Figure 1 | Scientific Reports

Figure 1

From: Difference of binding modes among three ligands to a receptor mSin3B corresponding to their inhibitory activities

Figure 1

Density \(Q_{cano} \left( {\lambda^{\left( \alpha \right)} ,\lambda^{\left( \beta \right)} ,\lambda^{\left( \gamma \right)} } \right)\) of (a) the sertraline–mSin3B, (b) YN3–mSin3B, and (c) acitretin–mSin3B systems in the 3D-RC space. In GA-guided mD-VcMD, the distribution is defined originally by \(Q_{cano} \left( {L^{\left( \alpha \right)} , L^{\left( \beta \right)} ,L^{\left( \gamma \right)} } \right)\), where \(L^{\left( \alpha \right)} ,\; L^{\left( \beta \right)}\), and \(L^{\left( \gamma \right)}\) are respectively indices to specify the positions \(\lambda^{\left( \alpha \right)}\), \(\lambda^{\left( \beta \right)}\), and \(\lambda^{\left( \gamma \right)}\) in the 3D-RC space. Then, we convert \(\left[ {L_{i}^{\left( \alpha \right)} , L_{j}^{\left( \beta \right)} ,L_{k}^{\left( \gamma \right)} } \right]\) to: \(\lambda_{i}^{\left( h \right)} = 0.5\left\{ {\left[ {\lambda_{i}^{\left( h \right)} } \right]_{min} + \left[ {\lambda_{i}^{\left( h \right)} } \right]_{max} } \right\}\), where \(i = 1, \ldots ,n_{vs} \left( h \right)\) (\(h = \alpha ,\;\beta ,\; \gamma\)). See Supplementary Table S3 for values of \(\left[ {\lambda_{i}^{\left( h \right)} } \right]_{min}\), \(\left[ {\lambda_{i}^{\left( h \right)} } \right]_{max}\), and \(n_{vs} \left( h \right)\). Then, \(Q_{cano} \left( {\lambda^{\left( \alpha \right)} ,\lambda^{\left( \beta \right)} ,\lambda^{\left( \gamma \right)} } \right)\) is normalized so that the highest density is set to 1. Contour levels are presented by colors in inset.

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