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In the example described below, vertices of the simplex (i.e. extreme pathways) were computed with standard linear-based methods in the bound case, and with probabilistic methods in the unbound case.
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On a test set of proteins the method identifies in 69% of the unbound cases and 85% of the bound cases the known ligand binding cavity as the top ranking prediction.
Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases.
While our protocol performs well in half of the unbound cases, examples like 1RXZ (described above and in Fig. 5) demonstrate the importance of including receptor flexibility in peptide docking, which is an ongoing work in our group.
The results show that MDockPeP successfully generated near-native peptide binding modes in 95.0% of the bound docking cases and in 92.2% of the unbound docking cases.
While the background results from diffuse unbound probe in the case of an antibody, specific binding on tumor cells yields intense punctate labeling.
In the case of unbound proteins, 70% of the predicted residues were correctly located at the protein protein interfaces.
In both cases the unbound fraction also blocked SRP function, however, indicating that other activities may contribute to the effect of the original sera.
The amount of unbound 3H-biotin in the case of dcAvd-Cys was 5.1±0.6% indicating a slightly reduced ability to bind 3H-biotin as compared to wt avidin.
In the case of the unbound ubiquinol oxidase docking results, only the interface between COX2 in subunit 2 and subunit 1 was considered.
MeHgCys and HgGS2 are not present to 100% in the standard, and thus the concentrations of the mercury reaching the plasma are diminished: in this case, signals for unbound Cys and GS should show also significant intensity.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com