Entering edit mode
7.6 years ago
Hamtaro
▴
50
Hello everybody!!
I have begun to study bioinformatics two month ago and I'm a little bit newbie in this field. In any case I've been always working with proteins, for that reason I'd like to know which tools do you recommend me to study them.
For example to know this kind of things:
- Which hypothetical cofactors can join them?
- A 3D protein structure compared to other
- Is it possible to "model" the protein?
Is it in SwissProt? In any case, Expasy-tool is really helpful;
3D-structure - PDB-site and PFam.
See this post, for example:
A: How make download in PDB file (Text)
The ability to model a protein depends upon what you have already known about it.
I just have the sequence because I'm working with an unknown protein.
You may want to start with a blast search at Uniprot. There are many protein related tools listed on this page that you can try.
Just a sequence - It's a lot, by the way.
First of all, run blastp, you will learn many details.
Start from www.ncbi.nlm.nih.gov, then https://blast.ncbi.nlm.nih.gov/Blast.cgi for protein - an icon on the right
If you don't know the organism, try nr (non-redundant) database for the initial rearch.
Try to find some proper tools in Expasy:
http://www.expasy.org/proteomics
This is modelling, you have mentioned:
https://swissmodel.expasy.org/interactive
etc...
To search Swiss-Prot from sequence, you have this site:
https://www.ncbi.nlm.nih.gov/Class/NAWBIS/Modules/Protein/protein9.html