Modelling of proteins

My objective is to model a protein for which the experimental structure is not known. I performed homology modeling using Modeller and performed Energy Minimisation (for 1ns) using GROMACS to improve the quality of the model. I have got 10000 pdb files from md.trr file using 'trjconv' command.

Now, the last pdb (that is, 10000th pdb file) has got 3 outliers when checked using Ramachandran plot. Is there any way, I can pick a better structure out of these 10000 structures generated, using any Bioinformatics tools?

proteins modelling

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updated 3.3 years ago by Ram

• written 9.5 years ago by shilpa.janarthanan •

If you just want to simulate a structure, based on homology (and/or ab initio methods if no suitable templates exist), why not try the I-TASSER suite? http://zhanglab.ccmb.med.umich.edu/I-TASSER/

It should perform all the energy minimisation etc you need and return 5 high scoring models.

(Your protein must be <1500AA

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written 9.5 years ago by Joe

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