Protein Lounge

Protein Lounge is a web-based resource designed to assist students, scientists, and researchers with the concepts of systems biology. The information provided in Protein Lounge focuses on clarifying the complex nature of biological pathways. Biological pathways consist of molecular actions that result in a cellular change: “There are many types of biological pathways. Some of the most common are involved in metabolism, the regulation of genes and the transmission of signals” 1.

Protein Lounge comprises multiple components that allow users to fully explore the area of biological pathways. The resource includes nine main databases: pathway, small interfering RNA (siRNA), peptide antigen, protein interaction, kinase-phosphatase, transcription factors, G-protein coupled receptor (GPCR), biochemical compound, and protein.

A major element of Protein Lounge is the pathway database, which contains 465 signal transduction and metabolic pathways. They are organized by signaling pathways and metabolic pathways. Users can also search by keywords or by organism categories (such as viruses or protozoa) or function categories (such as diseases or immunology).

One example found in the protein database is the airway pathology of chronic obstructive pulmonary disease (COPD). Protein Lounge provides an image at the molecular level of how smoke affects lung cells, resulting in emphysema or bronchitis. Also shown are the cellular changes that occur when an individual smokes and a description of the effects of COPD in addition to other basic information. Linked references to PubMed are provided for the description section as well as the last update date. A nice feature of Protein Lounge is that electronic presentation slides containing the same information are available for download for use in presentations and publications.

The pathway builder portion of Protein Lounge allows users to create their own signal transduction pathways. Users have the option of designing their own pathways or using a premade template. Some examples of premade pathways include the cellular apoptosis pathway or the innate immunity pathway. Users also have the option of saving pathway projects in an individual account. Saved pathway projects can then be downloaded as images.

The siRNA database provides individuals with a searchable listing of gene names and corresponding siRNA targets, which is useful to those who deal with gene expression analysis. The protein antigen database allows users to locate peptide sequences that correspond to a desired gene name. This particular database is helpful with creating pharmaceutical treatments. The protein interaction database contains information on the relationships that occur between human proteins. The kinase-phosphatase database comprises all of the possible kinases and phosphatases, including the substrates and organisms that they are located in. The transcription factors database provides users with transcription factor names as well as the organism, binding sequences, and elements. The GPCR database provides information on these receptors, incorporating the protein, organism, and function of the protein. The biochemical compound database is a resource that contains descriptions of molecules, such as their weight, location, function, type, and formula. The protein database contains data on all of the human proteins, including their specific function, chromosome location, and structure.

Protein Lounge provides users with a large and varying amount of information on biological systems. Those dealing with systems biology would benefit greatly from a resource such as this. The concepts are explained on a clear and detailed level. However, the help section of Protein Lounge leaves something to be desired.

Overall, this is an excellent product that would be useful for a specific audience of students, clinicians, and researchers. Although similar in nature to some of the resources in the National Center for Biotechnology Information (NCBI) suite, Protein Lounge provides a more graphical approach in visualizing pathways. Protein Lounge is an exceptional product that would be a useful tool for users in the areas of molecular biology and biochemistry.