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Exact(5)
For simplicity, only single molecular conformation was considered in this study although multiple conformations for a molecule should be taken into account to further improve the solvation free energy function.
We have demonstrated the presence of multiple conformations for trinucleotide repeat junctions in a short DNA oligo model.
Since then, structural studies of SHP-1, and its paralog phosphatase SHP-2, have revealed multiple conformations for the SHP phosphatases.
The water located between the iron and the distal histidine showed elongated density in both structures (Additional file 1: Figure S7B and D), which might indicate multiple conformations for this molecule (which also binds conserved R43).
Some applications also require a huge number of dockings, such as ensemble docking techniques using multiple conformations for flexible docking (Grünberg et al., 2004; Król et al., 2007), cross-docking for identification of protein interaction partners (Lopes et al., 2013; Matsuzaki et al., 2009; Wass et al., 2011; Zhang et al., 2014) and multiple docking (Karaca and Bonvin, 2011).
Similar(55)
One method for including flexibility in the docking experiment is to perform ensemble docking [ 15], which uses multiple conformations of the protein for evaluation.
First, the lack of a clear isosbestic point in HmHR suggested that there are either multiple binding sites for the chloride or multiple conformations of the protein, but not in HwHR.
At least three lines of evidence were proposed from experimental measurements for the co-existence of multiple conformations of P-Lec EGF domains.
There are multiple conformations of plasminogen and the protein populates the various forms.
If multiple conformations of the target protein are solved using NMR or X-Ray studies, these are good candidates for ensemble docking.
sdfMMConfAnalysis was used to analyze the strain energy for each conformation resulting in multiple conformations with energies for each input as described under "implementation".
Related(20)
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