The prediction of high-affinity and/or high-specificity protein–glycosaminoglycan (GAG) interactions is an inherently difficult task, due to several factors including the shallow nature of the typical GAG-binding site and the inherent size, flexibility, diversity, and polydisperse nature of the GAG molecules. Here, we present a generally applicable methodology termed Combinatorial Library Virtual Screening (CVLS) that can identify potential high-affinity, high-specificity protein–GAG interactions from very large GAG combinatorial libraries and a suitable GAG-binding protein. We describe the CVLS approach along with the rationale behind it and provide validation for the method using the well-known antithrombin–thrombin– heparin system.
CITATION STYLE
Sankaranarayanan, N. V., Sarkar, A., Desai, U. R., & Mosier, P. D. (2015). Designing “high-affinity, High-specificity” glycosaminoglycan sequences through computerized modeling. Methods in Molecular Biology, 1229, 289–314. https://doi.org/10.1007/978-1-4939-1714-3_24
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