PDBWiki: added value through community annotation of the Protein Data Bank.

Database : the Journal of Biological Databases and Curation
Henning StehrDan M Bolser

Abstract

The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. Currently, there are several such 'science-wikis' that aim to collect specialist knowledge from the community into centralized resources. However, there is no consensus about how to achieve this goal. For example, it is not clear how to best integrate data from established, centralized databases with that provided by 'community annotation'. We created PDBWiki, a scientific wiki for the community annotation of protein structures. The wiki consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows the user to attach categorized comments to the entries. Additionally, each page includes a user editable list of cross-references to external resources. As in a database, it is possible to produce tabular reports and 'structure galleries' based on user-defined queries or lists of entries. PDBWiki runs in parallel to the PDB, separating original database content from user annotations. PDBWiki demonstrates how collaboration features can be integrated with primary data from a biological database. It can be used as a system for better understanding how to capture...Continue Reading

References

Feb 27, 1975·Nature·M Levitt, A Warshel
Sep 19, 1998·Proteins·L Holm, C Sander
Oct 27, 1998·Trends in Biochemical Sciences·K Henrick, J M Thornton
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Apr 13, 2001·Bioinformatics·C Gille, C Frömmel
May 1, 1965·Journal of Molecular Biology·J MONODJ P CHANGEUX
Nov 9, 2006·Nucleic Acids Research·Bradley I ArshinoffRoy D Welch
Feb 6, 2007·Genome Biology·Steven L Salzberg
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Michael Levitt
Apr 25, 2007·Nucleic Acids Research·Ian W DavisDavid C Richardson
Jul 6, 2007·Nature
Aug 10, 2007·Nature·Bert J C JanssenPiet Gros
Aug 31, 2007·BMC Bioinformatics·Aleksey Porollo, Jaroslaw Meller
Feb 9, 2008·Nature Biotechnology·Suresh MathivananAkhilesh Pandey
May 30, 2008·Genome Biology·Barend MonsAmos Bairoch
Jun 10, 2008·Plant Physiology·Naama MendaLukas A Mueller
Jul 11, 2008·PLoS Biology·Jon W HussAndrew I Su
Jul 25, 2008·PLoS Biology·Alexander R PicoChris Evelo
Sep 5, 2008·Nature·Mitch Waldrop
Oct 7, 2008·Nucleic Acids Research·UNKNOWN UniProt Consortium
Oct 24, 2008·RNA·Jennifer DaubAlex Bateman

❮ Previous
Next ❯

Citations

Oct 1, 2011·Database : the Journal of Biological Databases and Curation·Khader ShameerRamanathan Sowdhamini
Mar 22, 2012·Database : the Journal of Biological Databases and Curation·Nicholas A StoverTheodore G Clark
Dec 7, 2011·Nucleic Acids Research·Robert D FinnAlex Bateman
Aug 19, 2010·BMC Bioinformatics·Dana WeekesJohn Wooley
Dec 15, 2011·BMC Genomics·Benjamin M GoodAndrew I Su
Jun 1, 2012·Genome Biology·Edward S DoveBartha M Knoppers
Nov 19, 2013·PLoS Computational Biology·Janez KoncDušanka Janežič
Sep 20, 2011·International Review of Psychiatry·Joel Paris
Oct 19, 2013·Nucleic Acids Research·Zhang ZhangJun Yu
Nov 28, 2013·Nucleic Acids Research·Ana Kozomara, Sam Griffiths-Jones
Jan 25, 2012·Journal of Chemical Information and Modeling·Janez KoncDušanka Janežič
Aug 27, 2014·PloS One·C Pawan K PatroXin-Yuan Fu
Aug 10, 2018·Physics in Medicine and Biology·Mailyn Perez-LivaBertrand Tavitian

❮ Previous
Next ❯

Methods Mentioned

BETA
protein folding

Software Mentioned

TOPSAN
Proteopedia
MediaWiki
MolProbity
Gene
OpenMMS
Polyview 3D
Open Protein Structure Annotation Network ( TOPSAN
WikiPathways
Splice

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.