Hina Bansal, Neetu Jabalia


Objective: The objective of our investigation is to apply computational tools for a protein sodium-dependent serotonin transporter (SERT). It plays a role in sudden infant death syndrome, aggressive behavior in Alzheimer disease, and depression-susceptibility. Although various conventional and experimental therapies have been directed for the treatment, still it needs attention for more effective treatments. Toward this pursuit, we performed in silico analysis of the protein using computational tools and servers.

Methods: Homology modeling approach has been used to define the tertiary structure of the protein using SWISS-MODEL workspace. Modal validation was done to verify the generated modal. Furthermore, primary and secondary structural and functional analysis was performed to provide more perceptions into the selected protein. The protein disorder analysis was performed using PrDOS server.

Results: The results of the primary structure analyses suggested that SERT is an acidic and hydrophobic protein in nature. It is structurally stable. The secondary structural analysis results revealed that random coils dominated among secondary structure elements. The homology modeling showed that the QMEAN score of the model was −5.17, and the sequence identity was 52%. Validation protein models using Rampage revealed that more that 95.9% residues were in favored regions. The protein disorder detected by PrDOS showed the total disorder amino acid residues were 89 (14.1%).

Conclusion: The study provides valuable clues for initiation of experimental characterization of this protein and throws light on some novel insights into the structural features of sodium-dependent SERT protein from Homo sapiens. This will also helpful in conducting docking studies for the receptor protein against various drug molecules.



Homology modeling, In silico analysis, Protein disorder analysis, Random coils.

| PDF |


Masson J, Sagné C, Hamon M, El Mestikawy S. Neurotransmitter transporters in the central nervous system. Pharmacol Rev 1999;51(3):439-64.

Hoyer D, Hannon JP, Martin GR. Molecular, pharmacological and functional diversity of 5-HT receptors. Pharmacol Biochem Behav 2002;71(4):533-54.

Roth BL. Irving Page Lecture: 5-HT(2A) serotonin receptor biology: Interacting proteins, kinases and paradoxical regulation. Neuropharmacology 2011;61(3):348-54.

Bansal H, Narang D, Jabalia N. Computational characterization of antifreeze proteins of Typhula ishikariensis - Gray snow mould. J Proteins Proteomics 2014;5(4):169-76.

Rebhan M, Chalifa-Caspi V, Prilusky J, Lancet D. GeneCards: Integrating information about genes, proteins and diseases. Trends Genet 1997;13(4):163.

Jabalia N, Bansal H, Mishra PC, Chaudhary N. In-silico investigation of cysteine proteases from Zingiber officinale. J Proteins Proteomics 2015;6(3):245-53.

Bansal H, Kriti, Kumar M, Narad P. homology modeling and docking studies on SEMA3A as a receptor for targeting multiple myeloma. Int J Pharm Sci Rev Res 2016;36(1):50-3.

Thomas S, Balaji PV. Understanding the relationship between the primary structure of proteins and its propensity to be soluble on overexpression in Escherichia coli. Protein Sci 2005;14(3):582-92.

Hirokawa T, Boon-Chieng S, Mitaku S. SOSUI: Classification and secondary structure prediction system for membrane proteins. Bioinformatics 1998;14(4):378-9.

Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4(4):406-25.

Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol Biol Evol 2007;24(8):1596-9.

Geourjon C, Deleage G. SOPMA: Significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 1995;11(6):681-4.

Garnier J, Gibrat JF, Robson B. GOR method for predicting protein secondary structure from amino acid sequence. Methods in enzymol 1996;266:540-53.

Dignya D, Vaibhav M, Manali D. In silico analysis of acral peeling skin syndrome: A proteomic approach Dinya Desai. Asian J Pharm Clin Res 2016;9(4):316-9.

Arnold K, Bordoli L, Kopp J, Schwede T. The SWISS-MODEL workspace: A web-based environment for protein structure homology modeling. Bioinformatics 2006;22(2):195-201.

Lovell SC, Davis IW, Arendall WB 3rd, de Bakker PI, Word JM, Prisant MG, et al. Structure validation by Calpha geometry: Phi, psi and Cbeta deviation. Proteins 2003;50(3):437-50.

Mukherjee S, Zhang Y. Protein-protein complex structure prediction by multimeric threading and template recombination. Structure 2011;19(7):955-66.

Dhanalakshmi R, Manavalan R. In silico docking approach for antiatherosclerotic activity of phytoconstituents of Corchoris aestuans and ADMET prediction. Asian J Pharm Clin Res 2015;8(2):350-3.

Ahmad S, Gromiha M, Fawareh H, Sarai A. ASAView: Database and tool for solvent accessibility representation in proteins. BMC Bioinformatics 2004;5(1):51.

Ishida T, Kinoshita K. PrDOS: Prediction of disordered protein regions from amino acid sequence. Nucleic Acids Res 2007;35:W460-4.

Tien MZ, Meyer AG, Sydykova DK, Spielman SJ, Wilke CO. Maximum allowed solvent accessibilites of residues in proteins. PLoS One 2013;8(11):e80635.

Vemulapati BM, Meghana C, Suharitha. In silico prediction of deleterious and non-deleterious nsSNPs in CFTR gene variants. Int J Pharm Pharm Sci 2016;8(12):303-6.

Medha D, Daga A, Rakesh R. Structural and functional analysis of AF9-MLL oncogeneic fusion protein using homology modeling and simulation based approach. Int J Pharm Pharm Sci 2015;7(12):155-61.

About this article




Homology modeling, In silico analysis, Protein disorder analysis, Random coils.





Additional Links

Manuscript Submission


Asian Journal of Pharmaceutical and Clinical Research
Vol 10 Issue 8 August 2017 Page: 299-303

Print ISSN


Online ISSN



162 Views | 202 Downloads

Authors & Affiliations

Hina Bansal
Department of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh, India.

Neetu Jabalia
Department of Biotechnology, Amity University, Sector 125, Noida, Uttar Pradesh, India.

Article Tools

Email this article (Login required)
Email the author (Login required)


  • There are currently no refbacks.