Next Article in Journal
Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy
Next Article in Special Issue
Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls
Previous Article in Journal
Protective Effect of Tulbaghia violacea Harv. on Aortic Pathology, Tissue Antioxidant Enzymes and Liver Damage in Diet-Induced Atherosclerotic Rats
Previous Article in Special Issue
Direct Observation of Protein Microcrystals in Crystallization Buffer by Atmospheric Scanning Electron Microscopy
Article Menu

Export Article

Open AccessCommunication
Int. J. Mol. Sci. 2012, 13(10), 12761-12772; doi:10.3390/ijms131012761

Proteins of Unknown Function in the Protein Data Bank (PDB): An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis

School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Malaysia
*
Author to whom correspondence should be addressed.
Received: 11 September 2012 / Revised: 21 September 2012 / Accepted: 21 September 2012 / Published: 8 October 2012
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
View Full-Text   |   Download PDF [664 KB, uploaded 19 June 2014]   |  

Abstract

Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference.
Keywords: Protein Data Bank; proteins of uncharacterized function; proteins of unknown function; structural similarity; 3D motifs Protein Data Bank; proteins of uncharacterized function; proteins of unknown function; structural similarity; 3D motifs
Figures

This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

Supplementary material

Scifeed alert for new publications

Never miss any articles matching your research from any publisher
  • Get alerts for new papers matching your research
  • Find out the new papers from selected authors
  • Updated daily for 49'000+ journals and 6000+ publishers
  • Define your Scifeed now

SciFeed Share & Cite This Article

MDPI and ACS Style

Nadzirin, N.; Firdaus-Raih, M. Proteins of Unknown Function in the Protein Data Bank (PDB): An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis. Int. J. Mol. Sci. 2012, 13, 12761-12772.

Show more citation formats Show less citations formats

Related Articles

Article Metrics

Article Access Statistics

1

Comments

[Return to top]
Int. J. Mol. Sci. EISSN 1422-0067 Published by MDPI AG, Basel, Switzerland RSS E-Mail Table of Contents Alert
Back to Top