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The cost of performing a peptide:MHC binding experiment, which is routinely feasible for less than $50, places a boundary on the amount of computation time that is justifiable in a real-world application.
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The standard SELEX procedure schedules the validation of certain found aptamers via binding experiments, which is not leading to any detailed specification of the aptamer enrichment during the screening.
In classical experimentation, gene expression analysis is frequently validated by in vitro DNA-binding experiments, which are classified as strong evidence.
Thus, our human ER binding affinity estimates are within about 10 kJ/mol of experiment which is within the expected error due to the atomic models [12].
This is atypical of an INPHARMA experiment, which is expected to specify the shared binding epitopes by indirect interligand NOEs through protein protons.[ 15] These interligand NOEs are observed even for experiments in which deuterated p38αI84A is used.
Thus, CLIPdb uniformly scores or ranks binding sites from various CLIP-seq experiments, which is important for the integrative analysis of these published CLIP-seq data.
Neither does it account for variation in the profiles at the same binding site across multiple replicate DNase I experiments, which are increasingly available.
Considering that there are conflicting reports regarding the order of binding of substrates to CaMKII [13] [15], our experiments provide direct binding data which is in agreement with the earlier reports that have indicated that CaMKII follows an ordered ternary complex formation mechanism [14], [15].
Decomposition of binding energies revealed that R129, R125, R327, R134 and R48 are important residues involved in substrate binding, which is useful for further site-directed mutagenesis experiments.
In this experiment, UBF which is known to be an rDNA binding transcription factor was used as a positive control.
A fine detail of this experiment is the surface binding of the antibody which is specific to the complex but which is added from outside of the cell.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com