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2 changes: 1 addition & 1 deletion pages/your_domain/structural_bioinformatics.md
Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,6 @@ Experimentally solved atomic structures of molecules can be obtained by several
* To extend molecular context, structure models can be visualised and analysed along with respective volume maps and {% tool "uniprot" %} sequences using data aggregators such as {% tool "3dbionotes" %}. This can be done independently of whether they have been published in PDB and EMDB. A collection of biochemical, biomedical and validation annotations would be mapped on the structure model coordinates and sequence to let the user better understand macromolecular function and interactions. Users can also use the {% tool "covid-19-structural-hub" %}, a dedicated summary view for all published SARS-CoV-2 structure models.
* As well as for computationally solved structures, model coordinates and metadata for experimentally solved structures are also preferably stored using the standard PDB archive format {% tool "pdbx-mmcif-format-and-tools" %} and the {% tool "pdbx-mmcif-modelcif-extension-dictionary" %}, respectively.
* Data model and metadata standards for submitting data underpinning macromolecular models depend on the experimental method used. EMDB map distribution format description has broadly followed [CCP4 map format](https://www.ccp4.ac.uk/html/maplib.html) and [MRC map format](https://www2.mrc-lmb.cam.ac.uk/research/locally-developed-software/image-processing-software/). Metadata is contained in a header file, an XML file that follows the XSD data model. EMPIAR data model schema consists of the main empiar.xsd XML schema file and additional requirements in empiar.sch in Schematron format (see [here](https://ftp.ebi.ac.uk/pub/databases/emtest/empiar/schema/) for more details). BMRB (meta)data distribution format is based on NMR-STAR, an extension of the Self-defining Text Archive and Retrieval (STAR) file format.
* As image processing framework, users can operate with workflow managers FAIR compliant such as {% tool "scipion" %} to obtain macromolecular models using Electron Microscopy (3DEM). It integrates several software packages while taking care of formats and conversions and data submissions to public repositories such as EMDB and EMPIAR. It is also possible to deploy a cloud-compatible version of Scipion either in a single server or in a cluster with {% tool "scipioncloud" %}. It can be also deployed in EOSC cloud infrastructures (see [here](https://marketplace.eosc-portal.eu/services/eosc.cnb-csic.scipioncloud?pv=search/all&q=scipioncloud) for details).
* As image processing framework, users can operate with workflow managers FAIR compliant such as {% tool "scipion" %} to obtain macromolecular models using Electron Microscopy (3DEM). It integrates several software packages while taking care of formats and conversions and data submissions to public repositories such as EMDB and EMPIAR. It is also possible to deploy a cloud-compatible version of Scipion either in a single server or in a cluster with {% tool "scipioncloud" %}.
* {% tool "aria" %} is a platform that projects and infrastructures can use to manage access, from proposal submission to reporting. It provides tools for facilities within a distributed infrastructure to manage their equipment. ARIA will soon allow linking of output data and metadata with proposals, publications and other outputs.