Sentence examples for from secondary structures from inspiring English sources

In this framework, there could be 64 distinct environments for a residue from the combination of structural features: four from secondary structures (α-helix, β-strand, coil and residue with positive φ main-chain torsion angle), two from solvent accessibility (accessible and inaccessible), and eight (23) from hydrogen bonds to main-chain carbonyl (CO) or amide (NH) or to another side chain.

For each exon, there was no statistical difference in the nucleotide accessibility and engaged scores computed from secondary structures predicted based on different sequence lengths of window of analysis (data not shown).

This is accommodated by novel approaches for predicting 3D RNA structures from secondary structures (Popenda et al., 2012).

Additionally, the accuracy of the trees benefitted from secondary structures: the number of false splits was significantly reduced compared to sequence as well as doubled sequence data.

Hickson et al. [ 84] showed that any multiple alignment method which works at the individual nucleotide level is incapable of recovering homology relationships inferred from secondary structures in rRNA sequences, and this is clear in Fig. 10.

The KalignP package, including automatic secondary structure prediction and ESPSGP calculation from secondary structures predicted by PSIPRED_single (Jones, 1999) (version 3.2), is about 15 times slower than Kalign2, but this speed is still comparable to many other MSA programs such as ClustalW and Muscle (Edgar, 2004), see Table 1 and Supplementary Material.

In their snapshots of "frozen" co-translational intermediates attached to ribosomes, these studies revealed compactly folded nascent chain fragments ranging in their level of structural organization from secondary structure elements to domains and/or correctly folded full-length proteins [ 4– 6].

Preliminary deduction of VerFtsZ protein structure from secondary structure comparisons using Cn3D database at NCBI resulted in reasonable alignment to the structural model of 1FSZ for FtsZ of Methanococcus jannaschii from Protein Data Bank (note that this species is synonymous with Methanocaldococcus jannaschii, the name used in some other databases employed for this study).

The structure of the peptide is probably rich in α-helix deduced from secondary structure predictions and the presence of basic amino acid residues appearing every few residues.

Finally, we demonstrate how by combining results from secondary structure prediction, different disorder predictors and MD, one can estimate the type of the predicted disorder region (Fig 4C D).

They may equally profit from secondary structure inclusion.