EasyModel: a user-friendly web-based interface based on MODELLER
Abstract Three-dimensional protein structures are invaluable sources of information for the functional annotation of protein molecules. Describing the function of a protein sequence is one of the most common problems in biology. Generally, this problem can be facilitated by studying the tertiary str...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-10-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-44505-9 |
| _version_ | 1797560177473355776 |
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| author | Seyed Shahriar Arab Alireza Dantism |
| author_facet | Seyed Shahriar Arab Alireza Dantism |
| author_sort | Seyed Shahriar Arab |
| collection | DOAJ |
| description | Abstract Three-dimensional protein structures are invaluable sources of information for the functional annotation of protein molecules. Describing the function of a protein sequence is one of the most common problems in biology. Generally, this problem can be facilitated by studying the tertiary structure of proteins. In the lack of protein structures, comparative modeling often provides a useful three-dimensional model of the protein associated with at least one known protein structure. Comparative modeling predicts the tertiary structure of a certain protein sequence (target) mainly based on its homological sequence to the sequence of one or more proteins with known structures (templates). MODELLER is one of the most widely used tools for homology or comparative modeling of three-dimensional protein structures. However, most users find it challenging to start with MODELLER as it is a command line based and requires knowledge of basic Python scripting to use it efficiently. In this study, a web-based interface has been designed to predict the tertiary structure of proteins based on Modeller, which does the comparative modeling automatically, and uses PHP and Python programming languages. This tool is called “EasyModel” and is available at http://bioinf.modares.ac.ir/software/easymodel/ . EasyModel provides a straightforward graphical interface for Modeller that can be used in only one browser. |
| first_indexed | 2024-03-10T17:55:41Z |
| format | Article |
| id | doaj.art-296d91933a724decb4636058b050fcb2 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-10T17:55:41Z |
| publishDate | 2023-10-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-296d91933a724decb4636058b050fcb22023-11-20T09:11:51ZengNature PortfolioScientific Reports2045-23222023-10-011311710.1038/s41598-023-44505-9EasyModel: a user-friendly web-based interface based on MODELLERSeyed Shahriar Arab0Alireza Dantism1Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares UniversityDepartment of Biophysics, Faculty of Biological Sciences, Tarbiat Modares UniversityAbstract Three-dimensional protein structures are invaluable sources of information for the functional annotation of protein molecules. Describing the function of a protein sequence is one of the most common problems in biology. Generally, this problem can be facilitated by studying the tertiary structure of proteins. In the lack of protein structures, comparative modeling often provides a useful three-dimensional model of the protein associated with at least one known protein structure. Comparative modeling predicts the tertiary structure of a certain protein sequence (target) mainly based on its homological sequence to the sequence of one or more proteins with known structures (templates). MODELLER is one of the most widely used tools for homology or comparative modeling of three-dimensional protein structures. However, most users find it challenging to start with MODELLER as it is a command line based and requires knowledge of basic Python scripting to use it efficiently. In this study, a web-based interface has been designed to predict the tertiary structure of proteins based on Modeller, which does the comparative modeling automatically, and uses PHP and Python programming languages. This tool is called “EasyModel” and is available at http://bioinf.modares.ac.ir/software/easymodel/ . EasyModel provides a straightforward graphical interface for Modeller that can be used in only one browser.https://doi.org/10.1038/s41598-023-44505-9 |
| spellingShingle | Seyed Shahriar Arab Alireza Dantism EasyModel: a user-friendly web-based interface based on MODELLER Scientific Reports |
| title | EasyModel: a user-friendly web-based interface based on MODELLER |
| title_full | EasyModel: a user-friendly web-based interface based on MODELLER |
| title_fullStr | EasyModel: a user-friendly web-based interface based on MODELLER |
| title_full_unstemmed | EasyModel: a user-friendly web-based interface based on MODELLER |
| title_short | EasyModel: a user-friendly web-based interface based on MODELLER |
| title_sort | easymodel a user friendly web based interface based on modeller |
| url | https://doi.org/10.1038/s41598-023-44505-9 |
| work_keys_str_mv | AT seyedshahriararab easymodelauserfriendlywebbasedinterfacebasedonmodeller AT alirezadantism easymodelauserfriendlywebbasedinterfacebasedonmodeller |