Introducing Protein Lounge: A New Bioinformatics Resource
HSLS is pleased to announce the addition of Protein Lounge to our collection of bioinformatics resources. Protein Lounge is a gene/protein centric Web portal that offers a collection of searchable databases and software tools, useful for researchers and students.
This collection features ten databases covering research organisms including human, mouse, rat, drosophila, C. elegans, zebrafish, and yeast, as well as nine biology-based research tools. Some noteworthy components:
Databases
• siRNA contains precomputed statistically validated siRNA targets against known genes.
• Peptide-Antigen offers computationally predicted antigenic peptide targets for antibody generation against known protein sequences.
• Pathway provides an extensive collection of 447 signaling and metabolic pathways subdivided into various functional categories such as adhesion, cell cycle, apoptosis, etc.
• Protein Interaction enables users to search for a protein, and then view the other proteins it activates, inhibits, or binds to.
• Kinase-Phosphatase stores a list of protein kinases and protein phosphatases organized with their substrates.
• Transcription Factors includes names, organism specification, binding sequences, binding elements, and cell type specification.
• Biochemical Compound contains text and graphics describing important molecules involved in cellular signaling, biosynthesis, and metabolism.
• Protein presents information categorized into subtopics such as reviews, pathways, disease relation, protein family members, sequence information, and publication.
Research Tools
• Pathway Builder 2.0 is a software application, downloadable to the desktop, that works on both Windows and Mac operating platforms. This easy-to-use “drag and drop” software allows users to make their own signaling or metabolic pathways using pre-configured membranes, organelles, proteins, and other necessary pathway structures. This tool is excellent for creating colorful publication quality graphics.
• Protein Hydroplotter allows viewing of hydrophilic and hydrophobic regions of a protein sequence. This tool is ideal for finding antibody and drug targets of a protein.
• Peptide Finder finds the best antigenic peptides of a protein sequence. Hydrophilic regions of the protein sequence are screened to find the best possible peptides that can be used as antibody or drug targets.
• Easy siRNA offers an efficient method of finding siRNA targets and cloning them online.
An additional feature of Protein Lounge is the Online Lab Book, which allows users to securely store information in a personal online lab book, viewable from any location.
To access Protein Lounge, type "Protein Lounge" into the search.HSLS quick search box at <www.hsls.pitt.edu/> .
For more information regarding Protein Lounge or for hands-on training on Pathway Builder, contact Ansuman Chattopadhyay, head of the Molecular Biology Information Service, at ansuman@pitt.edu or 412-648-1297.
--Ansuman Chattopadhyay
