cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.3814372
title: SIRAH-CoV2 initiative: ORF7A enconded accessory protein (PDB id:6W37)

description: This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 ORF7a encoded accessory protein (PDB id: 6W37). 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. The file 6W37_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. Additionally, the file 6W37_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W37_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6W37_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6w37_SIRAHcg_prot.prmtop 6w37_SIRAHcg_prot.ncrst 6w37_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Martín Soñora (msonora@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"]}
DOI: 10.5281/zenodo.3820673
title: SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)

description: This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). 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. The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar, contain 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. Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"]}
DOI: 10.5281/zenodo.3820672
title: SIRAH-CoV2 initiative: co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ)

description: This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of the co-factor complex of NSP7 and the C-terminal domain of NSP8 from SARS CoV-2 (PDBid:6WIQ). 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. The files 6WIQ_SIRAHcg_rawdata_0-5us.tar, and 6WIQ_SIRAHcg_rawdata_5-10us.tar, contain 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. Additionally, the file 6WIQ_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6WIQ_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6WIQ_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD using the command line: vmd 6WIQ_SIRAHcg_prot.prmtop 6WIQ_SIRAHcg_prot.ncrst 6WIQ_SIRAHcg_10us_prot_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)"]}
DOI: 10.6084/m9.figshare.13564859.v1
title: Result of MCMC run in disaggregation paper

description: MCMC result from paper entitled "disaggregation: An R Package for Bayesian Spatial Disaggregation Modelling"arXiv:2001.04847<br>Result of the 74 hour MCMC run that is compared with the result from the disaggregation package. Result is in RData format.
DOI: 10.6084/m9.figshare.13564859
title: Result of MCMC run in disaggregation paper

description: MCMC result from paper entitled "disaggregation: An R Package for Bayesian Spatial Disaggregation Modelling"arXiv:2001.04847<br>Result of the 74 hour MCMC run that is compared with the result from the disaggregation package. Result is in RData format.
DOI: 10.6084/m9.figshare.13542143.v1
title: Land surface temperature raster

description: Land surface temperature raster approximately 5x5km2 across Madagascar.
DOI: 10.6084/m9.figshare.13542143
title: Land surface temperature raster

description: Land surface temperature raster approximately 5x5km2 across Madagascar.
DOI: 10.6084/m9.figshare.13542137
title: Enhanced vegetation index raster

description: Enhanced vegetation index raster approximately 5x5km2 across Madagascar.
DOI: 10.6084/m9.figshare.13542116
title: Elevation raster

description: Elevation raster approximately 5x5km2 across Madagascar.
DOI: 10.6084/m9.figshare.13542116.v1
title: Elevation raster

description: Elevation raster approximately 5x5km2 across Madagascar.
DOI: 10.6084/m9.figshare.13542110
title: Population raster

description: Population raster approximately 5x5km2 across Madagascar.
DOI: 10.5281/zenodo.4434601
title: Herbarium of the University of Milan: The Sordelli Collection

description: <strong>Abstract</strong> This dataset contains the Sordelli collection of the Herbarium of the University of Milan. Specimens (<em>exsiccata</em>) were collected between 1851 and 1911 in Milan and its province and in Como lowland. <strong>Dataset content</strong> The dataset is composed by 5686 images in JPEG format. Their dimensions are 6000x4000 pixels and the resolution is about 305 DPI. For further information about image acquisition and digitization, please refer to the publication below. <br> The dataset has been divided into 14 ZIP archives sized 4GB each approx, but the last one. The whole dataset is almost 52 GB. A subset made of 20 random images is provided as example material in the file "example_copies.zip". Both the main dataset and the example subset are provided with CSV files containing details about specimens. <strong>Terms of use</strong> The dataset is open access for scientific research and non-commercial purposes.<br> The authors require to acknowledge their work and, in case of scientific publication, to cite the following paper: Baratè, A., Caccianiga, M., Caporali, E., Ludovico, L.A., Pinto, S., Presti, G., Sala, E., Testa, A.: Preserving and Promoting the Herbarium of the University of Milan through Digital Technologies. In: Proceedings of Florence HeriTech 2020, IOP Conference Series: Materials Science and Engineering, vol. 949, pp. 012066-1–012066-9. IOP (2020).<br> ISSN: 1757-899X (online), 1757-8981 (print)
DOI: 10.6084/m9.figshare.13542110.v1
title: Population raster

