Title:›› Transpath›››› BIND and››››› Prime

 

URL:

 

Transpath: http://www.biobase.de/pages/products/transpath.html

BIND: http://www.blueprint.org/bind/bind.php

PRIME: http://prime.ontology.ims.u-tokyo.ac.jp:8081/

 

 

Date Reviewed: May24, 2004

 

Description:

 

TranspathThis is a database that is a compilation of information on the various signaling pathways that are critical in the regulation of transcription factors.Transpath is very informative because not only does it give information about the pathways, but it also gives additional information about the extracellular signals that initiate the signaling cascade.

 

BIND (Biomolecular Interaction Network Database) is a database that contains information on molecular interactions, molecular complexes and the various biological pathways.

 

PRIME is a Japanese database that offers Kinase Pathways.It is useful in classifying protein kinases and their functional conservation.It offers orthologue tables of specific protein-protein interactions and also provides protein domain and structural information.

 

Strengths:

 

Transpath:The graphics on this database are very informative and extensive.There is a free available demo version that is restricted to the IL-1 pathway.The paid version, however, is a compilation of all the signaling pathways.This website is very user-friendly and gives one a guided tour of what to expect.The website can be searched by name of molecule, gene or the reaction pathway it is involved in and there are extensive references attached to each of these.The reaction pathway flowcharts are very detailed and can make great graphics to put in a presentation.There is also a browse button where you can become acquainted with the different molecules that are categorized as adaptor proteins, enzymes, co-factors, ligands, inhibitors, transcription factors etc.Very useful site to learn more about the signaling pathways that exist.Despite the complexity of the signaling pathways, this site does a very good job of putting it all together as lucidly as possible.

 

BIND (version 2.5)

The BIND website also has a tutorial.The tutorial does a decent job of explaining how the site works.You can enter a protein name in the Search field and the search results yield information that are organized into a description for the molecule, the biological processes it is involved in, the molecular function of it and also experiments and references that are available.You can also search a molecule based on what it interacts with and it gives a live graphic image of that.Each of the accompanying information on the moleculeŪs description, function or the biological processes it is involved in is further clickable to get more information.It has links to other labŪs website (e.g. Tony Pawson) which I found to be a very useful resource.And best of all, the site is completely free.

 

PRIME

With this website you are also able to enter a molecule name and search for the interacting partners as well as the pathway it is involved in.It gives a reference list along with the experimental data conducted.Free access.Information available for different species i.e can do a search based on specie.

 

Weaknesses:

 

Transpath: Unfortunately, the extensiveness of the website can only be made use of with a small fee.The demo version which is free is only restricted to the IL-1 pathway and therefore, much of the information on other signaling pathways can be accessed with a membership.

 

BIND:It took a very long time to get some of the graphics.Also, the site was notas user friendly as the Transpath site was.It took me some time to understand what to do despite the tutorial.Some of the information that the database spewed out was very extraneous and not necessary for the purposes of my search.The data that results from a search should be put together differently and not be so scattered.There seems to be too much information to go through when you do a search.However, it is misleading because half of the results are really not useful.

 

PRIME: I did not find this site to be very user friendly.It took me a very long time to figure out how to work the website.It didnŪt have a tutorial unlike the two other sites.Also, when I typed in the two proteins in a pathway, most of the time the machine would not give any results.I had to go into the alphabetical list and click on my protein to be able to get any data.Even though the information is pretty extensive, the organization of this website is poor.

 

Comprehensiveness:

 

Transpath-The new paid version seemed to be very comprehensive with over 20,000 entries of reactions listed and 35 pathways and almost 17000 molecules.The free demo version however was limited.

 

BIND-This site did not seem to be as comprehensive as TRANSPATH in terms of pathways probably because it is available free.There are 8 database pathways.However, it claimed that it had over 84,000 entries in the interaction database and roughly 1700 molecular complexes.

 

PRIME

Seemed to have a comprehensive list of pathways and protein interactions across species.

 

Timeliness

Transpath-the paid version is updated only 4 times a year.

BIND-not regularly at all.Last update was June 18,2003!

PRIME-this is the most updated of all three-last update was May21,2004

 

 

Ease of Use

Transpath:Demo version was very easy to use.I imagine the paid version is even better

BIND:Not very user friendly

PRIME: Least user friendly

 

Responsiveness

TranspathůDEMO version was very quick

BIND:quite slow during some instances

PRIME:quite slow as well.The graphics took a while to pull up.

 

Similar or related Sites:These sites are quite similar to each other in the type of information they hope to portray.BRITE, BBID and DIP are also other related sites.

 

Overall Evaluation

Transpath: 4

BIND:2.5

PRIME:2.5

 

Reviewer: Shweta Hakre

 

Email:shweta.hakre@tufts.edu