This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Which tools do you recommend me use to get the maximum information of a protein?

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:

  1. Which hypothetical cofactors can join them?
  2. A 3D protein structure compared to other
  3. Is it possible to "model" the protein?
protein software
• 2,792 views • link
updated by fileyfood • fileyfood • written by Hamtaro • Hamtaro

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.

• 0 views • link
written by natasha.sernova natasha.sernova

I just have the sequence because I'm working with an unknown protein.

• 0 views • link
written by Hamtaro • Hamtaro

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...

• 0 views • link
written by natasha.sernova natasha.sernova

1 answer

For modeling, check out the AlphaFold Server for predicting protein structure.

• 0 views • link
written by fileyfood • fileyfood

Log in to answer this question.

More posts like this