PMC:4331677 / 28243-29766 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4331677","sourcedb":"PMC","sourceid":"4331677","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4331677","text":"According to the hypothesis, the feature interactions reflect the chemical interaction, as a result, it is necessary to investigate whether the feature interactions response the hypothesis. Since the number of interactions is large, we only analyze the top twenty interactions (Figure 5C), the others could be analyzed similarly. In Figure 5C, the first letter of site fragment is the center amino acid of the trimer cluster, and the letters in the parenthesis represent the subordinate amino acids. The smarts (a kind of molecular patterns) represent ligand fragments. The Figure 5C suggest that the feature interactions reflect the chemical interaction well, which in consistent with the hypothesis. For example, the major amino acid of site fragment 147 (TF147) is Aspartic (short for D), which could interact with ligand fragment 92 (LF92, containing keto group) through hydrogen bond, if the distance and orientation are appropriate. In some situations, the major amino acid of a target feature could not form significant interaction with ligand feature, but the subsidiary amino acid could. For example, the major amino acid of site fragment 57 (TF57) is isoleucine (short for I), which is a hydrophobic amino acid. Isoleucine could not interact with ligand fragment 44 (LF44), which contains amino group. However, the subsidiary amino acid of site fragment 57, such as threonine (short for T) and arginine (short for R) can form hydrogen bond with ligand fragment 44, if the distance and orientation are appropriate.","tracks":[]}