I am having problem in the selection of monomeric human insulin pdb structure for the development of aptamer via molecular docking and molecular dynamics. How should I select the best suit one which represent the native structure of active insulin in human body. Which technique is preferred, is it X-ray diffraction or NMR structure? Based on the validation report, I found out that there are outliers in all the pdb structure, how should I fixed it. Before molecular analysis, the pdb structure should be properly checked and repaired, is there any detailed guidelines/protocol on this? I have no idea on how to identify the errors (things to be investigated) and the way to fix it. Your opinion is highly appreciated, thank you.
Hi Chong I would select the structure with a combination of best Resolution
and the least un-modeled residues that are pivotal to its activity. Subsequently I would model any un-modeled residues that are pivotal to its activity (Modeller etc.), hope this helps and feel free to inquire further:)
Hi Chong your very welcome:) and within your PDB Structure there may be unmodeled residues (see-attached screenshot example exhibiting unmodeled residues 88-99 in top right corner and exhibited in grey shading marked > UNMODELED); you will need to scan your PDB Structure similarly and literature search to select the best PDB Structure (i.e. a structure with pivotal and most residues modeled preferably) and then if you must, model the missing residues (MODELLER etc.).
Feel free to inquire further if needed:)
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