SwissDock is a web-based protein-small molecule docking service based on the EADock DSS engine. It provides a user-friendly interface for scientists to submit docking tasks and retrieve predicted complex structures. The service includes setup scripts to handle common issues and prepare target proteins and ligands. An efficient Ajax/HTML interface allows easy submission and retrieval of docking results. A SOAP interface is also available for automated tasks, with templates in Perl, Python, and PHP. The site offers access to a manually curated database of protein-ligand complexes and includes a wiki and forum for community interaction. SwissDock addresses challenges in docking by providing pre-curated protein structures and supporting various file formats. It allows users to select target proteins from the PDB or upload their own structures, and ligands from the ZINC database or upload their own files. The docking parameters can be set to different levels of accuracy, with options for fast, accurate, and very accurate docking. The results are visualized using Jmol and UCSF Chimera, and predicted binding modes can be downloaded. The performance of EADock DSS was evaluated using 251 test complexes from the Ligand Protein Database. With accurate parameters, the first predicted binding mode was within 2 Å of the crystal structure for 54.5% of the test complexes, increasing to 63.7% when considering the top five predictions. The success rate was higher for less flexible ligands, with 77% for SR0 and 86% for SR5. The performance was also influenced by the fraction of the ligand buried upon complexation. SwissDock is designed to be accessible to a wide audience, with automated setup of protein and ligand structures, multiple parameter presets, and convenient visualization and analysis tools. It is available at http://www.swissdock.ch and is intended to promote the use of docking tools beyond the traditional molecular modeling community. The service is supported by the Swiss Institute of Bioinformatics and provides computational resources through the VITAL-IT project.SwissDock is a web-based protein-small molecule docking service based on the EADock DSS engine. It provides a user-friendly interface for scientists to submit docking tasks and retrieve predicted complex structures. The service includes setup scripts to handle common issues and prepare target proteins and ligands. An efficient Ajax/HTML interface allows easy submission and retrieval of docking results. A SOAP interface is also available for automated tasks, with templates in Perl, Python, and PHP. The site offers access to a manually curated database of protein-ligand complexes and includes a wiki and forum for community interaction. SwissDock addresses challenges in docking by providing pre-curated protein structures and supporting various file formats. It allows users to select target proteins from the PDB or upload their own structures, and ligands from the ZINC database or upload their own files. The docking parameters can be set to different levels of accuracy, with options for fast, accurate, and very accurate docking. The results are visualized using Jmol and UCSF Chimera, and predicted binding modes can be downloaded. The performance of EADock DSS was evaluated using 251 test complexes from the Ligand Protein Database. With accurate parameters, the first predicted binding mode was within 2 Å of the crystal structure for 54.5% of the test complexes, increasing to 63.7% when considering the top five predictions. The success rate was higher for less flexible ligands, with 77% for SR0 and 86% for SR5. The performance was also influenced by the fraction of the ligand buried upon complexation. SwissDock is designed to be accessible to a wide audience, with automated setup of protein and ligand structures, multiple parameter presets, and convenient visualization and analysis tools. It is available at http://www.swissdock.ch and is intended to promote the use of docking tools beyond the traditional molecular modeling community. The service is supported by the Swiss Institute of Bioinformatics and provides computational resources through the VITAL-IT project.