Importance of protein 3D structure and its role in the progression of different diseases is well established. In terms of proteins, 3D structure is the most important as it controls the functionality of complete protein and plays an important part in the progression of the disease hence these 3D structures are better target for further drug designing and relative studies [39Mishra M, Pant AB, Srivastava P. Comparative modeling and binding site prediction of GP15/400 polyprotein of Wuchereria bancrofti by using computional approaches. IMTU Med J 2012; 3: 40-3.]. In case of parasitic disorder the selection of target protein is very specific as the drug is designed against the target protein that should not harm the host where as it could affect the vitality and pathogenicity of the parasite. These 3D structures of selected protein can be used as a better target for drug designing and relative studies against any parasitic disorder [39Mishra M, Pant AB, Srivastava P. Comparative modeling and binding site prediction of GP15/400 polyprotein of Wuchereria bancrofti by using computional approaches. IMTU Med J 2012; 3: 40-3.]. Different computational protocols were used for different studies at protein level viz;In silico characterization, homology modeling, docking etc.

It is important in deciphering the important physical and chemical properties along with the prediction of basic configuration of proteins in their secondary structure. Physicochemical characterization of proteins encodes better understanding about the properties like molecular weight, number of hydrogen bonds, theoretical isoelectric point (pI), helices, strands, turns, instability index, number of positive and negatively charged residues, extinction coefficient, grand average hydropathicity (GRAVY) and aliphatic index [39Mishra M, Pant AB, Srivastava P. Comparative modeling and binding site prediction of GP15/400 polyprotein of Wuchereria bancrofti by using computional approaches. IMTU Med J 2012; 3: 40-3.]. Above mentioned parameters are significantly playing an important role in analyzing the properties of protein. In silico characterization studies have drawn the positive and progressive relation and attention towards the advance approaches of protein characterization [40Pancaldi V, Bähler J. In silico characterization and prediction of global protein-mRNA interactions in yeast. Nucleic Acids Res 2011; 39(14): 5826-36.
[http://dx.doi.org/10.1093/nar/gkr160] [PMID: 21459850] ]. Different in silico characterization based studies related to filariasis and others disorders have already proven their significance and contributed a lot in the area of advance research.

In silico characterization of an RNA binding protein of cattle filarial parasite Setaria Digitata has been performed by Nagaratnam et al, 2014. In this study, a 549 bp long cDNA (sdrbp) has been sequenced and characterized in silico. Due to the difficulties in procuring WB parasite material, Setaria Digitata cDNA library has been constructed to identify novel drug targets against HLF and many of the cDNA sequences have been assigned structures and functions to interpret their importance in relation with this disorder [41Nagaratnam N, Karunanayake EH, Tennekoon KH, Samarakoon SR, Mayan K. In silico characterization of a RNA binding protein of cattle filarial parasite Setaria digitata. Bioinformation 2014; 10(8): 512-7.
[http://dx.doi.org/10.6026/97320630010512] [PMID: 25258487] ].

Another study revealed in silico structural and functional characterization of a Vibrio Cholerae O395 hypothetical protein containing a PDZ1 and an uncommon protease domain, Vibrio cholerae, the causative agent of epidemic cholera, has been a constant source of concern for decades. It has constantly evolved itself in order to survive the changing environment [42Dutta A, Katarkar A, Chaudhuri K. In silico structural and functional characterization of a V. cholerae O395 hypothetical protein containing a PDZ1 and an uncommon protease domain. PLoS One 2013; 8(2): e56725.
[http://dx.doi.org/10.1371/journal.pone.0056725] [PMID: 23441214] ]. In silico identification and characterization of novel drug targets and outer membrane proteins in the fish pathogen Edward siellatarda was a land mark for computational approaches with respect to helminths for identification of the new potential drug targets and novel vaccine candidates against it [43Mohammed N, Iddya K, Indrani K. In silico identification and characterization of novel drug targets and outer membrane proteins in the fish pathogen Edwardsiella tarda. Bioinformatics 2011; 3: 37-42.].

