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. Both, the eProtein Database and the ePathway Database are part of the ePath3D software, there are no additional charges for these database.

Getting Started

Opening Screen Shots of eProtein

Complete Protein Database includes all proteins, i.e., Pathway Proteins, Disease Proteins, Kinase-Phosphatase Proteins, Transcription Factor Proteins.



Each Protein has its own Datasheet, Review, Related Pathway List, Disease Relation, Sequence Information, Publications, siRNA Database, siRNA Finder, Protein Sequence Hydroplot, Peptide Antigen Database and Peptide Tool. You can click on the relative buttons to view the information.

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eProtein Databases

Introduction

Complete Protein Database includes all proteins, i.e., Pathway Proteins, Disease Proteins, Kinase-Phosphatase Proteins, Transcription Factor Proteins.

Opening Screen Shot of eProtein



Each Protein has its own Datasheet, Review, Related Pathway List, Disease Relation, Sequence Information, Publications, siRNA Database, siRNA Finder, Protein Sequence Hydroplot, Peptide Antigen Database and Peptide Tool. You can click on the relative buttons to view the information.

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Diseases

The disease folder contains Disease Descriptions and References of the selected protein. Click on the reference, to view Abstract and Full Text.

Modifying Diseases Description:

To modify a Disease description, of currently selected protein click “Modify Description” Button, then edit the information; click “Save Description” Button to save the changes.

Modifying References:

Edit: To edit References, of currently selected protein click “Modify References” Button, and then make changes as required. You can change Authors’ name, Journal’s Name, Title and Pubmed Id. Click “Save References” to save the changes.

Add: To add References, of currently selected protein click “Modify References” Button, and click on the blank row with asterisk mark (*). Fill in the following information in respective boxes, i.e., Authors’ Name, Journal’s Name, Title and Pubmed id. Click “Save References” button to save the changes.

Delete: To delete References, of currently selected protein click “Modify References” Button, and click on the row header (blank space showing the arrow mark to indicate currently selected Reference), and then press Keyboard delete button. To save the changes, click on “Save References” button.


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Reviews

The review folder contains Review Description and References of the selected protein. Click on the reference, to view Abstract and Full Text.

Modifying Review Description:

To modify Review description, of currently selected protein click “Modify Description” Button, then edit the information; click “Save Description” Button to save the changes.

Modifying References:

Edit: To edit References, of currently selected protein click “Modify References” Button, and then make changes as required. You can change Authors’ name, Journal’s Name, Title and Pubmed Id. Click “Save References” to save the changes.

Add: To add References, of currently selected protein click “Modify References” Button, and click on the blank row with asterisk mark (*). Fill in the following information in respective boxes viz. Authors’ Name, Journal’s Name, Title and Pubmed id. Click “Save References” button to save the changes.

Delete: To delete References, of currently selected protein click “Modify References” Button, and click on the row header (blank space showing the arrow mark to indicate currently selected Reference), and then press Keyboard delete button. To save the changes, click on “Save References” button.



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The pathways folder lists the pathways which are related to the selected protein. Click on the Pathway Title, to view 3D Pathway Image with its detail description and References. To Open Pre-made pathway on ePath3D, click on the Pathway Image.



Pathway Pop-Up window

Modifying Pathway Description:

To modify Review description, of currently selected protein click “Modify Description” Button, then edit the information; click “Save Description” Button to save the changes.

Modifying References:

Edit: To edit References, of currently selected protein click “Modify References” Button, and then make changes as required. You can change Authors’ name, Journal’s Name, Title and Pubmed Id. Click “Save References” to save the changes.

Add: To add References, of currently selected protein click “Modify References” Button, and click on the blank row with asterisk mark (*). Fill in the following information in respective boxes viz. Authors’ Name, Journal’s Name, Title and Pubmed id. Click “Save References” button to save the changes.

Delete: To delete References, of currently selected protein click “Modify References” Button, and click on the row header (blank space showing the arrow mark to indicate currently selected Reference), and then press Keyboard delete button. To save the changes, click on “Save References” button.



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The publications folder list the publications which are related to the selected protein. The publications are retrieved from the NCBI PubMed.



*Publication extracted from NCBI (The National Center for Biotechnology Information), Pubmed (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed)

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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.

Parameters:

The parameters for the siRNA Database are based on the methods developed for siRNA prediction by Dr. Thomas Tuschl (Max-Planck Institut).

BEST TARGET: The 'Best Target' for siRNA is nearest to the mRNA start sequence. Those siRNA targets which are nearest to the start sequence produce a better 'Knock-Down' due to cleavage of a great segment of the mRNA.

