Taken together, the results from Experiments 1 and 2 provide evidence of the effect of spatial analogies using a structural, progressive, and hierarchical alignment paired with corrective feedback, as instantiated within each instructor's teaching style.
Protein structural alignments were analyzed using a structural alphabet, Protein blocks (PBs) (18 20), which represent local structures that are recurrent in proteins.
In this study, we aimed, on the one hand, to classify all available sequences with significant similarity to Bet v 1 into subfamilies and, on the other hand, to determine all structural Bet v 1 homologues in the Protein Data Bank (PDB) using a sensitive structural alignment tool.
These results were produced using a novel structural alignment algorithm that will also be described.
Because protein structures are composed of amino acids whose side chains are linked by a common protein backbone, a number of different possible subsets of the atoms that make up a protein macromolecule can be used in producing a structural alignment and calculating the corresponding RMSD values.
Progressive multiple amino acid sequence alignments were performed with ClustalX version 2 ([ 55], http://www.clustal.org/clustal2/) using as a guide a structural alignment constructed with the VAST algorithm [ 56] that included all non-redundantALDH10 protein structures in the PDB [ 57].
Then, we reconstructed the phylogenetic tree of MIR159/319 from a structural alignment using RNA models for paired and unpaired nucleotides, thus revealing the evolutionary history of this miRNA gene family.
A structural alignment constructed using COMPARER 27 was used as a profile for the functional residue-based scoring scheme (Fig. 1).
We also revisited a structural alignment performed using the ProSup program to determine whether using LGA with a point of representation at the beta carbon would confirm a putative mis-alignment detected using the beta-carbon post-analysis filter of Lackner et al. (2000).
