https://3demmethods.i2pc.es/index.php?action=history&feed=atom&title=2023Krieger_ScipionPrody 2026-05-24T20:20:10Z Revision history for this page on the wiki MediaWiki 1.44.2 https://3demmethods.i2pc.es/index.php?title=2023Krieger_ScipionPrody&diff=4522&oldid=prev 2024-01-10T07:45:22Z

<p>Created page with &quot;== Citation == Krieger, James M. / Sorzano, Carlos Oscar S. / Carazo, Jose Maria. Scipion-EM-ProDy: A Graphical Interface for the ProDy Python Package within the Scipion Work...&quot;</p> <p><b>New page</b></p><div>== Citation ==<br /> <br /> Krieger, James M. / Sorzano, Carlos Oscar S. / Carazo, Jose Maria. 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. 2023. Intl. J. of Molecular Sciences, Vol. 24, No. 18, p. 14245 <br /> <br /> == Abstract ==<br /> <br /> Macromolecular assemblies, such as protein complexes, undergo continuous structural<br /> dynamics, including global reconfigurations critical for their function. Two fast analytical methods<br /> are widely used to study these global dynamics, namely elastic network model normal mode analysis<br /> and principal component analysis of ensembles of structures. These approaches have found wide use<br /> in various computational studies, driving the development of complex pipelines in several software<br /> packages. One common theme has been conformational sampling through hybrid simulations<br /> incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality<br /> is only available for experienced programmers with limited capabilities for other users. We have,<br /> therefore, integrated one popular and extensively developed software for such analyses, the ProDy<br /> Python application programming interface, into the Scipion workflow engine. This enables a wider<br /> range of users to access a complete range of macromolecular dynamics pipelines beyond the core<br /> functionalities available in its command-line applications and the normal mode wizard in VMD. The<br /> new protocols and pipelines can be further expanded and integrated into larger workflows, together<br /> with other software packages for cryo-electron microscopy image analysis and molecular simulations.<br /> We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made<br /> available by its development.<br /> <br /> == Keywords ==<br /> <br /> == Links ==<br /> <br /> https://www.mdpi.com/1422-0067/24/18/14245<br /> <br /> == Related software ==<br /> <br /> == Related methods ==<br /> <br /> == Comments ==</div>

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