The identification of heparin-binding sites is important for understanding the physiological function of many secreted proteins. Most of the experimental techniques for mapping these sites do not define them to atomic resolution. The use of automated docking methods can aid this process by facilitating both the design of experiments and visualization of their results. A method designed for a systematic search over the whole protein surface for heparin-binding sites, using heparin oligosaccharide structures as ligands, is described, with its validation and details of several published applications. The scope and limitations of this crude but effective computational chemistry method are discussed.
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Conference Article| May 22 2006
Computational approaches to the identification of heparin-binding sites on the surfaces of proteins
B. Mulloy 2
1NIBSC (National Institute for Biological Standards and Control), Blanche Lane, South Mimms, Potters Bar, Herts. EN6 3QG, U.K.
2To whom correspondence should be addressed, at Laboratory for Molecular Structure, NIBSC (email firstname.lastname@example.org).
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Publisher: Portland Press Ltd
Received: December 19 2005
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2006 The Biochemical Society
M. Forster, B. Mulloy; Computational approaches to the identification of heparin-binding sites on the surfaces of proteins. Biochem Soc Trans 1 June 2006; 34 (3): 431–434. doi: https://doi.org/10.1042/BST0340431
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