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We analyzed the binding mode between the inhibitors and 3MST.
The binding mode between the compound of interest and Abl 1 was elucidated using in silico docking.
Further, our analysis of the binding mode between the inhibitors and 3MST has provided the experimental support for the ping-pong enzymatic mechanism of 3MST with 3MP as a substrate.
In addition, docking simulation also carried out in this study to give a potent prediction binding mode between the small molecule and PKL1 (PDB code: 1umw) protein.
In addition, docking simulation also carried out in this study to give a potent prediction binding mode between the small molecule and ecKAS III (PDB code: 1hnj) protein.
In this paper, an intensive study on alkaloid ligand/G4 DNA interaction has been conducted, demonstrating that the end-stacking interaction is the favorable binding mode between the oncogene-related Pu22 G4 DNA and the heterocyclic alkaloid ligand.
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Molecular docking was employed to explore the binding mode between these compounds and the receptor, as well as help understanding the structure activity relationship revealed by CoMFA and CoMSIA.
The binding mode between this kind of compounds and the DHFR enzyme in addition to the key amino acid residues were explored by molecular docking simulation.
Protein structure prediction codes based on the associative memory Hamiltonian were used to probe the binding modes between the nuclear localization signal (NLS) polypeptide of NF-κB and the inhibitors IκBα and IκBβ.
The binding modes between the compound and aurora kinases were interpreted using in silico docking experiments to explain the selective inhibitory effects on aurora kinases A and B. These findings will facilitate the design of potent novel benzochalcones as anticancer agents.
Interestingly, the proposed binding modes between the nascent peptide and the β2 strands from the POTRA domains in the periplasmic ring are also in a parallel fashion (Fig. 1).
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