In molecular biology and structural genomics, protein structure determination has become an important area of research. Genome sequencing projects are producing linear amino acid sequences, but full understanding of the biological role of these proteins will require knowledge of their tertiary structures and functions [44Vyas VK, Ukawala RD, Ghate M, Chintha C. Homology modeling a fast tool for drug discovery: Current perspectives. Indian J Pharm Sci 2012; 74(1): 1-17.
[http://dx.doi.org/10.4103/0250-474X.102537] [PMID: 23204616] ]. 3D protein structures are precious sources of information for the functional annotation of protein molecules. These structures are best resolute by experimental methods such as X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. However, the experimental methods cannot always be applied. To overcome such issues, prediction of the protein structure by computational methods can frequently result in a useful model [45Madhusudhan MS, Marti-Renom MA, Eswar N, et al. Comparative Protein Structure Modeling The Proteomics Protocols Handbook 2005., 46Ul-Haq Z, Saeed M, Halim SA, Khan W. 3D structure prediction of human β1-adrenergic receptor via threading-based homology modeling for implications in structure-based drug designing. PLoS One 2015; 10(4): e0122223.
[http://dx.doi.org/10.1371/journal.pone.0122223] [PMID: 25860348] ]. The aim of comparative or homology protein structure modelling is to build a three-dimensional (3D) model for a protein of unknown structure (the target) on the basis of sequence similarity to proteins of known structure (the templates) [47Martí-Renom MA, Stuart AC, Fiser A, Sánchez R, Melo F, Sali A. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000; 29(1): 291-325.
[http://dx.doi.org/10.1146/annurev.biophys.29.1.291] [PMID: 10940251] ]. Homology modelling can create high-quality structural models when the target and template have close relationship. Like other methods of structure prediction, current run-through in homology modeling is evaluated in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction or CASP [48Moult J, Fidelis K, Kryshtafovych A, Schwede T, Tramontano A. Critical assessment of methods of protein structure prediction (CASP)--round x. Proteins 2014; 82(Suppl. 2): 1-6.
[http://dx.doi.org/10.1002/prot.24452] [PMID: 24344053] ].

Homology modelling is consistently becoming the method of choice for procuring three-dimensional coordinates for proteins because genome projects produce sequences at a much higher rate than NMR and X-ray laboratories can solve the three-dimensional structures [49Mizianty MJ, Fan X, Yan J, et al. Covering complete proteomes with X-ray structures: A current snapshot. Acta Crystallogr D Biol Crystallogr 2014; 70(Pt 11): 2781-93.
[http://dx.doi.org/10.1107/S1399004714019427] [PMID: 25372670] ]. There are some beautiful examples sowing homology modelling studies and their importance with reference to filariasis.

WB and BM three dimensional model of b-tubulin protein (BmBTP) was built using homology modeling approach [50Sharma OP, Pan A, Hot SL, Jadhav A, Kannan M, Mathur PP. Modeling, docking, simulation, and inhibitory activityof the benzimidazole analogue against b-tubulin protein from Brugiamalayi for treating lymphatic filariasis. Med Chem Res 2012; 21(9): 2415-27.
[http://dx.doi.org/10.1007/s00044-011-9763-5] ].

Another important 3D structure of Fatty Acid Retinal binding (FAR) protein in Wuchereria bancrofti was modelled because of its strong conservation of the biochemical activities with significant role [11Mishra M, Pant AB, Srivastava P. 3D Structure prediction with functional site identification of fatty acid retinal binding (FAR) protein: A target against filarial fight. Int J Curr Microbiol Appl Sci 2013; 2(11): 123-31.].

Filarial protein GP 15/400 poly protein which is an important pathogenic protein of Wuchereria Bancrofti was also modeled through in silico approaches [39Mishra M, Pant AB, Srivastava P. Comparative modeling and binding site prediction of GP15/400 polyprotein of Wuchereria bancrofti by using computional approaches. IMTU Med J 2012; 3: 40-3.]. It is a well-accepted fact that modelled structure are obtaining remarkable acceptance in scientific community. They have many related applications in virtual screening and drugs as well inhibitor designing based on structure activity relationship.

Synthesis and molecular modelling studies of 3-chloro-4-substituted-1-(8-hydroxy-quinolin-5-yl)-azetidin-2-ones as novel anti-filarial agents is generated an amazing understanding of problem [51Chhajed SS, Manisha P, Bastikar VA, et al. Synthesis and molecular modeling studies of 3-chloro-4-substituted-1-(8-hydroxy-quinolin-5-yl)-azetidin-2-ones as novel anti-filarial agents. Bioorg Med Chem Lett 2010; 20(12): 3640-4.
[http://dx.doi.org/10.1016/j.bmcl.2010.04.106] [PMID: 20483610] ]. These supportive findings are very important in helping and guiding of future lead discoveries and optimization efforts [52Jacobson M, Sali A. Comparative protein structure modeling and its applications to drug discovery. Annu Rep Med Chem 2004; 39.].

