GalaxyRefine is for refinement of single chain 3D structure. I normally use YASARA energy minimization to ensure stability of my predicted protein. Now if I want to use GalaxyRefine for energy minimization and refinement, will that be a good decision? Is there any other web server based tool for 3D pdb structure refinement, as I want to proceed further for molecular docking?
Please help. Thanks ---Sunzid.
You can use GalaxyRefine for structural refinement. It is a reliable tool. Many publications has mention of this tool.
Dear Sunzid,
Yes, of course. GalaxyRefine is very reliable and is highly recommended. It improves the structure conformation by reducing poor rotamers, unstable bond torsions and outliers by packing and reorienting the side chains by molecular dynamics simulations.
I myself have used this server for some of my publications.
For performing energy minimisations, you can use the standalone Swiss-PDV viewer which uses GROMOS96 force field mechanics to perform the same.
As an alternate server for structure refinement, you may delve into 3D-Refine server whose link is given below: http://sysbio.rnet.missouri.edu/3Drefine/faq.html#:~:text=3D%20refine%20server%20is%20a%20web%20service%20for,on%20the%20optimized%20model%20using%20a%20composite%20
Regards
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