PredictSuperFam-PSS-3D1D: A server for predicting superfamily for the annotation of twilight zone protein sequences

• Published in: Journal of structural biology Vol. 210; no. 2; p. 107479
• Main Authors: Muthuvel Prasath, K., Ganesan, K., Parthasarathy, S.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.05.2020
• Subjects: Hypothetical sequence annotation; PSS-3D1D method; Schistosoma haematobium; SCOP superfamily prediction; Twilight zone protein sequence; Twilight zone protein sequence; Schistosoma haematobium; SCOP superfamily prediction; PSS-3D1D method; Hypothetical sequence annotation
• ISSN: 1047-8477; 1095-8657
• DOI: 10.1016/j.jsb.2020.107479

[Display omitted] •The Prediction of SCOP Superfamily mainly for Twilight Zone Sequences.•Adding secondary structure data in 3D1D profile method improves predictions.•The performance and sensitivity of the method is analyzed by Twilight Zone dataset.•A case study has been done for the hypothetical protein sequences of Blood Fluke.•A web server is available online at http://bioinfo.bdu.ac.in/psfpss. Annotation of twilight zone protein sequences has been hitherto attempted by predicting the fold of the given sequence. We report here the PredictSuperFam-PSS-3D1D method, which predicts the superfamily for a given twilight zone (TZ) protein sequence. Earlier, we have reported that adding predicted secondary structure information into the threading methods could improve fold prediction especially for the TZ protein sequences. In this study, we have analysed the application of the same method to predict superfamilies. Here, in this method, the twilight zone protein sequence is threaded with the 3D1D profiles of the known protein superfamilies library. In addition, weightage for the predicted secondary structure (PSS) is also employed. The performance of the method is benchmarked with twilight zone sequences. In the benchmarks, 62 and 65 percentages of superfamily predictions are obtained with GOR IV and NPS@ predicted secondary structures, respectively. Receiver Operating Characteristic (ROC) curves indicate that the method is sensitive in predicting the superfamilies. A case study has been conducted with the hypothetical protein sequences of Schistosoma haematobium (Blood Fluke) using this method and the results are analyzed. Our method predicts the superfamily for TZ sequences for which, methods based on sequence similarity alone are inadequate. A web server has been developed for our method and it is available online at http://bioinfo.bdu.ac.in/psfpss.