Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing
Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal com...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-09-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/18/14245 |
| _version_ | 1797579627910135808 |
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| author | James M. Krieger Carlos Oscar S. Sorzano Jose Maria Carazo |
| author_facet | James M. Krieger Carlos Oscar S. Sorzano Jose Maria Carazo |
| author_sort | James M. Krieger |
| collection | DOAJ |
| description | Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development. |
| first_indexed | 2024-03-10T22:38:51Z |
| format | Article |
| id | doaj.art-1d9e26bbcf5d4460948b0a036807d35b |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T22:38:51Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-1d9e26bbcf5d4460948b0a036807d35b2023-11-19T11:09:56ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-09-0124181424510.3390/ijms241814245Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image ProcessingJames M. Krieger0Carlos Oscar S. Sorzano1Jose Maria Carazo2Biocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, SpainBiocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, SpainBiocomputing Unit, National Centre for Biotechnology (CNB CSIC), Campus Universidad Autónoma de Madrid, Darwin 3, Cantoblanco, 28049 Madrid, SpainMacromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common theme has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows, together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.https://www.mdpi.com/1422-0067/24/18/14245global protein dynamicssoftware integration workflowscryo-electron microscopynormal mode analysiselastic network modelsensemble analysis |
| spellingShingle | James M. Krieger Carlos Oscar S. Sorzano Jose Maria Carazo Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing International Journal of Molecular Sciences global protein dynamics software integration workflows cryo-electron microscopy normal mode analysis elastic network models ensemble analysis |
| title | Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing |
| title_full | Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing |
| title_fullStr | Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing |
| title_full_unstemmed | Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing |
| title_short | Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Workflow Engine Enabling Integration of Databases, Simulations and Cryo-Electron Microscopy Image Processing |
| title_sort | scipion em prody a graphical interface for the prody python package within the scipion workflow engine enabling integration of databases simulations and cryo electron microscopy image processing |
| topic | global protein dynamics software integration workflows cryo-electron microscopy normal mode analysis elastic network models ensemble analysis |
| url | https://www.mdpi.com/1422-0067/24/18/14245 |
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