All siRNA targets have been screened to remove any siRNA which shares homology with other sequences, thus producing targets which are specific to the gene of interest.

Target Selection Method:

Target Size: 19-22 Nucleotides

Nucleotide target from 5' and 3': 50 (Optimum). The search for target start after 50 nucleotide for sequences size more than 200. Ignored for sizes less than 200 nucleotide.

Nucleotide Target For siRNA: Either "AA" (Optimum) or "T"

G+C Content: 47-51% Optimum (10-90% are also taken in account if optimum fails)

'A' Repeats: < 4 (i.e motif will have less then or equal to 4 A's repeats)

'T' Repeats: < 4 (i.e motif will have less then or equal to 4 T's repeats)

'G' Repeats: < 3 (i.e motif will have less then or equal to 3 G's repeats)

'C' Repeats: < 3 (i.e motif will have less then or equal to 3 C's repeats)



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This database contains antigenic peptide targets against the protein sequence of the selected protein. The most important aspect in the production of antibodies or drug is the design of the peptide-antigen. The peptide-antigen is a small segment (15-18 amino acids) of the protein sequence of interest. These peptide-antigens can be used for immunization in order to produce antibodies against the protein for which the peptide is from or the peptides can be used as a basis for small-molecule/drug targeting. All peptide targets are linked to Protein Lounge's proprietary hyrdoplotting tool, which allows you to view an interactive version of the protein sequence on a hydrophilicity/phobicity plot.

Parameters:

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).

BEST TARGET: The 'Best Target' is the peptide which is the most hydrophilic, thus it is the region of the protein which has the best chance of surface exposure.

Target Selection Method:

Hydropathy Range (Kyte-Doolittle): (Less Hydrophilic)+5 to -5(Most Hydrophilic)

Peptide Length: 15-18

N-Term Forbidden: GPEDQNTSC

C-Term Forbidden: Q

Forbidden Repeats: Consecutive 5 Qs and 5 Es

Shorten By: 3

Lengthen By: 2

Overlap Peptide By: 1-10

Functionality:

View Hydroplot: When click on this button it'll pop up Kyte-Dolittle Graph window.



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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 the only currently available list of both kinases and phosphatases.

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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.

Transcription factors are proteins involved in the regulation of gene expression that bind to the promoter elements upstream of genes and either facilitate or inhibit transcription. Through this process they control and regulate gene expression. Transcription factors are composed of two essential functional regions: a DNA-binding domain and an activator domain. The DNA-binding domain consists of amino acids that recognize specific DNA bases near the start of transcription.

The Transcription Factor database contains all necessary information about the transcription factors such as its classification, specific functions, DNA sequence, domains, structures, interaction with other proteins, its allied members and role in specific diseases. One can also get information about the pathways related to the specific transcription factors. It is our goal to offer a reliable up-to-date resource on transcription factors that can be utilized by researchers in studying gene expression.

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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.

Modifying Datasheet:

To modify datasheet of currently selected protein click “Modify Datasheet” Button, then edit the information; then click “Save Datasheet” Button to save the changes.



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The parameters for the siRNA Database are based on the methods developed for siRNA prediction by Dr. Thomas Tuschl (Max-Planck Institute).

Functionality:

Enter DNA Sequence:

It contains the DNA sequence of selected Protein. The Sequence is editable and replaceable.

Parameters:

Region to Search for siRNA indicates the Coding Region of the Sequence to search for siRNA's. It can be changed by the user to select any portion from the sequence. This is the region of interest to search for siRNA's. The siRNA search will start from within this region taking into account other search values.

Nucleotide target from 5' and 3 value indicates that the search for siRNA fragments will not account for the number of nucleotide mention in this text box from the start of the DNA sequence & end of the Dna sequence between the Region to search for siRNA nucleotide. This option is neglected for sequences which are smaller than 200 bp.

siRNA Size is the length of siRNAs, program would attempt to generate.

First Nucleotide target of siRNA is the nucleotide for which the program would attempt to search with in the given nucleotide sequence. The program would search for nucleotide target after the 51(Region to Search for siRNA + Nucleotide target from 5' and 3'. Default is 'AA'.

G+C Content boxes displays the % of G's and C's the siRNA fragments should have.

The Avoid 'A' repeats, Avoid 'T' repeats, Avoid 'C' repeats, Avoid 'G' repeats displays the values which will be avoided while search. This implies that the siRNA fragments displayed will not have consecutive repeats of A's, T's, G's, C's for the values given.

