The method samples sequence and structure space in the vicinity of a known sequence and structure by alternately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbone for a fixed amino acid sequence using atomic-resolution structure prediction.
In a first in silico test, we show that by simultaneously optimizing the sequence and structure of three to nine residue peptide extensions starting from short (1 6 residue) peptide stubs in the binding pocket of a peptide binding protein, the approach can recover both the conformations and the sequences of known binding peptides.
Fatigue life in laser peened specimens was increased from +166% to +471% by optimizing the pulse sequence.
The improved thermal performance, a Tm increase of 4 °C for the cocaine-bound aptamer and 9 °C for the quinine-bound aptamer, was achieved by optimizing the DNA sequence in stem 2 of the aptamer to have the highest stability based on the nearest neighbor thermodynamic parameters and confirmed by UV and fluorescence spectroscopy.
Blocking construct was inseparably linked to the transgene of interest by optimizing the coding sequence and polyadenylation signal of barnase for a high AT content and placing it in the artificial second intron of the GUS gene in such way that the transcription of GUS and barnase proceeds in opposite directions.
These findings led us to hypothesize that in many cases, Cdk substrates might contain clusters of phosphorylation sites, and therefore that Cdk substrate prediction could be improved not only by optimizing the consensus motif sequence, but also by following consensus site identification with selection of proteins whose sequences are enriched for repeats of that motif.
An additional cost saving can possibly be achieved by optimizing the numbers of sequence reads necessary to obtain stable quantification results.
We address the twin issues of codon bias and possible improper folding by optimizing the hCNTF gene sequence for use in E. coli and adopting a factorial screening strategy.
The quay crane operating time is reduced by optimizing the loading and unloading sequence for the hatches and stacks in each ship-bay.
Consequently, the direct and label-free detection with the SPR technique and neutralized chimeric probe DNA can be realized for the SNP genotyping by optimizing the operation condition and sequence design.
