Computational protocol: Investigation of Estrogen Receptor (ESR1) for Breast Cancer from Traditional Chinese Medicine

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Protocol publication

[…] The LigandFit module [], a receptor-rigid docking algorithm program in Discovery Studio 2.5 (DS 2.5), was used for docking simulations of Raloxifene and TCM compounds to ESR1 in the CHARMm force field []. The docking site of ESR1 was designed on the basis of the research [, ]. Through docking simulation, the top two compounds with the highest docking scores of the TCM compounds were selected to make the analysis of the hydrophobic interactions by Ligplus [, ]. [...] The ligands of candidate complex must be reprepared before applying MD simulation by using SwissParam (http://swissparam.ch/) [] based on the reference force field [] of GROMACS 4.5.5 []. The ESR1, with ligands, was placed in a simulation box in an appropriate buffer or other solution at a minimum distance of 1.2 Å from the complex. The solution for simulation was based on the TIP3P water model in which sodium and chloride ions were added to neutralize complex charges. Based on the Steepest Descent method for 5,000 steps to minimize the complex, the structure with the lowest energy was transferred to MD simulation. The electrostatic interactions were calculated on the basis of the particle-mesh Ewald (PME) method []. The calculation with each time step was 2 fs and the numbers of steps were 5,000,000 times then the total simulation time of MD was 10,000 ps. The equilibration under the 100 ps constant temperature (PER ensemble) was based on the Berendsen weak thermal coupling method. The protocols in Gromacs used the MD data to calculate the MD trajectories, RMSD, energy variations, and eigenvector after MD. […]

Pipeline specifications

Software tools PHENIX, CHARMM, SwissParam, GROMACS
Applications Drug design, Protein structure analysis
Diseases Breast Neoplasms
Chemicals Estrogens, Hydrogen, Raloxifene Hydrochloride