A publicly available web resource that streamlines and simplifies the process of gleaning insight from protein structures. In contrast to most molecular graphics tools, the user interface of Aquaria is organized primarily by protein sequence, not structure. A user starts by specifying a protein of interest by name and organism, by identifier or by URL; Aquaria then generates a concise visual summary of all related PDB structures, using a precalculated all-against-all comparison of Swiss-Prot and PDB sequences (updated monthly). Aquaria is designed for biologists; its user interface creates clear and useful default views that show only the most relevant structural information tightly integrated with sequence, features and text that provide biological context.
Digital Productivity, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Sydney, Australia; Division of Genomics and Epigenetics, Garvan Institute of Medical Research, Sydney, Australia; School of Molecular Bioscience, The University of Sydney, Sydney, Australia; School of Information Technologies, The University of Sydney, Sydney, Australia; Department for Bioinformatics and Computational Biology, Technische Universität München, Munich, Germany; Instituto Superior Técnico, Universidade de Lisboa, Lisbon, Portugal; Instituto de Sistemas e Robótica, Lisboa, Lisbon, Portugal; St. Vincent's Clinical School, The University of New South Wales (UNSW), Sydney, Australia
Aquaria funding source(s)
This work was supported by CSIRO’s OCE Science Leader program and its Computational and Simulation Sciences platform, as well as the Alexander von Humboldt Foundation.