Protein Lounge ePath3D

Category Cross-Omics>Knowledge Bases/Databases/Tools and Cross-Omics>Pathway Knowledge Bases/Databases/Tools

Abstract ePath3D (The Complete Systems Biology Tool) is a suite of applications consisting of the ePathway Tool/Database (3D Pathway Drawing Tool and Pathway Database) and eProtein Database (Associated Protein Information Database and Protein Analysis Tools).

The ePathway (Tool/Database) is a 3D drawing tool, which also includes hundreds of pre-made pathways, which are linked to the eProtein database - (for additional info about the ePathway (Tool/Database) see below...).

The eProtein Database contains the proteins which are associated with the ePathway Database of ePath3D.

ePath3D Main features/capabilities:

1) Draw 3D signaling and metabolic pathway images


2) Ideal pathway illustration tool for publications and presentations.

3) Hundreds of pre-designed and editable signaling and metabolic pathways.

4) Thousands of annotated protein data.

5) Draw, store and link pathways to protein data.

6) New Pathways and Protein data updated monthly.

7) All ePath3D images are compatible with PowerPoint, MS Word, and other Microsoft Office software.

eProtein Database --

eProtein Database is the part of ePath3D which contains the proteins that are associated with the ePathway Database. One can also enter their own protein data into this database and link with pathways.

Note: Both, the eProtein Database and the ePathway Database are part of the ePath3D software, there are No additional charges for these databases.

eProtein Database features/capabilities:

1) eProtein Databases - Consist of complete Protein Databases includes all proteins, i.e., Pathway Proteins, Disease Proteins, Kinase-Phosphatase Proteins, and Transcription Factor Proteins.

2) Disease Folder - The disease folder contains Disease Descriptions and References of the selected protein.

3) Review Folder - The review folder contains Review Description and References of the selected protein.

4) Pathways - The pathways folder lists the pathways which are related to the selected protein.

5) Publications Folder - The publications folder list the publications which are related to the selected protein. The publications are retrieved from The National Center for Biotechnology Information (NCBI) PubMed.

6) siRNA Database - (see G6G Abstract Number 20191R) - The siRNA database contains siRNA targets against the selected protein's mRNA sequence. The program output is ranked by the degree of specificity of the predicted siRNAs.

7) Peptide Antigen Database - (see G6G Abstract Number 20194R) - This database contains antigenic peptide targets against the protein sequence of the selected protein.

8) Kinase and Phosphatase Database - (available at the manufacturer’s home page) - The Kinase and Phosphatase database is a list of all protein kinases and protein phosphatases. This database is of particular importance for drug discovery.

It is very important to understand the proteins which phosphorylate (kinases) and those which dephosphorylate (phosphatases) signaling proteins. The Protein Lounge Kinase/Phosphatase listing is one of the only currently available lists of both kinases and phosphatases.

9) Transcription Factor Database - (available at the manufacturer’s home page) - The Protein Lounge Transcription Factor Database is a resource housing information relating to transcription factors of humans and other organisms.

This database is organized by the transcription factor names, organism specification, binding sequences, binding elements, and cell type specification.

10) Datasheet - The Datasheet contains the basic protein information, i.e., Proteins Type, Family, Function, Protein Interactions (Inhibitory and Activation Effects), Protein Location, Cell Types, Protein Structure, Chromosome Location, Binding Site, Binding Element, and its allied proteins.

11) siRNA Finder - (see G6G Abstract Number 20195R) - The parameters for the siRNA Database are based on the methods developed for siRNA prediction by Dr. Thomas Tuschl (Max-Planck Institute).

12) Peptide Antigen Finder - (see G6G Abstract Number 20195R) - The parameters of the Peptide-Antigen Database are based on the methods for peptide selection developed by Dr. Philip Goulder (Oxford), Dr. Otto Yang (UCLA) and Dr. Andrew Bradbury (LANL).

This tool will find the regions on the entered protein sequence which are most antigenic, thus it will uncover good drug or antibody targets.

13) Hydroplotter (Kyte-Dolittle and Hopp-Wood Plots) - (see G6G Abstract Number 20195R) - These two plots display the hydrophilic and hydrophobic regions on a protein sequence. You can highlight the regions on the plot(s) to view the corresponding region on the protein sequence.

ePathway Database --

ePathway Database features/capabilities:

1) Pre-made Pathways - ePathway contains hundreds of pre-made signal transduction and metabolic pathways. All pathways have been created by the Protein Lounge biology team and are well referenced.

2) Drawing a Pathway from Scratch - In addition to modifying pre-made pathways, you can also draw a pathway from scratch by selecting from the biological membranes, protein images, and other accessory items.

3) Membranes - There are three (3) types of membranes available:

4) Organelles Folder - This folder contain cellular organelles, such as a nucleus, mitochondria, ribosomes, etc.

5) Receptors/Channels Folder - This folder contains the membrane receptors which will be necessary to draw a signaling pathway.

6) Accessory Items Folder - This folder contain other accessory items which are required to draw some pathways, such as Phosphates, Elements (Ca, K, Na, etc.), Scissors, Syringe, Capsules, etc.

7) Biochemical Compound Folder - This folder contains the basic units required to construct biochemical compounds.

8) Cells/Tissues Folder - This folder contains cells and tissue types which would be found in the body.

9) Organs/Systems Folder - This folder contains organs and organ systems which would be found in the body.

10) Organisms Folder - This folder contains organisms which may be necessary to draw pathways or diagrams.

System Requirements

Contact manufacturer.


Manufacturer Web Site Protein Lounge ePath3D and Protein Lounge Home

Price Contact manufacturer.

G6G Abstract Number 20174A

G6G Manufacturer Number 102215