BACKGROUND: To understand the molecular mechanisms that give rise to a protein's function, biologists often need to (i) find and access all related atomic-resolution 3D structures, and (ii) map sequence-based features (e.g., domains, single-nucleotide polymorphisms, post-translational modifications) onto these structures. RESULTS: To streamline these processes we recently developed Aquaria, a resource offering unprecedented access to protein structure information based on an all-against-all comparison of SwissProt and PDB sequences. In this work, we provide a requirements analysis for several frequently occuring tasks in molecular biology and describe how design choices in Aquaria meet these requirements. Finally, we show how the interface can be used to explore features of a protein and gain biologically meaningful insights in two case studies conducted by domain experts. CONCLUSIONS: The user interface design of Aquaria enables biologists to gain unprecedented access to molecular structures and simplifies the generation of insight. The tasks involved in mapping sequence features onto structures can be conducted easier and faster using Aquaria.

Abstract Summary: In this paper we present SRS 3D, a new service that allows users to easily and rapidly find all related structures for a given target sequence; structures can then be viewed together with sequences, alignments and sequence features (currently from UniProt, InterPro and PDB). Extensive user feedback confirms that SRS 3D is intuitive and useful especially for those not expert in structures. Availability: An SRS 3D server is provided at http://srs3d.ebi.ac.uk/ Supplementary information: Complete documentation is available (click the ‘Help’ button after login). Product information can be found at http://www.lionbioscience.com/SRS3D/products/srs/srs-3d

SRS is a widely used system for integrating biological databases. Currently, SRS relies only on locally provided copies of these databases. In this paper we propose a mechanism that also allows the seamless integration of remote databases. To this end, our proposed mechanism splits the existing SRS functionality into two components and adds a third component that enables us to employ peer-to-peer computing techniques to create optimized overlay-networks within which database queries can efficiently be routed. As an additional benefit, this mechanism also reduces the administration effort that would be needed with a conventional approach using replicated databases.