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However, in the absence of transposon ends, the drug adopts an unusual, compact binding mode distinct from that observed in the active site of the prototype foamy virus integrase.
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Our integrated analyses reveal that half of the marketed drugs and most of the drugs in clinical trials that interact with peptide GPCRs are small molecules with a wide range of binding modes distinct from those of large peptide ligands.
Crystal structures of LepB313-618 andne and the GAP domain of Legionella drancourtii LepB in complex with Rab1-GDP-AlF3 support the catalytic role of Arg444, and also further reveal a 3D architecture and a GTPase-binding mode distinct from all known GAPs.
The observed binding mode appears distinct from other single motif binding interactions, as well as from mechanisms that involve global conformational transitions, such as folding upon binding (Csermely et al., 2010; Wright and Dyson, 2009).
However, we do not observe the P+0 residue in any of our structures, which leaves open the possibility that the observed binding mode is distinct from that of true substrates.
More importantly, the structures reveal a 3D fold and a GTPase-recognition mode distinct from those of all known GAPs.
The observed SWI/SNF nucleosome binding mode is highly distinct from the prevailing model in which nucleosomes are either bound in a cleft of SWI/SNF (Dechassa et al., 2008) or are caged by RSC (Chaban et al., 2008).
b 2D binding mode found from XP P1. c 2D binding mode found from XP P1.
The binding mode obtained from the docking simulation was further used for structure optimization of vibralactone.
b 2D binding mode from SP P1. c 2D binding mode from SP P1.
The binding mode was proposed from a docking study.
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