Using molecular docking, molecular dynamics and analysis of conserved waters in the binding site, we identified a favourable binding mode for piperidin-4-yl and 4-cyclohexyl pyrrole-2-carboxamides while predicting unfavourable interactions with the active site for piperazine pyrrole-2-carboxamides.
Using ELISA-type solid phase binding assays, we identified a F3-binding site to a region between BBK32 residues 146 and 205 (data not shown).
Based on our analyses of the ES gene expression profiles and binding sites of potential cofactors in vicinity of the ChIP-seq TF binding locations, we identified a list of co-binding features that show significantly different characteristics between different gene expression patterns (activated or repressed gene expression in ES cells) at a false discovery rate of 10%.
With G-actin and F-actin binding assays, we identified a CapG nanobody that binds with nanomolar affinity to the first CapG domain.
From the 4 candidates of the Lq2-K+ channel binding models, we identified a good three-dimensional model of Lq2-K+ channel complex through triplet contact analysis, electrostatic interaction energy estimation by BD simulation and structural refinement by molecular mechanics.
So, combining surface and electron donor-acceptor profile of the selected region at ATP binding site, we identified a pharmacophore that can be potentially employed to design DDX3X specific ATP analog (Figure 4C).
Using isothermal titration calorimetry (ITC -based quantITC -basednding assays, we identified a 48-residue auto-inhibitory segment (residues 1577–1624, referred to as 'AS') as the complete ANK repeat-binding region.
Using the MatInspector program, which uses TRANSFAC transcription factor binding site matrices, we identified a number of putative transcription factor binding sites upstream of the Jab1 transcription start site.
We show that the nuclear localisation signal of EWS-Oct-4B is dependent on the POU DNA-binding domain, and we identified a cluster of basic amino acids, RKRKR, in the POU domain that specifically mediates the nuclear localisation of EWS-Oct-4B.
The nuclear localisation signal (NLS) of EWS-Oct-4B was dependent on the POU DNA-binding domain, and we identified a cluster of basic amino acids, RKRKR, in the POU domain that specifically mediates the nuclear localisation of EWS-Oct-4B.
