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  • To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite. To mitigate this issue, we developed eMatchSite, a new algorithm that performs sequence order-independent local binding site alignments using computer-generated protein models. The performance of eMatchSite is evaluated using several datasets and compared to other algorithms for binding site matching in large-scale benchmarking calculations.
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