PMC:1867812 / 15206-16270 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1867812","sourcedb":"PMC","sourceid":"1867812","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1867812","text":"To meet these requirements, we propose the following two-step approach to compare conformations of BBA5. First, we partition the 23 residues of BBA5 into four fragments: (i) F1: N-terminal 1–10 β-hairpin; (ii) F2: C-terminal 11 – 23 α-helix fragment; (iii) F3: the first half of F1 and the second half of F2; and (iv) F4: the second half of F1 and the first half of F2, i.e., the middle section in the primary sequence. This segmentation of is also summarized in Table 2. Second, we recognize the secondary structure propensity in each fragment. Two conformations are said to be similar if they demonstrate the same secondary structure propensity in the same fragment. For instance, the pair of conformations in Figure 3(a) are similar as residues in F1, F2 and F4 from both conformations indicate a β-turn like local motif. Please note that the orientation of local motifs does not affect the comparison. For instance, in Figure 3(d), we say the two conformations have a similar structure in F1 fragment, even though the β-turn motifs have different orientations.","tracks":[]}