Hi, I have a list of some genes and i want to check their interaction with my target. Anyone can suggest some bioinformatic tools that can predict the interaction?.
many thanks
Hello Arif
You may choose a docking approach by ClusPro server (Article The ClusPro web server for protein–protein docking
). Another way is to do a molecular dynamic simulation by GROMACS package. This require a high-end PC (or access to a server) + knowledge of programing.
I just recently used Stringv10.5 in a publication that shows the predictability of protein-protein interactions based on a variety of experimental and published databases.
David John Kowbel Thank you for your suggestion but i have already checked. i have some protein from mass spec data an i have to check their interaction with my protein of interest
Hi
One of the promising tools for protein-protein interaction is STRING database
(https://string-db.org/)
This database also provide "Functional Enrichment Analysis" which may usefull for your future analysis.
Thank you Amin for your suggestion, unfortunately STRING database contain those protein which are already predicted and my proteins not rely in this as i have some new protein list
If you got the expression level of these proteins, you may try Cytoscape to perform the network analysis.
I think is good choice many tools like : SIFT , polyphen , SNPs3D , SNPs&GO and MutPred .
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics