Search space reduction technique for molecular docking calculation

Abstract

To dock organic ligands in to protein binding sides by using devide-and-conqure method. The method can be used in the virtual screening process of designing a specific protein ligand. The molecular surface energy representation of protein and ligand can be used to filter out by sorting algorithm along with indexing method. Object oriented paradigm, a powerful tool for data abstraction and encapsulation, can be used for accessing all index in real time. Sorting algorithm by heap sort can guarantee the fastest and time consistency regardless of the variation of input data. Combining all of these can make sure that all possible data can be search in the complete and optimum way. Computer graphic calculation is a really good in parallel computing. Introducing computer graphic calculation can guarantee parallelizable in the most effective way. This paper will introduce the new method by using energy based virtual screening to do the complete search of autodock grid map energy. The result of program is a position and orientation of ligand in enzyme. However, there are some missing angle and interpolation area between the grid map corners. This problem can be solved by doing recursive search in the near area of the first output data.