PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences

Gray code representation of the universal genetic code: Generation of never born protein sequences using Toeplitz matrix approach

In this paper, we identify all possible Gray Code and Partitioned Gray Code representations of the Universal Genetic Code for n = 2-bit and 3-bit binary numbers. We analyse the Hamming Distance matrices of all these Gray code and Partitioned Gray Code possibilities for which we obtain the Toeplitz and Partitioned Toeplitz Matrices, respectively. We use this Gray Code and Partitioned Gray Code representations of the Universal Genetic Code combined with the novel Toeplitz matrix approach to generate many Never Born Protein (NBP) Sequences, which exhibit intrinsic structural stability. In general, Never Born Protein sequences may have many potential applications in synthetic biology and opens a new vista in understanding this new subset of proteins for better applications in drug discovery, synthesis of fine chemicals, etc.

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

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.