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Pancreatology 2009;9:4–5 DOI: 10.1159/000178767

Educational Websites – Bioinformatics Tools II

Gwen Lomberk

Gastroenterology Research Unit, Mayo Clinic College of Medicine, Rochester, Minn. , USA

Abstract

In this issue, the highlighted websites are a continuation of a series of education-al websites; this one in particular from a couple of years ago, Bioinformatics Tools [Pancreatology 2005; 5: 314–315]. These include sites that are valuable resources for many research needs in genomics and proteomics. Bioinformatics has become a laboratory tool to map sequences to databases, develop models of molecular interactions, evaluate structural compatibilities, describe differences between normal and disease-associated DNA, identify conserved motifs within proteins, and chart extensive signaling networks, all in silico.

Copyright © 2008 S. Karger AG, Basel and IAP

PANTHER: http://www.pantherdb.org/

The PANTHER ( P rotein AN alysis TH rough E volutionary R elationships) Classification System is a valuable website that classifies genes by their func-tions. This classification was accomplished using published scientific experi-mental evidence and evolutionary relationships to predict function, even without direct experimental evidence. Expert biologists have been consulted to classify proteins into families and subfamilies of shared function. From there, the proteins are then categorized by molecular function and biological process in ontological terms. As a result of these efforts, detailed biochemical interactions in canonical pathways have been predicted for an increasing number of proteins and can be viewed interactively.

Research Collaboratory for Structural Bioinformatics Protein Data Bank

(RCSB PDB): http://www.rcsb.org/pdb/home/home.do

The RCSB is a non-profit consortium focused on our understanding of the function of biological systems through the study of the 3-D structure of bio-logical macromolecules. This website integrates a variety of tools and re-sources for studying the structures of biological macromolecules and their

Published online: December 12, 2008

Gwen Lomberk, PhD Gastroenterology Research Unit Mayo Clinic College of Medicine Rochester, MN 55905 (USA) E-Mail lomberk.gwen@mayo.edu

© 2008 S. Karger AG, Basel and IAP1424–3903/09/0092–0004$26.00/0

Accessible online at:www.karger.com/pan

Pancreatology and the Web

Pancreatology and the Web Pancreatology 2009;9:4–5 5

relationships to sequence, function, and disease. The Protein Data Bank (PDB) archive is the single worldwide repository of information about the3-D structures of large biological molecules, including proteins and nucleic acids. Through a better understanding of the shape of a molecule, researchers gain better insight into how it works. In turn, this knowledge can be utilized to predict a structure’s role in human health and disease, and in drug devel-opment. The archive of structures available at the PDB ranges from small proteins and pieces of DNA to complex molecular machines like the ribo-some.

PeptideAtlas: http://www.peptideatlas.org/

The website covers multiple organisms and is a publicly accessible com-pendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Some of the experimental data have been published, while many others are still unpublished. The PeptideAtlas project has the long-term goal of full annotation of eukaryotic genomes through a thorough validation of expressed proteins. This database provides a method and frame-work to interpret proteome information coming from high-throughput pro-teomics technologies.

Human Protein Atlas: http://www.proteinatlas.org/

This website provides information regarding expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry images and immunofluores-cence confocal microscopy images. The website is part of the Swedish Human Proteome Resource (HPR) program, funded by the Knut and Alice Wallen-berg Foundation, which has the purpose of systematic exploration of the hu-man proteome using antibody-based proteomics. In order to provide this information, the project has combined high-throughput generation of affin-ity-purified antibodies with protein profiling in numerous tissues and cell types assembled in tissue microarrays.

With these tools, we are able to generate hypotheses, discover potential new drugs, and correlate DNA profiles and gene expression with various dis-eases before even performing an experiment at the lab bench or to enhance the experiments we have already performed at the bench. The databases are numerous and always growing in number during this age of the Internet, so be sure to take advantage of these cost-free reagents in your own research!