EasyModeller: A graphical interface to MODELLER
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MODELLER is a program for automated protein Homology Modeling. It is one of the most widely used tool for homology or comparative modeling of protein three-dimensional structures, but most users find it a bit difficult to start with MODELLER as it is command line based and requires knowledge of basic Python scripting to use it efficiently.
The study was designed with an aim to develop of "EasyModeller" tool as a frontend graphical interface to MODELLER using Perl/Tk, which can be used as a standalone tool in windows platform with MODELLER and Python preinstalled. It helps inexperienced users to perform modeling, assessment, visualization, and optimization of protein models in a simple and straightforward way.
EasyModeller provides a graphical straight forward interface and functions as a stand-alone tool which can be used in a standard personal computer with Microsoft Windows as the operating system.
KeywordsProtein Data Bank Template Structure Loop Modeling Protein Data Bank File Chain Information
Structural information of biological macromolecules is readily available in the Protein Data Bank (PDB) , http://www.pdb.org. By Sep 2009, the PDB contained ~ 60,713 experimental protein structures that can be grouped into ~ 3500 families . Considering that the number of non redundant amino acid sequence entries is around 408,000 http://www.expasy.org/sprot/, there is a huge gap between known annotated sequences and available 3 D structures. Developments in genomics have also spurred the developments in X-ray crystallography and NMR techniques to solve the new protein structure, which in turn has widened their use in drug discovery . However, these efforts are no where near in solving the 3 D structures of all the known proteins in any system. In the absence of experimental structures, computational methods are used to predict 3 D protein models to provide insight into the structure and function of these proteins. The steps involved in this process are : (1) identification of homolog that can be used as template(s) for modeling; (2) alignment of the target sequence to the template(s); (3) backbone generation; (4) loop modeling; (5) side-chain modeling; (6) model optimization; and (7) validation of the model. Repositories like The SWISS-MODEL http://swissmodel.expasy.org/SWISS-MODEL.html, Protein Model Portal http://proteinmodelportal.org and Modbase http://modbase.compbio.ucsf.edu, contain protein models generated using various auto-mated methods. However, without human intervention, errors as a result of inaccurate sequence alignment, and inability to identify and correctly model domains, such as loop and ligand-binding regions, are magnified, which results in the generation of low-accuracy models and thus limiting their applicability to drug discovery projects [7, 8]. In this context, the development of various user friendly and accurate tools for homology modeling is an active area of research such as new recent tools like HHPRED and Modeller at http://toolkit.tuebingen.mpg.de/sections/tertstruct toolkit, GeneSilico https://genesilico.pl/toolkit/[9, 10, 11, 12, 13, 14, 15]. MODELLER is one of the most widely used tools for homology or comparative modeling of protein three-dimensional structures. MODELLER stands apart from other packages due to its free availability, powerful features and reliable results. But most users find a bit difficult to start with MODELLER as it is command line based. Hence a freely available GUI for MODELLER would thus be very helpful to exploit the powers and advantages of this package more effectively. EasyModeller is a graphical user interface to MODELLER program.
The GUI eliminates the requirement of prior knowledge in the backend applications, thereby increasing the number of users of MODELLER and assists them to exploit the unique features of this great package more effectively. EasyModeller uses default parameters for most commands during software execution to make the process as simple as possible. User can change the parameters manually by editing the associated python script file (*.py) generated in the working directory.
EasyModeller will be updated by adding features like comparison and manual combination of multiple template structure and manual definition of spatial restraints into a more powerful GUI to MODELLER which could simultaneously display both alignment and structure windows, and have them interact with each other.
Availability and requirements
Project name: EasyModeller
Project homepage: http://www.uohyd.ernet.in/modellergui/
Operating system: Microsoft Windows (any)
Programming language: Perl (using Perl/Tk)
Other requirements: The system must have MODELLER (any version will work but preferably the latest version to get the best results) and Python (2.5 or 2.6 and not 3.11) preinstalled in the default installation directory (C://Program files/..). If the operating system is Windows Vista or Windows 7 then please run the executable file (.exe) of EasyModeller with administrative privilege (by right clicking it and selecting "Run as administrator"). Since EasyModeller uses the Microsoft Excel plot function to plot the profile graph, it is necessary to have Microsoft Excel installed in the system. A PDB viewer like Rasmol is required to visualize the generated model.
License: Free to use
Any restrictions to use by non-academics: None
We thank Centre for Modelling, Simulation and Design (CMSD), University of Hyderabad for the computational facilities. We duly acknowledge Council of Scientific and Industrial Research (CSIR), Govt. of India for providing senior research fellowship to PA and UGC for providing GATE fellowship to BKK.
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