description: Population raster approximately 5x5km2 across Madagascar.
DOI: 10.5281/zenodo.4434600
title: Herbarium of the University of Milan: The Sordelli Collection

description: <strong>Abstract</strong> This dataset contains the Sordelli collection of the Herbarium of the University of Milan. Specimens (<em>exsiccata</em>) were collected between 1851 and 1911 in Milan and its province and in Como lowland. <strong>Dataset content</strong> The dataset is composed by 5686 images in JPEG format. Their dimensions are 6000x4000 pixels and the resolution is about 305 DPI. For further information about image acquisition and digitization, please refer to the publication below. <br> The dataset has been divided into 14 ZIP archives sized 4GB each approx, but the last one. The whole dataset is almost 52 GB. A subset made of 20 random images is provided as example material in the file "example_copies.zip". Both the main dataset and the example subset are provided with CSV files containing details about specimens. <strong>Terms of use</strong> The dataset is open access for scientific research and non-commercial purposes.<br> The authors require to acknowledge their work and, in case of scientific publication, to cite the following paper: Baratè, A., Caccianiga, M., Caporali, E., Ludovico, L.A., Pinto, S., Presti, G., Sala, E., Testa, A.: Preserving and Promoting the Herbarium of the University of Milan through Digital Technologies. In: Proceedings of Florence HeriTech 2020, IOP Conference Series: Materials Science and Engineering, vol. 949, pp. 012066-1–012066-9. IOP (2020).<br> ISSN: 1757-899X (online), 1757-8981 (print)
DOI: 10.15468/cvhzp2
title: Report on species of the genus Tumicla Wallengren, 1863 in Gabon (Lepidoptera Erebidae: Arctiinae: Lithosiini)

description: This dataset contains the digitized treatments in Plazi based on the original journal article Durante, Antonio, Apinda-Legnouo, Emelie Arlette (2020): Report on species of the genus Tumicla Wallengren, 1863 in Gabon (Lepidoptera Erebidae: Arctiinae: Lithosiini). Zootaxa 4868 (1): 90-116, DOI: https://doi.org/10.11646/zootaxa.4868.1.5
DOI: 10.5281/zenodo.3865479
title: SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF)

description: This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). 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. Zinc ions were parameterized as reported in Klein et al. 2020. The files 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar, contain 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. Additionally, the file 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Martin Soñora (msonora@pasteur.edu.uy) Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano, JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano, Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", "Klein et al., JCIM, 2020 (DOI:10.1021/acs.jcim.0c00160)"]}
DOI: 10.5281/zenodo.3865478
title: SIRAH-CoV2 initiative: RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 (PDB id:7BTF)

description: This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 RNA-dependent RNA polymerase in complex with cofactors Nsp7 and Nsp8 and Zinc (PDB id: 7BTF). 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. Zinc ions were parameterized as reported in Klein et al. 2020. The files 7BTF_SIRAHcg_rawdata_0-2us.tar, 7BTF_SIRAHcg_rawdata_2-6us.tar, and 7BTF_SIRAHcg_rawdata_6-10us.tar, contain 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. Additionally, the file 7BTF_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 7BTF_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 7BTF_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 7BTF_SIRAHcg_prot.prmtop 7BTF_SIRAHcg_prot.ncrst 7BTF_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Martin Soñora (msonora@pasteur.edu.uy) Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano, JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano, Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", "Klein et al., JCIM, 2020 (DOI:10.1021/acs.jcim.0c00160)"]}
DOI: 10.5517/ccdc.csd.cc1pnzbn
title: CCDC 1569292: Experimental Crystal Structure Determination

description: Related Article: Jonathan Bould, Oleg Tok, Vincenzo Passarelli, Michael G. S. Londesborough, Ramón Macías|2020|Inorg.Chem.|59|17958|doi:10.1021/acs.inorgchem.0c02205
DOI: 10.5517/ccdc.csd.cc1pnzcp
title: CCDC 1569293: Experimental Crystal Structure Determination

description: Related Article: Jonathan Bould, Oleg Tok, Vincenzo Passarelli, Michael G. S. Londesborough, Ramón Macías|2020|Inorg.Chem.|59|17958|doi:10.1021/acs.inorgchem.0c02205
DOI: 10.5517/ccdc.csd.cc21xyhf
title: CCDC 1904655: Experimental Crystal Structure Determination

