I have six protein pdb structures obtained by Phyre2. The quality its okey but i need a bioinformatic program to perform the structure by energy minimization.
There are scors of bioinformatics software available onlike. Few of them are:
1. swiss-PDB Viewer
2. 3D refine (protein structure refine server)
3. Mod refiner (High resolution protein structure refinement)
and many more....
There are scors of bioinformatics software available onlike. Few of them are:
1. swiss-PDB Viewer
2. 3D refine (protein structure refine server)
3. Mod refiner (High resolution protein structure refinement)
and many more....
Hi,
Phyre2 will provide you modeled structures of the proteins (homology modeling). Just minimization is not enough rather MD simulations will suffice the need.
Im ussing chiron for the clashes in the structure. The validation tool in this program for the structures is not good enought.
In order to analyze and validate the models constructed, you can use SAVS Metaserver. This server is online tools for checking the stereo chemical quality of computationally constructed models, and includes the programs ProCheck, What_Check, Errat, VERIFY_3D, PROVE.
http://services.mbi.ucla.edu/SAVES/
I would use YASARA because it has a lot of different force fields, so you can try which one gives you the best results.
Thanks a lot Robbie and Anu. I decided to use Chiron and Verify_3D.
Regards.
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