I am trying to model a protein using swissmodel then assess it with Procheck. When I try to minimize the energy, ramachandran plot result shows that the quality of the protein has decreased compared with before the energy minimalization.
How you are doing energy minimization? Why you woun't use manual modelling method by Modeller as SWISS-MODELING is not a good way. please tell me what percentage of residues are contained in the conserved region and prohibited region of that plot if you finish it, otherwise i must say try manual methods.
Ashfaq Ahmad
Depending on your needs and time you have available I would recommend PyRosetta for modeling.
http://www.pyrosetta.org/home
We use this in our lab. The documentation is great and there is a good user support community.
Itasser is best modeling server, add hydrogen to ue protein model first then minimiz it under suitable force field, i,e AMBER99 normally for proteins.
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