ZDOCK predictions for the CAPRI challenge

• Published in: Proteins, structure, function, and bioinformatics Vol. 52; no. 1; pp. 68 - 73
• Main Authors: Chen, Rong, Tong, Weiwei, Mintseris, Julian, Li, Li, Weng, Zhiping
• Format: Journal Article
• Language: English
• Published: Hoboken Wiley Subscription Services, Inc., A Wiley Company 01.07.2003
• Subjects: Algorithms; alpha-Amylases - chemistry; alpha-Amylases - metabolism; Animals; Antibodies - chemistry; Antibodies - immunology; Antigens, Viral; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; blind test; CAPRI; Capsid Proteins - chemistry; Capsid Proteins - immunology; desolvation; electrostatics; Exotoxins - chemistry; Exotoxins - metabolism; Hemagglutinins - chemistry; Hemagglutinins - immunology; Macromolecular Substances; Membrane Proteins - chemistry; Membrane Proteins - metabolism; Models, Molecular; Phosphoenolpyruvate Sugar Phosphotransferase System - chemistry; Phosphoenolpyruvate Sugar Phosphotransferase System - metabolism; protein docking; Protein Interaction Mapping; Protein-Serine-Threonine Kinases - chemistry; Protein-Serine-Threonine Kinases - metabolism; Proteins - chemistry; Proteins - metabolism; Receptors, Antigen, T-Cell, alpha-beta - chemistry; Receptors, Antigen, T-Cell, alpha-beta - metabolism; shape complementarity; ZDOCK
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.10388

The CAPRI Challenge is a blind test of protein–protein‐docking algorithms that predict the complex structure from the crystal structures of the interacting proteins. We participated in both rounds of this blind test and submitted predictions for all seven targets, relying mainly on our Fast Fourier Transform based algorithm ZDOCK that combines shape complementarity, desolvation, and electrostatics. Our group made good predictions for three targets and had at least some success with three others. Implications of the treatment of prior biological information as well as contributions of manual inspection to docking predictions are also discussed. Proteins 2003;52:68–73. © 2003 Wiley‐Liss, Inc.