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MODELLER-Software for Protein Modelling
- June 22, 2018
- Posted by: rasa
- Category: Molecular Modelling & Simulation
Protein interactions play important role in biological field and hence their characterization to reveal their structure and functionhas become important.In absence of experimentally determined structures, proteins can be modeled using computational methods. There is an increase in number of known protein sequences since the computational tools for modelling have been built. Modeller is one of the software used for homology or comparative modelling of three dimensional structures of proteins .The software is available for free and can be easily downloaded on computers or laptops from https://salilab.org/modeller/download_installation.html. Recently, 9.20version of Modeller is availbale.
InComparative modelling, users just provide a sequence (target or query) to Modeller and based on alignment, Modeller calculates all the possible models (templates with known structures) containing all non-hydrogen atoms2. The input scripts of Modeller are Python scripts and there is not a necessity to have knowledge of Python to run this software. The scripts contain programs for template searching, its alignment with query sequence, and building of 3D model of protein and loop refining. For this, Modeller tutorial provides an example with all the steps of basic and advanced modelling and how to calculate the models.Modeller allows performing loop refinementfor n number of times. Also, with the help of Modeller one can create n number of protein models. The log file created in Modeller contains the whole information about modelled proteins. Based on the data in the log file, comparatively best protein model can be selected.
Study of proteins in lab is time consuming and complicated, butModeller makes it a bit easy and cost effective. With the help of basic modelling scripts beginners can start modelling protein in the Modeller.
1.Webb, Benjamin, and Andrej Sali. “Comparative Protein Structure Modeling Using MODELLER.” Current Protocols in Bioinformatics, 2014: 5.6.1-5.6.32.
2.Webb, Benjamin, and Andrej Sali. “Protein Structure Modeling with MODELLER.” Functional Genomics: Methods and Protocols, 2017: 39-54.