I have constructed a protein-carbohydrate complex based on available 3D structures. Since I did some manual adjustments in the carbohydrate structure, it is needed some kind of energy minimization in order to eliminate bad interactions and achieve a correct structure for this complex.
Most of the online servers for energy minimization and MD simulation are not suitable for structures with ligands, specially carbohydrates. GLYCAM-Web seems to have tools for carbohydrate docking and glycoprotein construction, but not specifically for energy minimization of protein-carbohydrate complexes.
It would be very useful if you can suggest any program or online server that can readily do energy minimization for these complexes.
I doubt there is a free, rigorous, energy minimization available online that especially doing a good job on protein-carbohydrate interaction. please share with me if you find out later. (A very powerful experimental approach for protein-carbohydrate interaction is STD NMR.)
Hi Shidong,
Yesterday I tried the YASARA force field minimization server. It seems that their programs are able to automatically recognize a parametrize pretty much any kind of molecule by using GAFF. So, it ended up working, though I don't know exactly how to evaluate the quality of this work. They don't give you the freedom to choose minimization parameters. I'm guessing that the best option is to run a MD simulation using AMBER/GLYCAM in order to relax the system...
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