Good morning, I have started to work with enzymes. For the one I am interested, I want to know the distribution of amino acids in its terciary structure. Sequence is reported (Uniprot A.N.Q9WYE2) as well as its 3d structure. But do you know any software that allows me visualize, one at time, every amino acid in its 3d structure, I mean first Tyr, then all Asp, and so on? I will appreciate your help.
If you just want to visualise the structure, then RASMOL is probably the easiest option, though it has fallen out of favour because it is so very basic and there is little else you can do apart from looking at the structure.
If you need more versatility then PYMOL is a better option. This is a molecular graphics programme for making pictures from pdb files and the basic instructions are fairly easy and there is a lot of information on the web on how to do more intricate pictures and movies with it.
If you are actually interested in manipulating the structure (mutating residues, changing the positions of atoms, working with the electron density maps that go with the structures, etc...) then COOT is the best option, but this programme can be a bit more difficult to master if you're not familiar with structural biology.
Hi Francisco,
The programme you should use (as mentioned by Antonio) is COOT. I allows you to go through your 3D structure and each amino acid one by one. Just 'go to atom' and select the first amino acid in the protein structure. You can also look at distances and angles of atoms you're interested in. It also allows you to mutate amino acids etc.
Best of all, it is free for academic use.
Best of luck
There are many different ways to compare distributions of residues compared to each other. 2 common approaches I think would be either to compare their absolute distribution or 3D distribution.
If you want to compare the absolute distribution of amino acids with respect to each other/domains/regions in a protein molecule, you can use a software I have recently published. Normally the software needs variation file to plot single nucleotide polymorphisms, but I have created a dummy variation file just to plot a single synonymous p.M1M variation. Open the .rar file and extract the html inside which shows the graph of your protein. You can use latest version of either chrome or firefox. To understand what the tracks are you can refer to examples in http://i-pv.org/. To be brief I also attached a gif file comparing distributions (log2 ratio) of tyrosine and aspartic acid.
If you want to compare distributions in 3D space, then you can go for Swiss PDB (http://spdbv.vital-it.ch/). Here you can show hide different amino acids and measure distances into each other.
Good luck
Note: click on the square icon below to view the gif file.
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