description: Related Article: Bingjie Zhang, Yueyan Zhang, Xiaodong Yang, Guoping Li, Sikun Zhang, Yanfeng Zhang, Demei Yu, Zishun Liu, Gang He|2020|Chem.Mater.|32|10575|doi:10.1021/acs.chemmater.0c03661
DOI: 10.5517/ccdc.csd.cc24ysjf
title: CCDC 1994835: Experimental Crystal Structure Determination

description: Related Article: Amani Toumi, Sarra Boudriga, Khaled Hamden, Mansour Sobeh, Mohammed Cheurfa, Moheddine Askri, Michael Knorr, Carsten Strohmann, Lukas Brieger|2020|Bioorg.Chem.|106|104507|doi:10.1016/j.bioorg.2020.104507
DOI: 10.5517/ccdc.csd.cc25c3b0
title: CCDC 2006671: Experimental Crystal Structure Determination

description: Related Article: Khalil Yamani, Hugo Pierre, Alexis Archambeau, Christophe Meyer, Janine Cossy|2020|Angew.Chem.,Int.Ed.|59|18505|doi:10.1002/anie.202008572
DOI: 10.5517/ccdc.csd.cc25vd5m
title: CCDC 2021360: Experimental Crystal Structure Determination

description: Related Article: Khanittha Walaijai, Stuart A. Cavill, Adrian C. Whitwood, Richard E. Douthwaite, Robin N. Perutz|2020|Inorg.Chem.|59|18055|doi:10.1021/acs.inorgchem.0c02505
DOI: 10.5517/ccdc.csd.cc25vd6n
title: CCDC 2021361: Experimental Crystal Structure Determination

description: Related Article: Khanittha Walaijai, Stuart A. Cavill, Adrian C. Whitwood, Richard E. Douthwaite, Robin N. Perutz|2020|Inorg.Chem.|59|18055|doi:10.1021/acs.inorgchem.0c02505
DOI: 10.5517/ccdc.csd.cc2122v2
title: CCDC 1878843: Experimental Crystal Structure Determination

description: Related Article: Chaima Boureghda, Raouf Boulcina, Vincent Dorcet, Fabienne Berrée, Bertrand Carboni, Abdelmadjid Debache|2020|Tetrahedron Lett.|62|152690|doi:10.1016/j.tetlet.2020.152690
DOI: 10.5517/ccdc.csd.cc266x1d
title: CCDC 2032423: Experimental Crystal Structure Determination

description: Related Article: Yu-Mei Wan, Qin-Long Hong, Hai-Xia Zhang, Jian Zhang|2020|Inorg.Chem.|59|17851|doi:10.1021/acs.inorgchem.0c02877
DOI: 10.5517/ccdc.csd.cc266x2f
title: CCDC 2032424: Experimental Crystal Structure Determination

description: Related Article: Yu-Mei Wan, Qin-Long Hong, Hai-Xia Zhang, Jian Zhang|2020|Inorg.Chem.|59|17851|doi:10.1021/acs.inorgchem.0c02877
DOI: 10.5517/ccdc.csd.cc267r5d
title: CCDC 2033233: Experimental Crystal Structure Determination

description: Related Article: Nabeela Kausar, Saeed Ullah, Maria Aqeel Khan, Humaira Zafar, Atia-tul-Wahab, M. Iqbal Choudhary, Sammer Yousuf|2020|Bioorg.Chem.|106|104499|doi:10.1016/j.bioorg.2020.104499
DOI: 10.5517/ccdc.csd.cc267ydt
title: CCDC 2033426: Experimental Crystal Structure Determination

description: Related Article: Minseok Kim, K. L. Dimuthu M. Weerawardene, Woojun Choi, Sang Myeong Han, Juwon Paik, Younghun Kim, Moon-Gun Choi, Christine M. Aikens, Dongil Lee|2020|Chem.Mater.|32|10216|doi:10.1021/acs.chemmater.0c03994
DOI: 10.5517/ccdc.csd.cc2693n9
title: CCDC 2034550: Experimental Crystal Structure Determination

description: Related Article: Ping Zhang, Wenju Chang, Yan-Shang Kang, Wenxuan Zhao, Pei-Pei Cui, Yong Liang, Wei-Yin Sun, Yi Lu|2020|Org.Lett.|22|9462|doi:10.1021/acs.orglett.0c03425
DOI: 10.5517/ccdc.csd.cc269mgm
title: CCDC 2035040: Experimental Crystal Structure Determination

