Example Jupyter notebook illustrating how mdciao can be used in API mode.
<p>In this case we compute the Gα-β2AR-interface contact frequencies. The 12 notebook cells are shown in two panels next to each other, A) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref001" target="_blank">1&...
Saved in:
| Main Author: | |
|---|---|
| Other Authors: | |
| Published: |
2025
|
| Subjects: | |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1852021181294575616 |
|---|---|
| author | Guillermo Pérez-Hernández (21156182) |
| author2 | Peter W. Hildebrand (374828) |
| author2_role | author |
| author_facet | Guillermo Pérez-Hernández (21156182) Peter W. Hildebrand (374828) |
| author_role | author |
| dc.creator.none.fl_str_mv | Guillermo Pérez-Hernández (21156182) Peter W. Hildebrand (374828) |
| dc.date.none.fl_str_mv | 2025-04-21T17:42:53Z |
| dc.identifier.none.fl_str_mv | 10.1371/journal.pcbi.1012837.g003 |
| dc.relation.none.fl_str_mv | https://figshare.com/articles/figure/Example_Jupyter_notebook_illustrating_how_mdciao_can_be_used_in_API_mode_/28833254 |
| dc.rights.none.fl_str_mv | CC BY 4.0 info:eu-repo/semantics/openAccess |
| dc.subject.none.fl_str_mv | Biochemistry Genetics Molecular Biology Biotechnology Science Policy Infectious Diseases Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Information Systems not elsewhere classified widely used concept jupyter notebook tutorials automatically producing annotated provides numerous examples div >< p advanced mdciao functions wide spectrum target residues source code simulation data sequence identity ready figures python application present mdciao packaged solutions online lookups molecular dynamics mdciao offers mdciao </ made possible keeping customizability including guides fly query expert users expert ones building upon |
| dc.title.none.fl_str_mv | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| dc.type.none.fl_str_mv | Image Figure info:eu-repo/semantics/publishedVersion image |
| description | <p>In this case we compute the Gα-β2AR-interface contact frequencies. The 12 notebook cells are shown in two panels next to each other, A) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref001" target="_blank">1</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref007" target="_blank">7</a>] and B) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref008" target="_blank">8</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref012" target="_blank">12</a>]. The outputs of cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref003" target="_blank">3</a>] and [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] have been edited out ([…]) but are analogous to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.g002" target="_blank">Fig 2A</a>) and can be found in the online documentation and the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook. The main computation is the generation of the mdciao object, intf, in cell [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] which can later be used to generate multiple text, tabular, and graphic reports of the frequencies, distributions, and time-traces anywhere else in the notebook. A full version of this notebook, with full outputs and high-res pictures can be found in the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook, and an online version can be found at <a href="https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples" target="_blank">https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples</a>. Locally, mdciao users can access this notebook (and others) by invoking the CLT mdc_notebooks.py (cf. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.t001" target="_blank">Table 1</a>).</p> |
| eu_rights_str_mv | openAccess |
| id | Manara_af42431acabdcb835ef26c287c464bb7 |
| identifier_str_mv | 10.1371/journal.pcbi.1012837.g003 |
| network_acronym_str | Manara |
| network_name_str | ManaraRepo |
| oai_identifier_str | oai:figshare.com:article/28833254 |
| publishDate | 2025 |
| repository.mail.fl_str_mv | |
| repository.name.fl_str_mv | |
| repository_id_str | |
| rights_invalid_str_mv | CC BY 4.0 |
| spelling | Example Jupyter notebook illustrating how mdciao can be used in API mode.Guillermo Pérez-Hernández (21156182)Peter W. Hildebrand (374828)BiochemistryGeneticsMolecular BiologyBiotechnologyScience PolicyInfectious DiseasesBiological Sciences not elsewhere classifiedChemical Sciences not elsewhere classifiedInformation Systems not elsewhere classifiedwidely used conceptjupyter notebook tutorialsautomatically producing annotatedprovides numerous examplesdiv >< padvanced mdciao functionswide spectrumtarget residuessource codesimulation datasequence identityready figurespython applicationpresent mdciaopackaged solutionsonline lookupsmolecular dynamicsmdciao offersmdciao </made possiblekeeping customizabilityincluding guidesfly queryexpert usersexpert onesbuilding upon<p>In this case we compute the Gα-β2AR-interface contact frequencies. The 12 notebook cells are shown in two panels next to each other, A) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref001" target="_blank">1</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref007" target="_blank">7</a>] and B) cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref008" target="_blank">8</a>] to [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref012" target="_blank">12</a>]. The outputs of cells [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref003" target="_blank">3</a>] and [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] have been edited out ([…]) but are analogous to <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.g002" target="_blank">Fig 2A</a>) and can be found in the online documentation and the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook. The main computation is the generation of the mdciao object, intf, in cell [<a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.ref005" target="_blank">5</a>] which can later be used to generate multiple text, tabular, and graphic reports of the frequencies, distributions, and time-traces anywhere else in the notebook. A full version of this notebook, with full outputs and high-res pictures can be found in the <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.s001" target="_blank">S1</a> Notebook, and an online version can be found at <a href="https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples" target="_blank">https://proteinformatics.uni-leipzig.de/mdciao/gallery.html#examples</a>. Locally, mdciao users can access this notebook (and others) by invoking the CLT mdc_notebooks.py (cf. <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1012837#pcbi.1012837.t001" target="_blank">Table 1</a>).</p>2025-04-21T17:42:53ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1012837.g003https://figshare.com/articles/figure/Example_Jupyter_notebook_illustrating_how_mdciao_can_be_used_in_API_mode_/28833254CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/288332542025-04-21T17:42:53Z |
| spellingShingle | Example Jupyter notebook illustrating how mdciao can be used in API mode. Guillermo Pérez-Hernández (21156182) Biochemistry Genetics Molecular Biology Biotechnology Science Policy Infectious Diseases Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Information Systems not elsewhere classified widely used concept jupyter notebook tutorials automatically producing annotated provides numerous examples div >< p advanced mdciao functions wide spectrum target residues source code simulation data sequence identity ready figures python application present mdciao packaged solutions online lookups molecular dynamics mdciao offers mdciao </ made possible keeping customizability including guides fly query expert users expert ones building upon |
| status_str | publishedVersion |
| title | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| title_full | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| title_fullStr | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| title_full_unstemmed | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| title_short | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| title_sort | Example Jupyter notebook illustrating how mdciao can be used in API mode. |
| topic | Biochemistry Genetics Molecular Biology Biotechnology Science Policy Infectious Diseases Biological Sciences not elsewhere classified Chemical Sciences not elsewhere classified Information Systems not elsewhere classified widely used concept jupyter notebook tutorials automatically producing annotated provides numerous examples div >< p advanced mdciao functions wide spectrum target residues source code simulation data sequence identity ready figures python application present mdciao packaged solutions online lookups molecular dynamics mdciao offers mdciao </ made possible keeping customizability including guides fly query expert users expert ones building upon |