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In [ 26], we have used these distribution distances to compare and correlate different methodologies of protein inter-residue contacts.
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The information entropy methodology for analysis of protein variability was modified to examine sequences of 9 amino acids or longer, instead of the more common application to single residues, as a means to relate the conserved sequences to the immune function of HLA-restricted peptides.
The most suitable methodology for study of protein complexes and PPI in these model systems has proven to be the affinity purification of protein complexes followed by MS identification (AP-MS).
Our computational experiments produced: (1) an evaluation of the methodology of representative proteins, (2) findings concerning which proteins make the best phylogenetic characters, and (3) a fairly complete and well-resolved phylogeny for sequenced Bacteria.
The lack of statistical significance may be an outcome of relative small sample size as well as the different methodologies of evaluating ATM protein expression and defining cut-points to divide ATM low and high groups.
The chapter discusses two methodologies for the evolution of protein function by domain swapping includes non-combinatorial and combinatorial.
However, for the time being, transcriptomic approaches are justified by the fact that the current methodologies for direct quantification of protein expression are either less reliable or more laborious and expensive than mRNA-based studies.
Mutagenesis represents a powerful methodology for the analysis of protein structural and functional relationships and dissection of complex protein protein interactions.
Damoulas and Girolami [ 15] offered the kernel combination methodology for the prediction of protein folds and the best accuracy was 70%.
Combined with strain collections, such as the GFP fusion collection for budding yeast, our methodology allows quantitative measurements of protein levels of up to hundreds of genes and therefore provides complementary data to high throughput studies of transcription.
In this section, we introduce BINDSURF [ 1], an efficient and fast blind methodology for the determination of protein binding sites depending on the ligand that uses the massively parallel architecture of GPUs for fast prescreening of large ligand databases.
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