The ZDOCK server is a user-friendly web-based tool for predicting the structures of protein-protein complexes and symmetric multimers. It is based on the rigid-body docking programs ZDOCK and M-ZDOCK, which use the Fast Fourier Transform algorithm for efficient global docking searches on a 3D grid. The server allows users to guide the scoring and selection of output models, and provides dynamic visualization of input structures and output docking models. The ZDOCK server is freely available to all academic and non-profit users at http://zdock.umassmed.edu. It has undergone major improvements to enhance docking performance, functionality, and user interface. The server allows users to generate sets of predictions in PDB format from job output files with a Java program. Jobs are run on a dedicated computer server at the University of Massachusetts Medical School with 128GB RAM and 64(2.2GHz) cores. Each ZDOCK and M-ZDOCK job is parallelized using Message Passing Interface (MPI) to run on eight cores. A Perl script on the backend server checks for jobs to submit, submits jobs, checks for completed jobs and sends results to users. The ZDOCK and M-ZDOCK executables and code were not modified for the server from the downloadable and published algorithms; default sampling levels are used for all jobs. The ZDOCK Server has established a sizable user base. Since its move to the dedicated computer server at the University of Massachusetts 7 months ago, the ZDOCK Server has completed >6200 jobs from >1000 unique users. The average running time for jobs is 11.5 min. While this is significantly faster than most docking servers, its predictive performance is comparable with recently developed docking servers. The ZDOCK Server provides a fast and effective means to produce models of protein–protein complexes and symmetric multimers, via a user-friendly web interface. In addition to generating and viewing structures of docking models through the server's tools and interface, users have the option of submitting ZDOCK Server output files directly to several available docking refinement and post-processing tools (linked from the server page). In the future, possible developments include clustering and post-processing functionality directly on the server itself, in addition to other improvements based on user requests.The ZDOCK server is a user-friendly web-based tool for predicting the structures of protein-protein complexes and symmetric multimers. It is based on the rigid-body docking programs ZDOCK and M-ZDOCK, which use the Fast Fourier Transform algorithm for efficient global docking searches on a 3D grid. The server allows users to guide the scoring and selection of output models, and provides dynamic visualization of input structures and output docking models. The ZDOCK server is freely available to all academic and non-profit users at http://zdock.umassmed.edu. It has undergone major improvements to enhance docking performance, functionality, and user interface. The server allows users to generate sets of predictions in PDB format from job output files with a Java program. Jobs are run on a dedicated computer server at the University of Massachusetts Medical School with 128GB RAM and 64(2.2GHz) cores. Each ZDOCK and M-ZDOCK job is parallelized using Message Passing Interface (MPI) to run on eight cores. A Perl script on the backend server checks for jobs to submit, submits jobs, checks for completed jobs and sends results to users. The ZDOCK and M-ZDOCK executables and code were not modified for the server from the downloadable and published algorithms; default sampling levels are used for all jobs. The ZDOCK Server has established a sizable user base. Since its move to the dedicated computer server at the University of Massachusetts 7 months ago, the ZDOCK Server has completed >6200 jobs from >1000 unique users. The average running time for jobs is 11.5 min. While this is significantly faster than most docking servers, its predictive performance is comparable with recently developed docking servers. The ZDOCK Server provides a fast and effective means to produce models of protein–protein complexes and symmetric multimers, via a user-friendly web interface. In addition to generating and viewing structures of docking models through the server's tools and interface, users have the option of submitting ZDOCK Server output files directly to several available docking refinement and post-processing tools (linked from the server page). In the future, possible developments include clustering and post-processing functionality directly on the server itself, in addition to other improvements based on user requests.