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

• Published in: International journal of molecular sciences Vol. 24; no. 18; p. 14245
• Main Authors: Krieger, James M, Sorzano, Carlos Oscar S, Carazo, Jose Maria
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 18.09.2023; MDPI
• Subjects: Applications programming; Biophysics; cryo-electron microscopy; Cryoelectron Microscopy; Databases, Factual; Deformation; elastic network models; Electron microscopy; ensemble analysis; Equipment and supplies; Flexibility; global protein dynamics; Image processing; Image Processing, Computer-Assisted; Microscopy; Molecular dynamics; Motion; normal mode analysis; Signal transduction; Simulation; Simulation methods; software integration workflows; Software packages; Workflow; hybrid simulations; normal mode analysis; ensemble analysis; elastic network models; software integration workflows; global protein dynamics; principal component analysis; cryo-electron microscopy
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms241814245

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.