Hi. Im Beginner in Bioinformatics. Need an opinion from Professional. I was about to model a 3D structure of hypothetical protein for my MSc study. I have succesfully model a 3D structure by using SWISS-MODEL and go through some refinement and validation protocal such as Ramachandran plot, energy minimization by Using SAVES, GROMACS, etc. Actually, I would like to Publish a paper for MSc Study . The things that was bear in my mind is;
1)To publish any homology based protein models, what kind of structural assessment needs to be done? OR what are the minimum requirements to publish homology based protein models?
2) what is good software for Calculating RMSD (Root Mean Square Deviation)?. Do I need to calculate this ?
Thanks (Sorry for my poor english).