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

Concepts

Life SciencesBioinformaticsBiophysicsComputational BiologyStructural BioinformaticsStructural BiologyMolecular DockingProtein DockingProtein StructureProtein-ligand DockingProtein-protein DockingProtein-protein Interaction ModelingComputational Protein-protein DockingMultimer DockingProtein ComplexesProtein-protein-ligand DockingRigid-body DockingRigid-body Protein-protein Docking

TL;DR

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. The authors present a user‑friendly protein docking server to predict structures of protein–protein complexes and symmetric multimers. The server is based on the rigid‑body docking programs ZDOCK and M‑ZDOCK and offers an accessible interface that allows users to guide scoring, select output models, and dynamically visualize input structures and docking results. The server enables researchers to quickly and easily generate structural models of protein–protein complexes and symmetric multimers for their own analysis. The ZDOCK server is freely available to all academic and non‑profit users at http://zdock.umassmed.edu; no registration is required, and contact emails are brian.pierce@umassmed.edu or zhiping.weng@umassmed.edu.

Abstract

Abstract Summary: 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