As a point of reference, we also induced rules based on domain-specific global structural similarity in terms of orientations and connectivity of the main secondary structure elements (CATH fold, see Materials and Methods) [33].
The core structure comprising the main secondary structure elements of the CNX lectin domain [10] was used as a starting search model.
Fig. 1 shows a cartoon representation of NS in its native conformation, where such main secondary structure features are highlighted.
The main secondary structure prediction tool is RNAfold, which computes the minimum free energy (MFE) and backtraces an optimal secondary structure.
We characterize structural environments of the amino acid variants by the following properties: i) side-chain solvent accessibility, ii) main-chain secondary structure, and iii) hydrogen bonds from a side chain to a main chain or other side chains.
The debate has come to a head as asbestos removal has begun, and part of the main centerpiece building, along with other secondary structures, has been knocked down.
Usually, three to six classes may be rationally defined (e.g. VILFMYW for the strong hydrophobic class, mainly present within the internal sides of regular secondary structures, GPDSN as main loop-forming residues and ARC-QTEKH for the intermediate class (Callebaut et al. 1997; Hennetin et al. 2003)).
These mRNAs often contain a 5'-UTR considerably longer than the average cellular 5'-UTR [13], [14], may contain AUG codons upstream of the initiation codon for the main open reading frame, and have complex secondary structures [15].
The NH region reflects the predominance of NH NH interactions and lack of other main-chain interactions characteristic of the common secondary structures.
To test how these substitutions could affect mRNA folding, the secondary structures of mRNA for the main haplotypes of BGa, BGp, and SG were predicted.
