Insights into the Molecular Mechanisms of Protein-Ligand Interactions by Molecular Docking and Molecular Dynamics Simulation: A Case of Oligopeptide Binding Protein

Algorithm 3

Pseudocode of LRDPSO.

(1)	Initialize the positions and velocities of all the particles randomly;
(2)	Evaluate the docking energy value f(Xi,n);
(3)	Set the personal best position of each particle to be its current position;
(4)	Set n = 0;
(5)	While (termination condition = false) do
(6)	n = n + 1;
(7)	Compute mean best position Cn according to equation (3);
(8)	For (i = 1 to M)
(9)	Update the personal best position (Pi,n) and global best position (Gn);
(10)	Calculate the velocity Vi,n+1 using equation (1);
(11)	Calculate the position Xi,n+1 using equation (2);
(12)	Evaluate the docking energy value f(Xi,n+1);
(13)	End for
(14)	Apply the Solis and Wets to the best particle among all Xi,n+1;
(15)	For (i = 1 to M)
(16)	if Xi,n+1 better than Pi,nthen
(17)	Pi,n+1 = Xi,n+1;
(18)	else
(19)	Pi,n+1 = Pi,n;
(20)	End for
(21)	End while
(22)	Return the best position among all Pi,n as optimal solution;