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This automated webserver enables docking of small molecules with a broad range of Protein Structures available in the Protein Drug Target Database (PDTD) (http://www.dddc.ac.cn/pdtd/) [ 4].
(271) This enables docking of the ubiquitin E3 ligase complex(111) consisting of Skp1, Cul-1, Roc1, and βTrCP that ubiquitylates IκBα on adjacent lysine residues 21 and 22, leading to the destruction of the inhibitor protein by the proteasome and translocation of the NFκB dimer to the nucleus to activate transcription.
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This study will also enable docking its known interactors, such as ApoER2 and VLDLR, perhaps involving domains R3 and R4 or R7 and R8, as R5 R6 is implicated in dimer formation.
These dimers become phosphorylated and enable docking of cytoplasmic proteins involved in signal transduction (Negro et al., 2004).
This development enables the docking process to be quantified in terms of the number and identities of the pharmacophoric hypotheses that can be matched by a compound or a library of compounds.
The conformation selection theory thereby affords parallel computing and enables a docking study to be performed on thousands of IBM Blue Gene processors with high processor utilization [6] [8].
The conformation selection theory thereby affords parallel computing and enables a docking study to be performed using thousands of IBM Blue Gene processors with high processor utilization [6] [8].
These findings suggest that small molecules prefer to adopt local minimum conformations when binding to proteins and theoretically support the virtual screening methods that use local minimum conformations to enable massively parallel docking [6], [8], [14].
This would enable blind docking of peptides without any prior knowledge about either the binding site location or the peptide backbone conformation.
Clear rod-like densities of transmembrane helices enabled accurate docking of an atomic homology model of E. coli SecYEG (Bostina et al., 2005; Deville et al., 2011; Figures 2A and 2C 2E).
To benefit from this concept, which has been known since 2000, it is essential to develop and improve new tools that enable molecular docking simulations of fully-flexible receptor models.
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