Dear Gromacs Users, I want to do some simulations of the protein (its N anc C terminals) which crystal structure does not exist. I submitted the sequence to www.proteinmodelportal.org obtaining different structures based on different proteins from Protein Data Bank. For instance my N terminal has 180 aa. Obtained models covers %Seq id of 78% for 36 residues, 68% for 36 different residues, 62% of 36 another residues and many other models below 50%. The website provides you with the PDB files of your query so sounds perfect as you do not have to mutate every residue one by one. The question is whether this is efficent and provide a good result to use such protein in my simualtions? Is this app. too big? What are the other ways to overcome this problem (obtain structure of the protein which crystal structure does not exist?
Thank you in advance, Steven
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