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By exploring the binding interface of molecular interaction, the amino acids in the binding interface between Ang2 and an aptamer can be analyzed for finding out whether the aptamer with the best pose binds with the Ang2 receptor-binding domain or not.
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Systematic search generates all possible ligand binding conformations by exploring the whole conformational space.
To validate the robustness of our general observations, we constructed several predictive transcriptional binding networks by exploring the parameter space.
We gained insight into the dynamics of sodium ion transport and the possible location of the principal binding site by exploring the Na+ concentration dependence of the photocycle transitions monitored at characteristic wavelengths.
By exploring the protein sulfate complex, we have defined the sulfate binding site architecture.
By exploring the geometry of contact distribution at protein-protein interfaces, we provide an improved model of binding energy.
DOI: http://dx.doi.org/10.7554/eLife.00691.010 To further analyze the apparent membrane affinity loss conferred by PTEN tail phosphorylation, we explored the binding interactions of semisynthetic PTENs with vesicles containing anionic phospholipids.
Scoring function is at the heart of molecular docking by assisting a docking program to efficiently explore the binding space of a ligand.
Additionally, molecular docking of compounds explored the binding affinity of highly active and least active compounds with its receptor by using GOLD docking suit [12].
Our molecular docking platform explored the binding association of various drugs inside the binding pocket, but did not analyze the peptide's binding affinity for these drugs.
The research involved virtual screening of 37 different molecules by molecular docking studies performed by Molecular Design Suite (MDS) into the ligand binding domain of PPAR-γ receptor to explore the binding affinity and conformations of the molecules.
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