How can I study the effect of a ligand on the enzyme structure using computational tools?

Najmeh Hadizadeh Shirazi @Najmeh_Hadizadeh_Shirazi

11 November 2013 1 3K Report

The enzyme is obtained from wild bacteria. Its crystallographic structure has not been determined, but the structure of similar enzymes have been determined. How can I study the effect of a ligand on the enzyme structure using computational tools?.

Hamed Haghshenas

Dear Miss Hadizadeh,

Actually you have two problem with your protein.First you need a molecular modelling software (such as MODELER,etc) for modelling your protein. Then you need a molecular dynamics software such as Amber , gromacs , .....

this packages can compute effect of ligands on protein structure using RMSD , do-dssp ,... analysis.If you need more information about details contact with me using below email:

[email protected]

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