Protein modeling by homology using the example of tick-borne encephalitis serine protease NS3

Homology modeling is a process of obtaining a 3D structure of a protein using various algorithms based on already known structures of homologous proteins. The spatial structure of protein is required for in silico protein evaluation. 3D structures can be obtained using different methods: NMR, Xray crystallography (XRC), and cryo-electron microscopy (cryo-EM), but these methods require a lot of time and money. At the same time, the speed of nucleotide sequences analysis is increasing, thereby creating a mismatch between the number of decoded genomes and the investigated 3D protein structures that are encoded by these sequences. Also, homology modeling is the easiest and fastest way to obtain the model of the desired protein. This review describes free software for homology modelling — SWISS-MODEL and MODELLER, how to use it and how to evaluate the results.