I predicted a protein structure using Robetta server and I got 5 models.I tried to validate these structures to know which one is good I used both Rampage web server and SAVES server.The allowed and disallowed region for Rampage web server and SAVES server is different?Can u suggest me which one is better ?
Hello Jyotilipsa Mohanty ,
All the server have there own protocol for validating the protein structure, Hence we get different score.
One approach may be run MD simulation to check its stability or one may try to compare the modeled structure with its template structure to pick best among five.
Both servers represent the structure of proteins backbone by their dihedral angles using Ramachadran plot, but applies different algorithms. I suggest to optimize your protein structure using an atomic-level refinement algorithm, such as ModRefiner (see reference below).
Article Improving the Physical Realism and Structural Accuracy of Pr...
Another strategy would be to submit the model to MD simulations to optimize your protein structure.
- Badges
- Science topic
- Similar topics
- Biological Science
- Biochemistry
- Enzymology
- Enzymes