Package: scipion-em-prody
This plugin provide a wrapper aroundProDysoftware: A Python Package for Protein Dynamics AnalysisInstallationYou will need to use 3.0+ version of Scipion to be able to run these protocols. To install the plugin, you have one option so far:Developer’s versiondownload repositorygit clone https://github.com/scipion-em/scipion-em-prody.gitinstallscipion3 installp -p ./scipion-em-prody --develProDy software will be installed automatically with the plugin but you can also use an another version
by installing that one in your scipion3 environment.Important:you need to have conda (miniconda3 or anaconda3) pre-installed to use this program.Configuration variablesCONDA_ACTIVATION_CMD: If undefined, it will rely on conda command being in the
PATH (not recommended), which can lead to execution problems mixing scipion
python with conda ones. One example of this could can be seen below but
depending on your conda version and shell you will need something different:
CONDA_ACTIVATION_CMD = eval “$(/extra/miniconda3/bin/conda shell.bash hook)”ProtocolsProDyANM for anisotropic network model (ANM) normal mode analysisProDyRTB for rotation and translation blocks (RTB) normal mode analysisProDyDefvec for calculating deformation vectors between two structuresProDyEdit to edit normal modes to different nodes/atoms, including slice and extendProDyCompare for comparing motions between different calculations including from continuousflexProDySelect for atom selectionProDyAlign for alignment two structures, including atom matching and superpositionProDyBiomol for building biologically relevant molecular assembliesProDyAddPDBs for adding multiple structures into one PDB fileProDyPDBFixer for fixing missing atomsProDyImportModes for importing modes calculated outside Scipion, including from GromacsProDyBuildPDBEnsemble for building ensembles from heterogeneous atomic structuresProDyImportEnsemble for importing ensembles calculated outside ScipionProDyPCA for principal component analysis based on ensembles of atomic structuresProDyProject for projecting ensembles of structures onto principal components or normal modesProDyGNM for Gaussian network model (GNM) analysisProDyDomainDecomp for dynamical domain decomposition based on GNM modesProDyClustENM for ClustENM and ClustENMD hybrid SimulationsProDyRMSD for RMSD clustering and reorderingViewersProDyComparisonsViewer for viewing matrices and bar graphs quantifying motion similaritiesProDyModeViewer for viewing modes of motion in the VMD plugin NMWizProDyGNMViewer for viewing GNM mode shapes and covariance or cross-correlation matricesProDyDomainViewer for viewing dynamical domainsProDyProjectionsViewer for viewing conformational landscapes from projecting ensembles onto modesReferencesKrieger, J.M.; S. Sorzano, C.O.; Carazo, J.M. 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. Preprints 2023, 2023080828Zhang S, Krieger JM, Zhang Y, Kaya C, Kaynak B, Mikulska-Ruminska K, Doruker P, Li H, Bahar I (2021). ProDy 2.0: Increased scale and scope after 10 years of protein dynamics modelling with Python. Bioinformatics, btab187.Bakan A, Meireles LM, Bahar I ProDy: Protein Dynamics Inferred from Theory and Experiments 2011 Bioinformatics 27(11):1575-1577Bakan A, Dutta A, Mao W, Liu Y, Chennubhotla C, Lezon TR, Bahar I Evol and ProDy for Bridging Protein Sequence Evolution and Structural Dynamics 2014 Bioinformatics 30(18):2681-2683