description: Related Article: Mariana Rocha, Gustavo A. Echeverrí, Oscar E. Piro, Jorge L. Jios, Sonia E. Ulic, Diego M. Gil|2021|J.Fluorine Chem.|242|109697|doi:10.1016/j.jfluchem.2020.109697
DOI: 10.5517/ccdc.csd.cc26kn3k
title: CCDC 2042748: Experimental Crystal Structure Determination

description: Related Article: Mengyao Bian, Hamdulla Mawjuda, Hui Gao, Huiying Xu, Zhi Zhou, Wei Yi|2020|Org.Lett.|22|9677|doi:10.1021/acs.orglett.0c03734
DOI: 10.5517/ccdc.csd.cc26lk0d
title: CCDC 2043613: Experimental Crystal Structure Determination

description: Related Article: Damian Szymor-Pietrzak, Muhammad N. Khan, Anaïs Pagès, Ajay Kumar, Noah Depner, Derrick L. J. Clive|2020|J.Org.Chem.|86|619|doi:10.1021/acs.joc.0c02284
DOI: 10.5517/ccdc.csd.cc26lk1f
title: CCDC 2043614: Experimental Crystal Structure Determination

description: Related Article: Damian Szymor-Pietrzak, Muhammad N. Khan, Anaïs Pagès, Ajay Kumar, Noah Depner, Derrick L. J. Clive|2020|J.Org.Chem.|86|619|doi:10.1021/acs.joc.0c02284
DOI: 10.5517/ccdc.csd.cc261pwv
title: CCDC 2027427: Experimental Crystal Structure Determination

description: Related Article: Hong Li, Bing Liu, Ling Xu, Huan Jiao|2021|Dalton Trans.|50|143|doi:10.1039/D0DT03626A
DOI: 10.5517/ccdc.csd.cc269j46
title: CCDC 2034937: Experimental Crystal Structure Determination

description: Related Article: Mengyu Niu, Xiaoping Yang, Yanan Ma, Xilong Leng, Wenxin Hao, Ya Chen, Zanqing Chen, Desmond Schipper|2021|J.Lumin.|231|117807|doi:10.1016/j.jlumin.2020.117807
DOI: 10.15468/jj4yna
title: New species of black corals (Cnidaria: Anthozoa: Antipatharia) from deep- sea seamounts and ridges in the North Pacific

description: This dataset contains the digitized treatments in Plazi based on the original journal article Opresko, Dennis M., Wagner, Daniel (2020): New species of black corals (Cnidaria: Anthozoa: Antipatharia) from deep- sea seamounts and ridges in the North Pacific. Zootaxa 4868 (4): 543-559, DOI: https://doi.org/10.11646/zootaxa.4868.4.5
DOI: 10.5281/zenodo.3874825
title: SIRAH-CoV2 initiative: SARS-Cov2 Spike´s RBD / ACE2-B0AT1 complex (PDB id:6M17)

description: This dataset contains the trajectory of a 3 microseconds-long coarse-grained molecular dynamics simulation of the hexameric complex between SARS-CoV2 Spike´s RBD, ACE2, and B0AT1 (PDB id: 6M17). 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. Zinc ions were parameterized as reported in Klein et al. 2020. The files 6M17_SIRAHcg_rawdata_0-1.tar, 6M17_SIRAHcg_rawdata_1-2.tar, and 6M17_SIRAHcg_rawdata_2-3.tar contain 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. Additionally, the file 6M17_SIRAHcg_3us_prot.tar contains only the protein coordinates, while 6M17_SIRAHcg_3us_prot_skip10ns.tar contains one frame every 10ns. To take a quick look at the trajectory: 1- Untar the file 6M17_SIRAHcg_10us_prot_skip10ns.tar 2- Open the trajectory on VMD 1.9.3 using the command line: vmd 6M17_SIRAHcg_prot.prmtop 6M17_SIRAHcg_prot.ncrst 6M17_SIRAHcg_3us_prot_skip10ns.nc -e sirah_vmdtk.tcl Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. This dataset is part of the SIRAH-CoV2 initiative. For further details, please contact Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).
description: {"references": ["Machado et al. JCTC 2019 (DOI: 10.1021/acs.jctc.9b00006)", "Machado & Pantano JCTC 2020 (DOI:10.1021/acs.jctc.9b00953)", "Machado & Pantano Bioinformatics 2016 (DOI:10.1093/bioinformatics/btw020)", "Klein et al. 2020 (DOI:10.1021/acs.jcim.0c00160)"]}