I am preparing receptor files for docking.
I have a crystal structure which is a homodimer. It has some residues missing in 1of the monomer but resolved in the other. It also has some residues absent in both monomers( 10 in the N-terminus & 3 residues at C-terminus). I modelled the protein's missing portions with Modeller and the resulting structure has the following problems :
1. There is a 3-10 helix in 1 of the loops in the original PDB 's A chain but this is not being modelled by Modeller in the B chain in which it is missing .....
I checked the documentation of Modeller but could not find anything about modelling 3-10 helices .....
2. The model is poor in quality compared to original PDB...There are 5 ramachandran outliers while the original PDB has none.
I used Molprobity to fix the model but still I am getting the same 5 outliers in Ramachandran Plot.
How to improve the quality of the model ?
Is there any tool to model 3-10 helices ?
Creating the secondary structure is possible in Ambertools and Avogadro softwares.
Dear jay
Missing terminal residues of a protein is not a big deal.I have seen this problem in almost 90 percent of pdb structures.You can simply ignore that due to the small effect of terminal residues on protein structure. To further ensure, check your protein structure using a visualization software like VMD. your terminal residues should be far away from active site of protein.
Do not worry about it !! Just ignore terminal residues.
Best
I am not sure but I guess Discovery studio Visualizer has the capability to model 3-10 helix. Just have a look at it.
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