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This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Nucleocapsid protein N-terminal RNA binding domain (PDB id:6M3M). Simulations have been 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.
\n\nThe files 6M3M_SIRAHcg_rawdata.tar contains all the raw information required to visualize (on VMD), analyze, backmap, and eventually continue the simulations using Amber18 or higher. Step-By-Step tutorials for running, visualizing, and analyzing CG trajectories using SirahTools can be found at www.sirahff.com.
\n\nAdditionally, the file 6M3M_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6M3M_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.
\n\nTo take a quick look at the trajectory:
\n\n1- Untar the file 6M3M_SIRAHcg_10us_prot_skip10ns.tar
\n\n2- Open the trajectory on VMD using the command line:
\n\nvmd 6W4B_SIRAHcg_prot.prmtop 6W4B_SIRAHcg_prot.ncrst 6W4B_SIRAHcg_prot_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 Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
", "languages": [ { "id": "eng", "title": { "en": "English" } } ], "publication_date": "2020-04-17", "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": "drug design" }, { "subject": "simulation" }, { "subject": "SIRAH" }, { "subject": "coarse-grain" }, { "subject": "CoV2 nucleocapsid" }, { "subject": "COVID-19" }, { "subject": "SARS" } ], "title": "SIRAH-CoV2 initiative: Nucleocapsid protein N-terminal RNA binding domain (PDB id:6M3M)", "version": "SIRAH version 2.2, 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.
\r\n\r\nIf after its acceptance, a record is subsequently found not to be compliant, we reserve the right to remove it from the community.
\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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