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In fact, when NQTrp is involved in hydrogen bonds with the backbone of the Phe20-Glu22 region, the naphthoquinone and the indole ring are able to "clamp" the phenyl ring of either Phe19 or Phe20, as shown in three of the four most frequent binding modes (Figure 7).
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In the most frequent binding mode that was generated for core fragment B in the kinases of the docking panel the exocyclic amino group pointed toward the gatekeeper and the nitrogen atom bridging the heterocycles was placed next to the hinge region.
The binding modes depicted in Figure 6 were determined by selecting the simultaneous and most frequent hydrogen bonds between the peptide backbone and NQTrp (see Table S4).
NF-κB dimers bind to different κB sequences with different binding affinities and binding modes.
The sampling component generates sufficient putative binding modes.
Reportedly, conventional SFs are able to predict binding modes while mostly failed to predict binding affinities.
The probable mechanisms and the proposed binding modes were discussed.
The two types of binding interfaces differ also in their binding modes to HBGAs.
We also found the binding modes with lowest energy generated from other 5 trials shared some common features with the native binding mode in the last trial.
Cohesin:Dockerin dual binding modes.
Different ATP binding modes in ELK groups.
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