Structural Bioinformatics is concerned with computational methods for the analysis and modeling of three-dimensional molecular structures. There is a plethora of computational tools available to work with structural data on a large scale. Using these tools on distributed computing infrastructures (DCI), however, is often hampered by a lack of suitable interfaces. The MoSGrid (Molecular Simulation Grid) science gateway provides an intuitive user interface to several widely used tools in structural bioinformatics. It ensures the confidentiality, integrity and availability of data via a granular security concept which covers all layers of the infrastructure. The concept applies SAML (Security Assertion Markup Language) and allows trust delegation from the user interface layer across the high-level middleware layer and the grid middleware layer down to the HPC facilities. SAML assertions had to be integrated into the MoSGrid infrastructure in several places: the workflow-enabled grid portal WS-PGRADE, the gUSE (grid User Support Environment) DCI services, and the cloud file system XtreemFS. The security infrastructure presented here allows single sign-on and thus lowers the hurdle for users to utilize large HPC infrastructures for structural bioinformatics.