Abbreviations β<sub>2</sub>m β<sub>2</sub>-microglobulin 3D three dimensional AD Alzheimer's disease ADT AutoDock Tools DRA Dialysis-related amyloidosis DSSP dictionary of secondary structure of proteins FEL free energy landscape GROMACS GROningen MAchine for Chemical Simulations LGA Lamarckian Genetic Algorithm LINCS LINear Constraint Solver MC main chain MD molecular dynamics MHC-I major histocompatibility complex class I MM-PBSA molecular mechanics Poisson-Boltzmann surface area PME nanometer (nm); particle mesh ewald PCA principal component analysis PDB protein data bank <i>R</i><sub>g</sub> radius-of-gyration RSV rifamycin SV RMSD root-mean-square deviation RMSF root-mean-square fluctuation SC side chain SPC simple point charge SASA Solvent accessible surface area VMD visual molecular dynamics Communicated by Ramaswamy H. Sarma.
In the present study, four synthetic flavonoid derivatives (1, 2, 3 and 4) were examined for docking studies with Amyloid beta (PDB Code: 1IYT) and Amyloid fibril (PDB Code: 2BEG).