Abstract
The increasing number of uncharacterized protein structures necessitates the development of computational approaches for function annotation using the protein tertiary structures. Protein structure database search is the basis of any structure-based functional elucidation of proteins. 3D-SURFER is a web platform for real-time protein surface comparison of a given protein structure against the entire PDB using 3D Zernike descriptors. It can smoothly navigate the protein structure space in real-time from one query structure to another. A major new feature of Release 2.0 is the ability to compare the protein surface of a single chain, a single domain, or a single complex against databases of protein chains, domains, complexes, or a combination of all three in the latest PDB. Additionally, two types of protein structures can now be compared: all-atom-surface and backbone-atom-surface. The server can also accept a batch job for a large number of database searches. Pockets in protein surfaces can be identified by VisGrid and LIGSITEcsc. The server is available at http://kiharalab.org/3d-surfer/.
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Acknowledgments
This work has been supported by grants from the National Institutes of Health (R01GM075004 and R01GM097528), National Science Foundation (EF0850009, DBI1262189, IOS1127027), and National Research Foundation of Korea Grant funded by the Korean Government (NRF-2011-220-C00004). The authors thank Kristen Johnson for proofreading the manuscript.
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Xiong, Y., Esquivel-Rodriguez, J., Sael, L., Kihara, D. (2014). 3D-SURFER 2.0: Web Platform for Real-Time Search and Characterization of Protein Surfaces. In: Kihara, D. (eds) Protein Structure Prediction. Methods in Molecular Biology, vol 1137. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-0366-5_8
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DOI: https://doi.org/10.1007/978-1-4939-0366-5_8
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