Pocket extraction on proteins via the Voronoi diagram of spheres.
Proteins consist of atoms. Given a protein, the automatic recognition of depressed regions, called pockets, on the surface of proteins is important for protein-ligand docking and facilitates fast development of new drugs. Recently, computational approaches have emerged for recognizing pockets from the geometrical point of view. Presented in this paper is a geometric method for the pocket recognition which is based on the Voronoi diagram for atoms. Given a Voronoi diagram, the proposed algorithm transforms the atomic structure to meshes which contain the information of the proximity among atoms, and then recognizes depressions on the surface of a protein using the meshes.
Kim
Donguk
D
Voronoi Diagram Research Center, Hanyang University, Seoul, Republic of Korea.
Cho
Cheol-Hyung
CH
Cho
Youngsong
Y
Ryu
Joonghyun
J
Bhak
Jonghwa
J
Kim
Deok-Soo
DS
D000465:Algorithms; D001665:Binding Sites; D017076:Computer-Aided Design; D015195:Drug Design; D008024:Ligands; D008958:Models, Molecular; D015394:Molecular Structure; D004364:Pharmaceutical Preparations / Q000737:chemistry* / Q000378:metabolism; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D013499:Surface Properties; D009626:Terminology as Topic
D008024:Ligands; D004364:Pharmaceutical Preparations; D011506:Proteins