**Author details**

50 Bioinformatics

**4.5. Our further direction** 

**5. Conclusion** 

unknown.

organelle can also inhibit the protein's function.

*In silico* approach offers various advantages over *in vivo* and *in vitro* approaches such as non-use of animals, low costs, and reduced execution time. This approach allows identification of proteins of interest from a particular biological study. From a protein function standpoint, transfer of annotation from known proteins to a novel target is currently the only practical way to convert vast quantities of raw sequence data into meaningful information. Many bioinformatics tools now provide more sophisticated methods to transfer functional annotation, integrating sequence, family profile and structural search methodology. Thus, in addition to data mining for protein-protein interaction, further *in silico* approach should also consider structural alignment, molecular docking and pathway modeling in order to obtain a comprehensive and more reliable

The availability of protein databases and computer-aided softwares to identify probable components of cellular mechanisms has become a new trend in the present scientific era. We demonstrate here a computational analysis of nuclear transport in *T. brucei* as an initial step and proof of concept for further investigation. Our approach successfully identified 22 *T. brucei* proteins essential for nuclear transport. All those parasite proteins were found to contain relevant functional domains that drive the translocation of macromolecules in the parasite. The phosphorylation and O-glycosylation sites were also detected in all identified parasite proteins. This has given us an insight into the regulatory aspect of parasite nuclear transport. The database mining of protein interaction has shown that nine out of 22 parasite proteins possess relevant functional interactions for nuclear transport activities. However, more functional interactions from nuclear transport constituents of *T. brucei* are required to elucidate the exact mechanism. The homology between the parasite proteins and human counterparts was shown by BLASTp analyses. Whether there are structural differences between them remain

The nuclear transport in *T. brucei* has been characterized by using the *in silico* approach. The predicted functionalities and regulatory aspects of parasite nuclear transport constituents were in agreement with the previous reports. Moreover, the protein interaction data derived from the public database has made the participation of parasite proteins in the mechanism more convincing. Thus, we have laid a path for understanding the nuclear transport machinery in *T. brucei*. The development of drugs that target as well as alter nuclear import and export will undoubtedly become beneficial in controlling Trypanosomiasis in future. Drugs that have a direct effect on a single protein must be able to localize to the same site as the protein and interact with one or more of its domains. Alternatively, a drug that effectively blocks the target protein from reaching its proper

insight into protein-protein interaction of *T. brucei* nuclear transport.

Mohd Fakharul Zaman Raja Yahya\* and Umi Marshida Abdul Hamid *School of Biology, Faculty of Applied Sciences, MARA University of Technology Shah Alam, Shah Alam Selangor, Malaysia* 
