Disease Motifs
Investigating the Biomechanics of Disease
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Resources

I intend to populate this page with useful links to sites that might be of interest. There will of course be links in the rest of the site too but it seems like a good idea to put a complete collection here with a little explanation about what these online resources are. I use the SwissProt protein. If you have suggestions of useful sites please let me know. For now though I am just going to keep things basic and not put sites on that are far too complicated to use.

ExPASy One of the first ports of call is the database and facilities at Expasy or should I say the ExPASy (Expert Protein Analysis System) proteomics server which can be found at http://expasy.org and has been developed by the Swiss Institute of Bioinformatics (SIB).

I like to use their BLAST program which can be found at http://expasy.org/tools/blast. I also like to use the scan prosite tool at http://expasy.org/tools/scanprosite. Look at the http://expasy.org/sprot and search the Swiss-prot/TrEMBL database and you can search for any protein you like. For example if you type in Human Prion Protein in to the search box you will be given a human prion protein data sheet which is located at http://www.expasy.org/uniprot/P04156 .


NCBI Another favourite site of mine is at the NCBI at http://www.ncbi.nlm.nih.gov and I like to use their Protein BLAST program which is well worth a look.

They have a 3D viewer called Cn3D 3-D Structure Viewer that can be downloaded on to your pc at http://www.ncbi.nlm.nih.gov/Structure/CN3D/cn3dinstall.shtml that you can use to look at the 3D structure of proteins. You select the one for your platform although I noticed they didn't mention Vista but I downloaded it anyway and it seems to work fine. You can visit the library of proteins structures at http://www.ncbi.nlm.nih.gov/Structure/MMDB/mmdb.shtml and enter a protein name like 'prion protein human' in the 'search structure for' box select one of the values returned and save the file to your computer and open with the viewer. I selected http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=72075 which shows the E200K mutant or variation of the Human Prion Protein. You can once you have downloaded the viewer just click on the little icon at the side of each image of the returned proteins (and there usually quite a few proteins returned) to see the structure of the protein.

There is an option do view the molecule with Rasmol which will need to be downloaded before hand at http://www.rasmol.org/?gclid=CO-Qz9KbkJ4CFZQA4wodghq9qg and you have to select 'RasMol Latest Windows Installer' for windows. You then don't have to download file to view.


European Bioinformatics Institute (EBI) There is a protein alignment tool at the European Bioinformatics Institute (EMBL-EBI), which is part of the European Molecular Biology Laboratory (EMBL). This tool is the ClustalW2 and can be found at http://www.ebi.ac.uk/Tools/clustalw2/index.html.


ActivePerl If you are interested in doing some Perl programming on your PC you might want to consider downloading the Perl Manager. http://www.activestate.com/Products/activeperl/feature_list.mhtml

I am an amateur Perl programmer and do like to mess around with databases. I won't advise you to download any of the databases at this link as these databases are huge and will probably slow your pc down if not make it crash. But if you do know what you are doing with this very large downloads, here is a site where I download the databases that I use ftp://ftp.ebi.ac.uk/pub/databases/

To download the complete database Complete Database

To download some of the Taxonomic divisions Taxonomic Divisions

To download the BLAST program from the NCBI Blast Program

To download the BLAST program I use which is several years old Blastall.exe. Click on the link and 'SAVE AS'.




Networks

There are some sites that help in building a network image.

GeneMANIA, which will build up a network of genes diagram, has to be viewed by any browser other than IE which I think is very unfortunate (and discriminatory) as IE is my preferred browser. So just in case like me you work in IE you will need to copy the link into another browser for this occasion the url is http://www.genemania.org