Dear modellers,
I have started my Ph.D in the field of Molecular modelling and
drug design.So,i need some comments about my modelling procedure.Please
verify the modelling protocol
that i am following to build the model and post-modelling procedures and
give some good comments.
1. Obtaining the models with the help of modeller
2.Choose the model that is having lowest objective function.
3.Verify the model using Verify3D- program.
4.The regions that shows below the threshold value.Do the loop modelling
and try to improve that region.
5.After improving the regions check it with also PORCHECK results for
stereochemical evaluation.
6.Do the energy minimization with 50 cycles with fixing backbone and
without charges.Then release the backbone and without charges for 50
cycles.Then with charges for 50 cycles.
7. Then verify it with PROSAII energy verification program.
Expecting for your reply.Thanks in advance.
Yours friendly,
Senthil kumar.R