Introduction

Dear students,

We have already seen several aspects of bioinformatics computation(s). Examples are:

• Predicting point mutations using an HSSP file;
• Predicting how a helix sticks through a membrane (upside-up or upside-down);
• Protein dynamics and energy minimization;
• Comparing protein structures with CATH, SCOP, DALI;
• The use of the Ramachandran plot;
• Softwares like Yasara, BLAST, MRS;
• The WHAT IF structure computation servers.

But there is much, much more that can be computed. In the remainder of this course we will look at a series of databases and computational facilities, and you will get ample time to work out one project yourself in great detail.

First we will make a tour along a few of the more useful sites. This tour cannot be complete for the very simple reason that that would take the rest of our lives...

The journal NAR has every year a special volume on databases. How many databases did they list in the most recent volume? How many BLAST servers are listed in the SwissProt (expasy) list of proteomics and sequence analysis tools? Look at the CBS prediction servers. Describe in your own words what the TargetP server does; which biological process does it calculate? Find the fructose catabolism pathway in the EBI reactome system.

Question 44: The journal NAR has every year a special volume on databases. How many databases did they list in the most recent volume?

Question 45: How many BLAST servers are listed in the SwissProt (expasy) list of proteomics and sequence analysis tools?

Question 46: Look at the CBS prediction servers. Describe in your own words what the TargetP server does; which biological process does it calculate?

Question 47: Draw (cut-n-paste) the fructose catabolism pathway.