PMC:1867812 / 13880-15205 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 compare two trajectories, one must address the following key issue: how can we compare two protein conformations? Several measures have been commonly used towards such a purpose, including RMSD (root mean squared distance) [13], contact order [14], and native contacts [15]. However, all these measures are designed to quantify the global topology of a conformation. Furthermore, based on our empirical analysis of these measures, we notice that they are generally too coarse and thus can often be misleading. Even more importantly, such measures fail to identify similar local structures (or motifs) between conformations. This is especially crucial for small proteins like BBA5. As demonstrated in both experimental and theoretical studies, small proteins often fold hierarchically and begin locally [16]. For instance, it has been shown that BBA5 tends to first form secondary structures such as β-turns and α-helices, then conform to its global topology [9]. Finally, as suggested by Pande [8], both sterics (local motifs) and global topology might play an important role in protein folding. Therefore, to compare conformations of (small) proteins, a more reasonable comparison should consider both local and global structures. Moreover, it should also take the native topology of the protein under study into account.","tracks":[{"project":"2_test","denotations":[{"id":"17407611-12368107-1692920","span":{"begin":227,"end":229},"obj":"12368107"},{"id":"17407611-9545386-1692921","span":{"begin":247,"end":249},"obj":"9545386"},{"id":"17407611-10087919-1692922","span":{"begin":806,"end":808},"obj":"10087919"},{"id":"17407611-12422224-1692923","span":{"begin":962,"end":963},"obj":"12422224"}],"attributes":[{"subj":"17407611-12368107-1692920","pred":"source","obj":"2_test"},{"subj":"17407611-9545386-1692921","pred":"source","obj":"2_test"},{"subj":"17407611-10087919-1692922","pred":"source","obj":"2_test"},{"subj":"17407611-12422224-1692923","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93baec","default":true}]}]}}