Circular Cone: A novel approach for protein ligand shape matching using modified PCA

Nowadays in modern medicine, computer modeling has already become one of key methods toward the discovery of new pharmaceuticals. And virtual screening is a necessary process for this discovery. In the procedure of virtual screening, shape matching is the first step to select ligands for binding protein. In the era of HTS (high throughput screening), a fast algorithm with good result is in demand. Many methods have been discovered to fulfill the requirement. Our method, called “Circular Cone”, by finding principal axis, gives another way toward this problem. We use modified PCA (principal component analysis) to get the principal axis, around which the rotation is like whirling a cone. By using this method, the speed of giving score to a pocket and a ligand is very fast, while the accuracy is ordinary. So, the good speed and the general accuracy of our method present a good choice for HTS.