Generate siRNA:

When clicked on this button, program would start searching for the siRNA in the given DNA sequence. It would display the results just below.



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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). The tool will find the regions on the entered protein sequence which are most antigenic, thus will make good drug or antibody targets.

Functionality:

Sequence:
Enter Sequence contains the Amino Acid sequence of selected Protein. The Sequence is editable and replaceable.

Parameters:
Peptide Length is the length of peptide, program would attempt to generate. Default is 15 AAs. It can be change as per requirement.

Peptide Overlap By determines, how many AAs will be included while generating the next peptide. Default is 10 AAs.

krhgpgpreargar
        gpreargarpglrv

Shorten By determines how much the program will shorten the peptide, in case it find N-Forbidden AAs or C-Forbidden AAs. Here, the default is 3. That's why peptide length may vary between 12 and 17, if Lengthen By is 2 and Shorten By is 3 and Peptide

Lengthen By determine how much the program will lengthen the peptide, if it find 15 down to 12 are forbidden (in default case).

C-Term Forbidden AAs restrict peptides which ends with these AAs. If program find C-Forbidden peptides at the end of peptide it'll shorten or lengthen the peptide to find Non-Forbidden peptide. Default is GPEDQNTSC.

N-Term Forbidden AAs restrict peptides which start with these AAs. Default is 'Q'.

Generate Peptide:

When click on this button, it will start searching for best possible peptides using given parameters. The Program will automatically discard any Peptides with less then -1 hydrophilicty. The results of this are presented in the below screen shot.

Hydroplot:

It'll display a pop-window with Kyte-Dolittle Graph aligned with the peptide and protein sequences. You can highlight the plot to view the corresponding region on protein sequence.



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The two plots below display the hydrophilic and hydrophobic regions on the protein sequence. You can highlight the regions on the plot to view the corresponding region on the protein sequence.

Kyte-Dolittle Hydroplot



Hopp-Wood Hydroplot



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Changing Organism Database: Select the organism from drop-down list, to view the protein database of that Organism.



Changing Database Type: To Change the currently selected database to any other database(i.e. Kinase, Phosphatase, Pathway Proteins, Transcription Factor and All Proteins), select it from drop-down list.



View By Pathways: Select any Pathway from drop-down list, it would show the list of proteins related to the selected Pathway.



View By Category: Select any Protein Category from drop-down list, to view the list of protein exist in that Category.



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To Search protein, specify the protein name or gen bank no or Full Name in "Enter Search Term" box. And then click "Go" Button to search for specified protein. The results will me displayed in Protein Data Grid.



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To Open ePathway Drawing Tool, click on the ePathway button at the top of the Screen.



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To Save Currently selected Protein data, click on Save button of Tool Bar or Menu bar(File -> Save). The data would be saved in .CSD file, which only open with eProtein.



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Edit: To edit Protein data, click on “Modify Protein” Button, and then make changes as required. You can modify Protein name, Gen Bank No. and Full Name of Protein but cannot edit Organism. Click “Save Protein” to save the changes.

Add: To add Protein, click on “Add Protein” Button, and click on the blank row with asterisk mark (*); it is always the last record. Fill in the following information in respective boxes viz.Protein’ Name, Gen Bank No., and Full Name. Click “Save Protein” button to save the changes.

Delete: To delete protein click on “Modify Protein” Button, then select the protein you want to delete, and then press Keyboard delete button. To save the changes, click on “Save Protein” button.



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Open: It would open the existing eProtein (.CSD) File

Save: It would Save the Protein Information into the computer hard drive.

Copy: To Copy selected text, click on Copy.

Cut: To Cut selected text, click on Cut.

Paste: To Paste the Copied text, click on Paste.

Print Preview: It would show Print Preview window with the selected Protein Information.

Page Setup: Use this button to setup the page before printing.

Print: Click on this button to print the content of selected Protein.



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File:

Open: It would open the existing eProtein (.CSD) File

Save: It would Save the Protein Information into the computer hard drive.

Print Preview: It would show Print Preview window with the selected Protein Information.

Page Setup: Use this button to setup the page before printing.

Print: Click on this button to print the content of selected Protein.

Exit: Click on this button to exit from the eProtein Application.



Edit:

Copy: To Copy selected text, click on Copy.

Cut: To Cut selected text, click on Cut.

Paste: To Paste the Copied text, click on Paste.



Tools:

Options: Here you can specify your preferences, like what will start first i.e ePathway or eProtein when the ePath3D Start.



About:

About: It will display the copy right information and names of developers.

Help: When click on this option, it will display the help file.



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