I am new to MD simulation for Protein - protein complex , sorry for asking some basic questions !
1. What Kind of information it will provide if I do MD simulation for protein complex after docking ?
2. How to analyses results if i use MD softwares like AMBER , NAMD or Gromacs ?
3.How to compare these simulation result with Experimental result ( if any ) ?
Dear Mr. Penumutchu, hear are my answer for your questions. Hope these answer satisfies you.. :)
1. If you conduct a MD simulation for protein complex after docking, you may predict its stability based on the curve of simulation time versus potential energy of the complex. This complex stability calculation thus very important to obtain the best ligands or lead compounds.
2. To answer this question maybe you have to see the software manual. Usually, to analyze the MD simulation results you have to draw curve between potential energy of the complex versus simulation time or RMSD/RMSF (root mean square deviation/fluctuation) versus simulation time.
3. You could compare the RMSD/RMSF curve between simulation result and experimental result from protein data bank (PDB) and then you could conclude is your simulation result valid or not.
Dear Mr. Penumutchu, hear are my answer for your questions. Hope these answer satisfies you.. :)
1. If you conduct a MD simulation for protein complex after docking, you may predict its stability based on the curve of simulation time versus potential energy of the complex. This complex stability calculation thus very important to obtain the best ligands or lead compounds.
2. To answer this question maybe you have to see the software manual. Usually, to analyze the MD simulation results you have to draw curve between potential energy of the complex versus simulation time or RMSD/RMSF (root mean square deviation/fluctuation) versus simulation time.
3. You could compare the RMSD/RMSF curve between simulation result and experimental result from protein data bank (PDB) and then you could conclude is your simulation result valid or not.
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