Missing segments of protein and minimization

Question

[chemistry1233]

I have problem with pdb file when I want to use for docking becuase they have missing segments and it`s neccessary to minimize energy. I know for Chimera, SwissPDB and Modeller. I want to ask you which is better and how to work with it

[Deepak Tanwar]

Go through this manual: http://www.bioinformatics.bbsrc.ac.uk/training.html#deepview

Answer 1

[João Rodrigues]

You should use either MODELLER or another homology modelling / loop modelling software. Chimera and SwissPDB (Viewer) are visualisation tools and are not suited for this task. The energy minimisation can also be done with MODELLER (if you provide a complete protein and its sequence). Have a look at the manual and/or the tutorial.

To avoid installing and running it locally, you can use the MODELLER interface on the HHpred website.

Answer 2

[chemistry1233]

Can anyone to tell step by step for add missing segments and minimization throught SwissPDB and Chimera

[João Rodrigues]

No. Besides the other answers, I pointed you to the HHpred website that does a pretty simple job at adding missing segments. You just need to learn the basics of homology modelling.