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{ "affiliations": [ { "name": "Institut Pasteur de Montevideo" } ], "person_or_org": { "family_name": "Florencia Klein", "identifiers": [ { "identifier": "0000-0003-4099-9907", "scheme": "orcid" } ], "name": "Florencia Klein", "type": "personal" } }, { "affiliations": [ { "name": "Institut Pasteur de Montevideo" } ], "person_or_org": { "family_name": "Mat\u00edas Machado", "identifiers": [ { "identifier": "0000-0002-9971-4710", "scheme": "orcid" } ], "name": "Mat\u00edas Machado", "type": "personal" } }, { "affiliations": [ { "name": "Institut Pasteur de Montevideo" } ], "person_or_org": { "family_name": "Mart\u00edn So\u00f1ora", "identifiers": [ { "identifier": "0000-0003-3872-6117", "scheme": "orcid" } ], "name": "Mart\u00edn So\u00f1ora", "type": "personal" } }, { "affiliations": [ { "name": "Institut Pasteur de Montevideo" } ], "person_or_org": { "family_name": "Sergio Pantano", "identifiers": [ { "identifier": "0000-0001-6435-4543", "scheme": "orcid" } ], "name": "Sergio Pantano", "type": "personal" } } ], "description": "
This dataset contains the trajectories of 10 microseconds-long coarse-grained molecular dynamics simulations of SARS-CoV2 Spike´s RBD glycosylated at Asn331 and Asn343. The initial coordinates correspond to amino acids 327 to 532 taken from the PDB structure 6VSB. Missing loops and glycosylation trees were added with CHARMM-GUI (http://www.charmm-gui.org).
\n\nThere are two different sets of simulations corresponding to Core Complex and High Mannose. Simulations were performed using the SIRAH force field running with the Amber18 package at the Uruguayan National Center for Supercomputing (ClusterUY) under the conditions reported in Machado et al. JCTC 2019, adding 150 mM NaCl according to Machado & Pantano JCTC 2020. Glycan parameters are available upon request.
\n\nThe files RBD-Man9_SIRAHcg_rawdata_0-6us.tar and RBD-Man9_SIRAHcg_rawdata_6-10us.tar, contain all the raw information required to visualize (on VMD), analyze, and backmap the simulations of High Mannose glycosylated RBD. Analogous information for Core-complex glycosylations is contained in files RBD-Core-complex_SIRAHcg_rawdata_0-6us.tar and RBD-Core-complex_SIRAHcg_rawdata_6-10us.tar
\n\nStep-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.
\n\nAdditionally, files with names ending in SIRAHcg_10us_glycoprot.tar contain only the protein coordinates, while file names ending with SIRAHcg_10us_glycoprot_skip10ns.tar contains one frame every 10ns.
\n\nTo take a quick look at a trajectory:
\n\n1- Untar the file RBD-Core-complex_SIRAHcg_10us_prot_skip10ns.tar
\n\n2- Open the trajectory on VMD 1.9.3 using the command line:
\n\nvmd glyco-RBD_SIRAHcg_glycoprot.prmtop glyco-RBD_SIRAHcg_glycoprot.ncrst glyco-RBD_SIRAHcg_glycoprot_10us_skip10ns.nc -e sirah_vmdtk.tcl
\n\nNote that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc.
\n\nThis dataset is part of the SIRAH-CoV2 initiative.
\n\nFor further details, please contact Pablo Garay (pgaray@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
", "languages": [ { "id": "eng", "title": { "en": "English" } } ], "publication_date": "2020-06-22", "publisher": "Zenodo", "references": [ { "reference": "Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)" }, { "reference": "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)" }, { "reference": "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)" } ], "resource_type": { "id": "dataset", "title": { "de": "Datensatz", "en": "Dataset" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "Coronavirus" }, { "subject": "simulation" }, { "subject": "glycosylation" }, { "subject": "SIRAH" }, { "subject": "coarse-grain" }, { "subject": "COVID-19" }, { "subject": "SARS" } ], "title": "SIRAH-CoV2 initiative: Glycosylated RBD", "version": "SIRAH version 2.3, Amber18" }, "parent": { "access": { "owned_by": { "user": 96953 } }, "communities": { "default": "10f33f78-3f29-41b6-bb10-f757a8f03cb8", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-03-16T11:40:44.487619+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "10f33f78-3f29-41b6-bb10-f757a8f03cb8", "links": {}, "metadata": { "curation_policy": "The Coronavirus Disease Research Community - COVID-19 is curated by a selected team of experts nominated by OpenAIRE* (see list below). Each time a Zenodo user wants to add a record into the community, an email is sent to the curators that will decide whether to include the record or not.
\r\n\r\nOnly records that may be relevant to the Corona Virus Disease (COVID-19) or the SARS-CoV-2 should be included in this community. The Community curators are not able to edit records, therefore they may ask the corresponding authors to modify the record metadata when necessary, to provide the readers/users with more detailed information according to the FAIR principle of Open Science.
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\r\n\r\nThe curation team is reachable through the following email address for further clarification or information: covid19@openaire.eu.
\r\n\r\nCurator List:
\r\n\r\n* OpenAIRE: open access and open science training and support since 2009. OpenAIRE is the largest aggregator of European Commission funded research outputs and beyond, also delivering on-demand services for research communities.
\r\n", "page": "This community collects research outputs that may be relevant to the Coronavirus Disease (COVID-19) or the SARS-CoV-2. Scientists are encouraged to upload their outcome in this collection to facilitate sharing and discovery of information. Although Open Access articles and datasets are recommended, also closed and restricted access material are accepted. All types of research outputs can be included in this Community (Publication, Poster, Presentation, Dataset, Image, Video/Audio, Software, Lesson, Other).
\r\n\r\nThe recent Corona Virus Disease (COVID-19) outbreak is requiring unseen efforts of collaboration of the scientific community that need to act fast and to share results in an unpredictable manner. In order to facilitate the Scientist efforts, this community was created to collect all research results that could be relevant for the scientific community working on the Corona Virus Disease (COVID-19) and SARS-CoV-2.
\r\n\r\nAlthough Open Access articles and datasets are recommended, also closed and restricted access material are accepted. All types of research outputs can be included in this Community (Publication, Poster, Presentation, Dataset, Image, Video/Audio, Software, Lesson, Other).
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