PSS-3D1D: an improved 3D1D profile method of protein fold recognition for the annotation of twilight zone sequences
- 130 Downloads
Annotation of any newly determined protein sequence depends on the pairwise sequence identity with known sequences. However, for the twilight zone sequences which have only 15–25% identity, the pair-wise comparison methods are inadequate and the annotation becomes a challenging task. Such sequences can be annotated by using methods that recognize their fold. Bowie et al. described a 3D1D profile method in which the amino acid sequences that fold into a known 3D structure are identified by their compatibility to that known 3D structure. We have improved the above method by using the predicted secondary structure information and employ it for fold recognition from the twilight zone sequences. In our Protein Secondary Structure 3D1D (PSS-3D1D) method, a score (w) for the predicted secondary structure of the query sequence is included in finding the compatibility of the query sequence to the known fold 3D structures. In the benchmarks, the PSS-3D1D method shows a maximum of 21% improvement in predicting correctly the α + β class of folds from the sequences with twilight zone level of identity, when compared with the 3D1D profile method. Hence, the PSS-3D1D method could offer more clues than the 3D1D method for the annotation of twilight zone sequences. The web based PSS-3D1D method is freely available in the PredictFold server at http://bioinfo.bdu.ac.in/servers/.
KeywordsProtein fold Twilight zone Sequence annotation
This work forms part of the research project funded by the Department of Information Technology (DIT), Govt. of India, New Delhi. One of the authors (KG) gratefully acknowledges the support provided by the DIT in the form a senior research fellowship.
- 1.Doolittle RF (1986) Of urfs and orfs: a primer on how to analyze derived amino acid sequences. University Science Books, Mill ValleyGoogle Scholar
- 16.Meller J, Elber R (2002) Protein recognition by sequence-to-structure fitness: bridging efficiency and capacity of threading models. Adv Chem Phys 120:77130Google Scholar
- 31.Fano R (1961) Transmission of information: a statistical theory of communications. University Science Books, CambridgeGoogle Scholar