ZDOCK server: interactive docking prediction of protein–protein complexes and symmetric multimers

• Published in: Bioinformatics (Oxford, England) Vol. 30; no. 12; pp. 1771 - 1773
• Main Authors: Pierce, Brian G., Wiehe, Kevin, Hwang, Howook, Kim, Bong-Hyun, Vreven, Thom, Weng, Zhiping
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 15.06.2014
• Subjects: Algorithms; Applications Notes; Molecular Docking Simulation - methods; Multiprotein Complexes - chemistry; Protein Multimerization; Software
• ISSN: 1367-4803; 1367-4811; 1367-4811
• DOI: 10.1093/bioinformatics/btu097

Protein–protein interactions are essential to cellular and immune function, and in many cases, because of the absence of an experimentally determined structure of the complex, these interactions must be modeled to obtain an understanding of their molecular basis. We present a user-friendly protein docking server, based on the rigid-body docking programs ZDOCK and M-ZDOCK, to predict structures of protein–protein complexes and symmetric multimers. With a goal of providing an accessible and intuitive interface, we provide options for users to guide the scoring and the selection of output models, in addition to dynamic visualization of input structures and output docking models. This server enables the research community to easily and quickly produce structural models of protein–protein complexes and symmetric multimers for their own analysis. Availability: The ZDOCK server is freely available to all academic and non-profit users at: http://zdock.umassmed.edu. No registration is required. Contact:  brian.pierce@umassmed.edu or zhiping.weng@umassmed.edu