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8 results for “NSP3”
SIRAH-CoV2 initiative: Apo ADP ribose phosphatase of NSP3 from SARS CoV-2 (PDB id: 6W02)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 ADP ribose phosphatase of NSP3 from SARS CoV-2 in its APO form (PDB id: 6W02, Bioassembly 1). 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 <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00006">Machado et al. JCTC 2019</a>, adding 150 mM NaCl according to <a href="https://pubs.acs.org/doi/10.1021/acs.jctc.9b00953">Machado & Pantano JCTC 2020</a>. </p> <p>The file 6W02_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 <a href="https://academic.oup.com/bioinformatics/article/32/10/1568/1743152">SirahTools</a> can be found at www.sirahff.com.</p> <p>Additionally, the file 6W02_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W02_SIRAHcg_10us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6W02_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6W02_SIRAHcg_prot.prmtop 6W02_SIRAHcg_prot.ncrst 6W02_SIRAHcg_prot_10us_skip10ns.nc -e sirah_vmdtk.tcl</p> <p>Note that you can use normal VMD drawing methods as vdw, licorice, etc., and coloring by restype, element, name, etc. </p> <p>This dataset is part of the SIRAH-CoV2 initiative.</p> <p>For further details, please contact Exequiel Barrera (ebarrera@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
PanDDA analysis of fragment screen against the Nsp3 macrodomain of SARS-CoV-2 - P43 crystals at UCSF
<p>This deposition contains the X-ray diffraction data used for the PanDDA analysis of the fragment screen against the NSP3 macrodomain of SARS-CoV-2 described in Schuller et al. 2021 (DOI: 10.1126/sciadv.abf8711).</p> <p>A description of the files can be found in the "README" text file. </p> <p>The data in this deposition is from the fragment screen performed at UCSF using P43 crystals. The data from the fragment screen performed at UCSF using C2 crystals can be found here - https://zenodo.org/record/4716363 - in the zipped directory named "ucsf_nsp3_mac1_C2.zip". </p>
PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from fragment merging/linking and virtual screening
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Gahbauer et al. 2022 (doi: https://doi.org/10.1101/2022.06.27.497816).</p> <p>mac1_pandda.zip contains the structure factor intensities, PanDDA input/ouput and refined models/maps. A description of the files can be found in the README file. </p> <p>mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files. </p>
Nsp3 macrodomain of SARS-CoV-2 ; A Target Enabling Package
<p>The conserved macrodomain encoded as non-structural protein 3 (Nsp3 Mac1) is employed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to remove host-derived ribosylation, which is a post-translational modification involved in the production of antiviral cytokines. This TEP provides early tools to develop Nsp3 Mac1 inhibitors, including purification protocols of recombinant proteins, reproducible crystallisation condition suitable for X-ray crystallography fragment screening, biophysical (activity and binding) assays and over 200 fragment hits representing a wide range of chemotypes, that are a starting point for the development of more selective and potent compounds.</p>
Molecular dynamics trajectories related to manuscript: SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle
<p>This dataset contains two folders, each with sequentially numbers coordinates files for all-atom molecular dynamics trajectories related to the manuscript "SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle" by Zimmermann et al. Each folder contains PDB and PSF files specifying the components of each system depicted in Fig. S10 of that manuscript as well as 200 sequentially named DCD files, each containing 5 nanoseconds of a 1 microsecond trajectory.</p>
PanDDA analysis of ligand screen against the NSP3 macrodomain of SARS-CoV-2: ligands from FrankenROCS fragment-linking pipeline and subsequent optimization of AVI-313
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in Correy et al. 2024 (doi: https://doi.org/10.1101/2024.08.25.609621). Compounds were from fragment linking using FrankenROCS and subsequent optimization of AVI-313. </p> <p>frankenROCS_mac1.tar.gz contains structure factor intensities, PanDDA input/output and refined models/maps.</p> <p>frankenROCS_mac1_ligand-bound-states.tar.gz contains the ligand-bound states extracted from the multi-state PDB files.</p>
PanDDA files from a ligand screen against the NSP3 macrodomain of SARS-CoV-2 - ligands from linking with FRESCO
<p>This deposition contains the X-ray diffraction data used to run PanDDA in the ligand screen against the NSP3 macrodomain of SARS-CoV-2 described in McCorkindale et al. 2022 (https://doi.org/10.1101/2022.11.21.517375).</p> <p>mac1_pandda.zip contains the structure factor intensities, PanDDA input/ouput and refined models/maps. A description of the files can be found in the README file. </p> <p>mac1_ligand-bound_states.zip contains the ligand-bound states extracted from the multi-state PDB files. </p>
Data from: Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication
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