For my protein 3D structure prediction, I already used MODELLER 9.12 and built about 500 models, then chose the best model base on TM-score and RMSD. But when I do superimposition with my template, I find that all the models have a problem in superimposing one aminoacid residue that is in the active site .
It is difficult to give an exact answer without analyzing the set of structures, but superimposition can use all the atoms, just the alpha carbons or just the atoms around a part of the molecule. You could superimpose the structures using just the atoms next to the active site, for example around 5 to 8 angstroms apart. This can tell you if a mayor distortion on the rest of the structure occurs or if the deviation is due to a local deformation of the active site itself.
If the difference is that you posted on a picture, it seems not relevant to me. But if this is important for your work another source of dissimilarity might be the force field used for building the crystallographic structure respect to that used for modelling. Maybe most important, to a specific ligand to the amino acid in the crystal structure, absent in the model. This might be an inhibitor, ions or even water molecules. Please check your crystal structure for these type of interactions.
Good luck!
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