Homology modeling of antioxidant proteins in spinach was adopted to explore Physico-chemical properties and structure of spinach antioxidant proteins [53Sahay A, Shakya M. In silico analysis and homology modelling of antioxidant proteins of spinach. J Proteomics Bioinform 2010; 3: 148-54.
[http://dx.doi.org/10.4172/jpb.1000134] ].

Another study regarding molecular modelling, dynamics and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies explored new interventions of this issue. In this current study, a putative cofactor-iPGM gene was identified in the protein sequence of the Wuchereria bancrofti [54Sharma OP, Vadlamudi Y, Liao Q, Strodel B, Suresh Kumar M. Molecular modeling, dynamics, and an insight into the structural inhibition of cofactor independent phosphoglycerate mutase isoform 1 from Wuchereria bancrofti using cheminformatics and mutational studies. J Biomol Struct Dyn 2013; 31(7): 765-78.
[http://dx.doi.org/10.1080/07391102.2012.709460] [PMID: 22908983] ].

Docking technique is used to form a stable complex between protein and ligand. Molecular docking is one of the most accepted protocol for the computer aided drug designing and structural molecular biology. Prediction of binding orientation with reference to drug candidate and protein targets to calculate the affinity and activity is mostly used by following the detailed docking procedure. This reason justifies the significance of molecular docking or protein ligand interaction in rational drug design [55Sliwoski G, Kothiwale S, Meiler J, Lowe EW Jr. Computational methods in drug discovery. Pharmacol Rev 2013; 66(1): 334-95.
[http://dx.doi.org/10.1124/pr.112.007336] [PMID: 24381236] ]. During the docking methodology preferred orientations of different molecules are used to predict in the term of binding affinity association of the molecules through scoring functions [56Lengauer T, Rarey M. Computational methods for biomolecular docking. Curr Opin Struct Biol 1996; 6(3): 402-6.
[http://dx.doi.org/10.1016/S0959-440X(96)80061-3] [PMID: 8804827] ]. The most interesting and demanding case of the protein-ligand interaction are seen in application of medical sciences. Ligand is a small molecule, which interacts with proteins binding sites. This methodology is used to model the interaction between a small molecule and a protein at the atomic level. This interaction characterizes the behaviour of small molecules with the binding site of target proteins as well as to explicate elementary biochemical processes.

Molecular docking is the most important master program used in structural molecular biology as well as for computer-aided drug design.

Kalani et al, 2014 proved the importance of docking study in filariasis by establishing the importance of ursolic acid against the human lymphatic filarial parasite Brugia malayi through targeting Glutathione-S-Transferase (GST) parasitic enzyme [57Kalani K, Kushwaha V, Sharma P, et al. In vitro, in silico and in vivo studies of ursolic acid as an anti-filarial agent. PLoS One 2014; 9(11): e111244.
[http://dx.doi.org/10.1371/journal.pone.0111244] [PMID: 25375886] ].

Studies on filarial GST as a target for antifilarial drug development in silico and in silico inhibition of filarial GST by substituted 1, 4-naphthoquinones reveals a good computational contribution in filiarial issues [58Mathew N, Srinivasan L, Karunan T, Ayyanar E, Muthuswamy K. A target for antifilarial drug development in silico andin silico inhibition of filarial GST by substituted 1,4-naphthoquinones. J Mol Model 2011; 17(10): 2651-7.
[http://dx.doi.org/10.1007/s00894-010-0952-9] [PMID: 21267750] ].

Structural insights on Brugia malayi transglutaminase with cinnamoyl derivatives also proved importance of molecular docking approach [59Srikumar PS, Rohini K. Structural insights on Burgia malayi transglutaminase with cinnamoyl derivatives- A molecular docking approach. Int J Pharma Bio Sci 2012; 3(3): 998-1006.].

Another study related to filariasis is a systematic study on structure and function of ATPase of Wuchereria bancrofti because as till date no effective drug or vaccine has been discovered to treat lymphatic filariasis (LF) and ATPase is one of the most important proteins of Wuchereria bancrofti that could be a good target to develop these [60Islam MS, Patwary NI, Muzahid NH, Shahik SM, Sohel M, Hasan MA. A systematic study on structure and function of ATPase of Wuchereria bancrofti. Toxicol Int 2014; 21(3): 269-74.
[http://dx.doi.org/10.4103/0971-6580.155357] [PMID: 25948965] ].