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Two Complementary Methods for Relative Quantification of Ligand Binding Site Burial Depth in Proteins: The "Cutting Plane" and "Tangent Sphere" Methods
[article]
2015
arXiv
pre-print
We describe two complementary methods to quantify the degree of burial of ligand and/or ligand binding site (LBS) in a protein-ligand complex, namely, the "cutting plane" (CP) and the "tangent sphere" (TS) methods. To construct the CP and TS, two centroids are required: the protein molecular centroid (global centroid, GC), and the LBS centroid (local centroid, LC). The CP is defined as the plane passing through the LBS centroid (LC) and normal to the line passing through the LC and the protein
arXiv:1505.01142v1
fatcat:qznfsp3gavcf5d7o7fmcdpis5u