hello everyone , i just like to ask the bioinformatic professionals here about the best free validation software to validate my 3D structures... i'm still new in the bioinformatic field and i'd like to know more validation bcoz i need to apply protein docking later .. have a nice day
I'm so thankful for ur reply , the problem is i'm still new in this field that's why i'm getting confused bcoz i feel its really hard to understand
You may use TM-score or GDT-TS to measure the similarity of two protein structures. For your ref:
https://zhanglab.ccmb.med.umich.edu/TM-score/
Hello
For 3D Structure and Cavity you can use:
CASTp, Autodock vina, Swissmodel, Qsite, Chimera, RasMol or JMOL, MOE, BIOVIA Discovery Studio.
Good Luck.
Baraa Adil In-silico validation of three-dimensional structures of a protein is a very significant step in computational protein modelling.
When working with experimental protein structures or predicted homology models, the first question is usually about its quality.
Is the structure roughly correct?
The general approach is to validate the structure. Therefore, tools for validating many criteria have been developed, including Ramachandran plot outliers, all-atom clash scores, deviations from bonding geometry, and rotamers etc.
As you're a newbie i would suggest you to validate your modelled protein using provided server;
1. Ramachandran plot analysis use RAMPAGE: http://mordred.bioc.cam.ac.uk/~rapper/rampage.php
2.SAVE 5.0 it has alot of other tool such as;
Verify 3D,
ERRAT,
PROVE,
PROCHECK,
WHATCHECK
http://servicesn.mbi.ucla.edu/SAVES/
3.Then PROSA
https://prosa.services.came.sbg.ac.at/prosa.php
4.Swiss structure assessment
https://swissmodel.expasy.org/assess
5.Molprobity
http://molprobity.biochem.duke.edu/
Please, read each tools' original published paper to understand the concept behind the tool.
I recommend Jmol and swissmodel . Was very easy to use it for myself. But autodock and chimera i hear also are good havent tested them yet.
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