ProteMiner-SSM: a web server for efficient analysis of similar protein tertiary substructures.
Analysis of protein-ligand interactions is a fundamental issue in drug design. As the detailed and accurate analysis of protein-ligand interactions involves calculation of binding free energy based on thermodynamics and even quantum mechanics, which is highly expensive in terms of computing time, conformational and structural analysis of proteins and ligands has been widely employed as a screening process in computer-aided drug design. In this paper, a web server called ProteMiner-SSM designed for efficient analysis of similar protein tertiary substructures is presented. In one experiment reported in this paper, the web server has been exploited to obtain some clues about a biochemical hypothesis. The main distinction in the software design of the web server is the filtering process incorporated to expedite the analysis. The filtering process extracts the residues located in the caves of the protein tertiary structure for analysis and operates with O(nlogn) time complexity, where n is the number of residues in the protein. In comparison, the alpha-hull algorithm, which is a widely used algorithm in computer graphics for identifying those instances that are on the contour of a three-dimensional object, features O(n2) time complexity. Experimental results show that the filtering process presented in this paper is able to speed up the analysis by a factor ranging from 3.15 to 9.37 times. The ProteMiner-SSM web server can be found at http://proteminer.csie.ntu.edu.tw/. There is a mirror site at http://p4.sbl.bc.sinica.edu.tw/proteminer/.
Chang
Darby Tien-Hau
DT
Department of Computer Science and Information Engineering, National Taiwan University, Taipei, Taiwan, ROC.
Chen
Chien-Yu
CY
Chung
Wen-Chin
WC
Oyang
Yen-Jen
YJ
Juan
Hsueh-Fen
HF
Huang
Hsuan-Cheng
HC
D001665:Binding Sites; D020169:Caspases / Q000737:chemistry / Q000378:metabolism; D015195:Drug Design; D016023:Integrins / Q000737:chemistry / Q000378:metabolism; D020407:Internet; D008024:Ligands; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D012984:Software; D012985:Software Design; D040681:Structural Homology, Protein
D016023:Integrins; D008024:Ligands; D011506:Proteins; D020169:Caspases