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. 2017 Apr 20;45(12):e110. doi: 10.1093/nar/gkx255

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© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 1. — Quantification of binding specificity. (A) Representative nucleic acid–ligand binding complex (PDB ID: 3NPN) with the RNA structure shown in molecular surface and the ligand shown in sticks, the native pose of the ligand is colored in red and the conformation ensemble is distributed within the docking box covering the binding pocket as well as its surrounding surface. (B) Binding energy spectrum for the conformation ensemble, the line for native conformation is colored in red. The binding energy of the conformation ensemble follow a statistical Gaussian-like distribution, from which the binding specificity is quantified with the dimensionless intrinsic specificity ratio (ISR) by (18,21,23,27). The energy gap (δE) is computed with <E > −E_N and the energy fluctuation or roughness (ΔE) is computed with , E_N is the binding energy of the native conformation and S is the conformational entropy of the ligand.

Inline graphic — Quantification of binding specificity. (A) Representative nucleic acid–ligand binding complex (PDB ID: 3NPN) with the RNA structure shown in molecular surface and the ligand shown in sticks, the native pose of the ligand is colored in red and the conformation ensemble is distributed within the docking box covering the binding pocket as well as its surrounding surface. (B) Binding energy spectrum for the conformation ensemble, the line for native conformation is colored in red. The binding energy of the conformation ensemble follow a statistical Gaussian-like distribution, from which the binding specificity is quantified with the dimensionless intrinsic specificity ratio (ISR) by (18,21,23,27). The energy gap (δE) is computed with <E > −E_N and the energy fluctuation or roughness (ΔE) is computed with , E_N is the binding energy of the native conformation and S is the conformational entropy of the ligand.