PMC:1867812 / 37180-40525 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":"SOAP-based Trajectory Summarization\nThe previous mining phase discovers a collection of frequent (minLink = 1) SOAPs and the associated episodes in each trajectory. Therefore, it identifies all the conformations in the trajectories that contain at least one frequent (minLink = 1) SOAPs. For instance, the last conformation in trajectory T23 (Figure 1(c)) has two SOAPs of size 2:(5 8) (i.e., association of a type 5 and a type 8 bit-pattern) and (7 8), and three SOAPs of size 1: (5), (7), and (8), while the last conformation in trajectory T24 has three SOAPs: (7 8), (7) and (8). This leads to our SOAP-based approach for folding trajectory summarization.\nTo summarize a folding trajectory, we perform the following three steps. First, for each conformation, we identify all the frequent SOAPs that appear in it and use these SOAPs to represent this conformation. Note that not every conformation contains frequent SOAPs, especially when minSupp is set high. Second, for each SOAP-representable conformation, we carry out two tasks on its associated SOAPs. We next use the folding trajectories of BBA5 to explain how these two tasks are carried out.\nIn the first task, for each SOAP, we mark the relative location of each involved bit-pattern in the primary sequence of BBA5. This is done by identifying the segment of BBA5 where the majority of a bit-pattern's α-carbons are located. The segment can be one of the following as described in Section 2.2: F1, residues 1 – 10; F2 , residues 11 – 23; F3, residues 6–17; and F4: residues 1–5 and 18–23. Let us again take the last conformation in T24 as an example. It can be summarized by three SOAPs: (7 8), (7) and (8). When we look at the list of α-carbons involved in these bit-patterns, we find out that 7 is mainly located in F2 and 8 in F1. Therefore, we mark the three SOAPs as follows: (8.1 7.2), (7.2) and (8.1). We re-arrange the bit-patterns in a SOAP by their relative locations in BBA5. This super-imposes BBA5-specific spatial information to a SOAP. In the second task, we prune away redundant SOAPs after marking each bit-pattern with its relative location in BBA5. A SOAP is redundant if it is embedded in another SOAP. For instance, in the previous example, we can prune away (8.1) and (7.2) as both are embedded in (7.2 8.1). After pruning, most conformations in such a small protein can often be represented by a single SOAP. We can even take this summarization a step further, where we replace a bit-pattern with its corresponding 3D motif, as illustrated in Figure 5. For instance, SOAP (7.2 8.1) will be transformed into (β.1 α.2). We refer to such SOAPs as generalized SOAPs, and the corresponding trajectory as a generalized trajectory. Note that in a generalized trajectory, multiple types of bit-patterns can be mapped into a single type of 3D motif. For instance, the α-motif corresponds to three types of bit-patterns 4, 7, and 9 (Figure 5). Figure 9 shows a segment in each summarized BBA5 folding trajectory before and after being generalized with 3D motifs.\nFigure 9 SOAP-based folding trajectory summarization. An sample segment in each of the two BBA5 folding trajectories is presented, (a) After superimposing the relative location of each bit-pattern and pruning away redundant SOAPs. (b) After further generalizing each bit-pattern by corresponding 3D motif.","divisions":[{"label":"title","span":{"begin":0,"end":35}},{"label":"p","span":{"begin":36,"end":658}},{"label":"p","span":{"begin":659,"end":1152}},{"label":"p","span":{"begin":1153,"end":3038}},{"label":"label","span":{"begin":3039,"end":3047}}],"tracks":[]}