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Aquaria: Simplifying discovery and insight from protein structures

Abstract

Viewing 3D models of a protein?s molecular structure can give insight into function, especially when mapped with sequence features (e.g., domains, SNPs, or post-translational modifications). Homology-based 3D models are now available for many proteins, however it is often difficult to find the most relevant models and to map sequence features onto them. Thus we developed Aquaria, a new web resource that provides 46 million models (more than double the number previously available) derived from a systematic all-against-all comparison of SwissProt and PDB sequences. Aquaria provides at least one model for 87% of SwissProt proteins, with a median of 35 models per protein. Aquaria has been designed for ease of use, so that more life scientists can advance their research by taking advantage of the wealth of structural data now available. We demonstrate its utility by applying Aquaria to derive new insight into the human proteins p53 and GLUT-4. Aquaria is freely available at http://aquaria.ws.

Type Journal
Authors O'Donoghue, S. I.; Sabir, K. S.; Kalemanov, M.; Stolte, C.; Wellmann, B.; Ho, V.; Roos, M.; Perdigao, N.; Buske, F. A.; Heinrich, J.; Rost, B.; Schafferhans, A.
Garvan Authors Dr Sean O'Donoghue
Publisher Name NAT METHODS
Published Date 2015-02-01 00:00:00
Published Volume 12
Published Issue 2
Published Pages 98-99
URL http://www.ncbi.nlm.nih.gov/pubmed/25633501
Status Published in-print