEMBL), protein structure (MSD), whole genomes  ...  As the amount of biological data grows, so does the need for biologists to store and access this information in central repositories in a free and unambiguous manner.  ...  Protein structure submissions PDB-AutoDep Three-dimensional structure submissions to the Protein Data Bank.  ... 
doi:10.1093/nar/gkg066 pmid:12519944 pmcid:PMC165513 fatcat:46gy4lg2v5ak7mdns47kaelgpu

Structure and the genome

1997 Nature Structural & Molecular Biology  
Data bank blues The responsibility for the dissemination of such information must fall to the various structure and sequence data banks.  ...  But what of annotation-or the provision of additional information associated with each item of stored data, be it DNA or protein sequence-in the various data banks?  ... 
doi:10.1038/nsb0597-329 fatcat:3otvrn2gjjdm3onbjymiv64phm

Development of Protein Structure Databases and their Applications to Functional Annotation

H. Nakamura
2008 Journal of Proteomics & Bioinformatics  
We manage the Protein Data Bank Japan (PDBj), curating, editing and distributing protein structural data, as a member of the worldwide Protein Data Bank (wwPDB) and currently process about 25-30% of all  ...  targets from structural genomics projects [4] .  ...  the worldwide Protein Data Bank (wwPDB) and currently process about 25-30% of all deposited data in the world [1] .  ... 
doi:10.4172/jpb.s1000038 fatcat:p5lzdo35pjfsjkrrpildlrsyae

The definitive source for protein structures

Melanie Nelson
2000 Genome Biology  
Protein Data Bank (PDB) is the recognized public repository for protein structure information. Mirror sites Protein Data Bank mirror sites are available. Content  ...  Protein Data Bank (PDB) is the recognized public repository for protein structure information.  ...  Related websites The PDB website includes an excellent page of links to Protein Data Bank mirror sites, particularly resources about protein structure, sequence and function.  ... 
doi:10.1186/gb-2000-1-6-reports2056 fatcat:drt72t727jb7xmozeny2ahtuxq

The European Bioinformatics Institute's data resources: towards systems biology

C. Brooksbank
2004 Nucleic Acids Research  
Genomic and post-genomic biological research has provided fine-grain insights into the molecular processes of life, but also threatens to drown biomedical researchers in data.  ...  Acids Research, we have launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI).  ...  EMBL-Bank provides access to completed and partially completed genome sequence data through its Genomes Pages (www.ebi.ac.uk/genomes/).  ... 
doi:10.1093/nar/gki026 pmid:15608238 pmcid:PMC539980 fatcat:ccwgkwuws5fsjaz7zp7i5jfjzy

Protein circular dichroism data bank (PCDDB): Data bank and website design

Lee Whitmore, Robert W. Janes, B. A. Wallace
2006 Chirality  
It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures.  ...  In the case of a protein whose crystal structure and sequence are known, the PCDDB entry will be linked to the appropriate PDB and sequence data bank files, respectively.  ...  It is named in parallel with the Protein Data Bank (PDB), a long-existing valuable reference data bank for protein crystal and NMR structures.  ... 
doi:10.1002/chir.20267 pmid:16612804 fatcat:642qdrxervcrfntalz3xsvle6e

Biological Databases- Integration of Life Science Data

Nishant Toomula,, Arun Kumar, Sathish Kumar D, Vijaya Shanti Bheemidi
2012 Journal of computer science and systems biology  
Over the past few decades, major advances in the field of molecular biology, coupled with advances in genomic technologies, have led to an explosive growth in biological information generated by the scientific  ...  This article presents information on some popular bioinformatic databases available online, including sequence, phylogenetic, structure and pathway, and microarray databases.  ...  Protein Data Bank: The PDB (Protein Data Bank) is the single worldwide archive of Structural data of Biological macromolecules, established in Brookhaven National Laboratories in 1971.  ... 
doi:10.4172/jcsb.1000081 fatcat:fuijh5offzcgdbqr6cvfj6xsj4

Basics of Bioinformatics in Biological Research

Ashwini Kamble, Rajesh Khairkar
2017 International Journal of Applied Sciences and Biotechnology  
of the data.  ...  But there are various problems while doing this like it's always challenging to develop proper and sophisticated analysis method which can properly use genomic data bases considering its and heterogeneity  ...  to DNA and protein sequences, genome mapping data, 3D macromolecular structures and the PubMed bibliographic database.  ... 
doi:10.3126/ijasbt.v4i4.16252 fatcat:fjx7lsr4zbgjdnfcltsqmkia4m

Saccharomyces Genome Database (SGD) provides biochemical and structural information for budding yeast proteins

S. Weng
2003 Nucleic Acids Research  
The PDB Homologs page provides structural information from the Protein Data Bank (PDB) about yeast proteins and/or their homologs.  ...  The Saccharomyces Genome Database (SGD: http:// genome-www.stanford.edu/Saccharomyces/) has recently developed new resources to provide more complete information about proteins from the budding yeast Saccharomyces  ...  The Protein Data Bank (PDB) Homologs page provides a list of structures available in PDB (7) relevant to a given S. cerevisiae protein (Fig. 1A) .  ... 
doi:10.1093/nar/gkg054 pmid:12519985 pmcid:PMC165501 fatcat:gkbattftdnhovdzkjhbiqij6ca

Oncogenes and cell proliferation Web alert

TyraG Wolfsberg, Izabela Makalowska, Wojciech Makalowski
1998 Current Opinion in Genetics and Development  
Oncogenes and cell proliferation The World Wide Web Wnt Window (WWWWW) http://www-leland.stanford.edu/-rnusse/wntwindow.html These pages are intended to keep track of the profusion of data on Wnt genes  ...  They provide lists of Wnt genes, phenotypes, pathways, and sequence alignments, most linked to the corresponding GenBank or Medline record.  ...  SWISS-PROT http://www.ebi.ac.uk/ebi_docs/swissprot_db/swisshome.html The SWlSS-PROT Protein Sequence Data Bank is a nonredundant database of protein sequences which contains high-quality annotation and  ... 
doi:10.1016/s0959-437x(98)80054-3 pmid:9599044 fatcat:kfddrau43be5bhlyhvlz2io774

Archiving activities of the Protein Data Bank at Osaka university

T. Kosada, M. Kusunoki, R. Igarashi, Y. Kengaku, S. Saeki, H. Nakamura
2002 Acta Crystallographica Section A Foundations of Crystallography  
The Protein Data Bank (PDB) is the sole international repository for threedimensional data of biological macromolecules and is managed by the Research Collaboratory for Structural Bioinformatics (RCSB)  ...  The PDB activities at Osaka is now operated by the PDBj (The protein Data Bank of Japan, http://pdbj.protein.osaka-u.ac.jp/) and have been supported by grants ACT-JST and BIRD-JST from Japan Science and  ... 
doi:10.1107/s0108767302099695 fatcat:2gwpqmbrwnamffwtun3jkxrbmq
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