Sometime this may be a silly question because I'm new to this field.
In 3Drefine server, it mentioned that it applies atomic-level energy minimization on the optimized model using a composite physics and knowledge-based force fields. My question is,is that refinement and energy minimization both do the same change to a structure or they are different. If these servers do different changes in structure, shall i need to go through both servers before do my protein-protein molecular docking
Dear Shamali Abeywardhana ,
I would like to recommend you the following articles:
https://dx.doi.org/10.3390%2Fijms20092301
https://dx.doi.org/10.1093%2Fnar%2Fgkx249
Article 3Drefine: an interactive web server for efficient protein st...
Article Princeton_TIGRESS: ProTeIn Geometry REfinement using Simulat...
Hope it helps
Shamali Abeywardhana
Hope you doing well
After modelling your model you can align and minimize by PyMOL and SPDB viewer.
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