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Dataset results
9 results for “CoV2 Protease”
SIRAH-CoV2 initiative: Main Protease (PDB id:6LU7)
<p>This dataset contains the trajectory of a 15 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Main protease in its APO form (PDB id: 6LU7, 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 files 6LU7_SIRAHcg_rawdata1.tar, 6LU7_SIRAHcg_rawdata2.tar, and 6LU7_SIRAHcg_rawdata3.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 <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 6LU7_SIRAHcg_15us_prot.tar contains only the protein coordinates, while 6LU7_SIRAHcg_15us_prot_skip10ns.tar contains one frame every 10ns.</p> <p>To take a quick look at the trajectory:</p> <p>1- Untar the file 6LU7_SIRAHcg_15us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6LU7_SIRAHcg_prot.prmtop 6LU7_SIRAHcg_prot.ncrst 6LU7_SIRAHcg_prot_15us_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 Sergio Pantano (spantano@pasteur.edu.uy).</p>
SIRAH-CoV2 initiative: Papain-like Protease (PDB id:6W9C)
<p>This dataset contains the trajectory of a 10 microseconds-long coarse-grained molecular dynamics simulation of SARS-CoV2 Papain-like protease in its APO form with Zn ions bound (PDB id: 6W9C). 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>. Zinc ions were parameterized as reported in <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.0c00160">Klein et al. 2020</a>.</p> <p>The files 6W9C_SIRAHcg_rawdata_0-5us.tar, 6W9C_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 <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 6W9C_SIRAHcg_10us_prot.tar contains only the protein coordinates, while 6W9C_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 6W9C_SIRAHcg_10us_prot_skip10ns.tar</p> <p>2- Open the trajectory on VMD using the command line:</p> <p>vmd 6W9C_SIRAHcg_prot.prmtop 6W9C_SIRAHcg_prot.ncrst 6W9C_SIRAHcg_10us_prot_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 Florencia Klein (fklein@pasteur.edu.uy) or Sergio Pantano (spantano@pasteur.edu.uy).</p>
Simulation results for Sars-CoV2 3C-like main protease: TRAPP analysis of the binding site flexibility and results of the docking study
<p>Collection of data and scripts related to the paper:</p> <p>Jonas Gossen et al. "A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics" </p> <p>https://www.biorxiv.org/content/10.1101/2020.12.14.422634v2 doi: https://doi.org/10.1101/2020.12.14.422634</p> <p>ACS Pharmacology and Translational Science 2021 DOI: 10.1021/acsptsci.0c00215</p> <p> </p> <p> </p> <p><strong>1. TRAPP simulation results for Sars-CoV2 3C-like main protease:</strong></p> <p>include simulation of the binding pocket druggability, physical-chemical properties, and the binding site composition</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/Protease_clean.ipynb">Protease_clean.ipynb</a> - Jupyter Notebook containing analysis of the generated data</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/allTables.zip">allTables.zip</a> - results of TRAPP simulations of the binding site flexibility using LRIP and tConcoord methods</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/Every10-ligand_6LU7_R3.5.zip">Every10-ligand_6LU7_R3.5.zip</a> - results of TRAPP pocket analysis on the MD frames</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/PDB-Giulia.zip">PDB-Giulia.zip</a> - TRAPP pocket analysis of 40 PDB complexes of main protease</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/TRAPP_properties_PDB.xlsx">TRAPP_properties_PDB.xlsx</a> - binding pocket properties for 40 PDB complexes of main protease summarized in a table</p> <p><a href="https://zenodo.org/api/files/f6c0a0ae-d53a-4e78-aaaf-b3ff674171a5/DrugPDB_3structures.xlsx">DrugPDB_3structures.xlsx</a> - binding pocket properties for 3 PDB structures </p> <p><strong>2. Docking & Screening Results</strong></p> <p><a href="https://zenodo.org/api/files/9165535d-aec5-4f1e-8ad1-6ca11a90e595/TRAPP_secondSelection_VS.csv">TRAPP_secondSelection_VS.csv</a> - docking/screening of selected structures from TRAPP analysis</p> <p><a href="https://zenodo.org/api/files/9165535d-aec5-4f1e-8ad1-6ca11a90e595/Fred_VS.csv">Fred_VS.csv</a> - docking of PDB structures using Fred</p> <p><a href="https://zenodo.org/api/files/9165535d-aec5-4f1e-8ad1-6ca11a90e595/Glide_VS.csv">Glide_VS.csv</a> - docking of PDB structures using Glide</p> <p><a href="https://zenodo.org/api/files/77b1679d-ccc9-4e30-add2-5f7420e04ed1/TableS1.xlsx">TableS1.xlsx</a> - Available structures of SARS-CoV-2 Mpro selected for binding site analyses. </p> <p><a href="https://zenodo.org/api/files/77b1679d-ccc9-4e30-add2-5f7420e04ed1/TableS2A.xlsx">TableS2A.xlsx</a> - SiteScore analysis of all the deposited X-ray crystal structures for the Mpro.</p> <p><a href="https://zenodo.org/api/files/77b1679d-ccc9-4e30-add2-5f7420e04ed1/TableS2B.xlsx">TableS2B.xlsx</a> - SiteScore analysis of the MSM ensemble (4-macrostates).</p>
All Atom Molecular Dynamics Simulations of Lopinavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of lopinavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulations.</p>
TOP-100 DOCKING POSES OF FDA APPROVED DRUGS AND DRUGS IN CLINICAL INVESTIGATION AT SARS-CoV2 MAIN PROTEASE
<p>7922 compounds were downloaded from NPC database (https://tripod.nih.gov/npc/). In order<br> to eliminate the non-specific binders, some criteria including molecular weight, between 100 to<br> 1000 g/mol; number of rotatable bonds, <100; number of atoms, between 10 and 100; number<br> of aliphatic and aromatic rings, <10; number of hydrogen-bond acceptor and donors, <10 were<br> set and as a result the total number of compounds was decreased to 6654. These ligands were<br> prepared using LigPrep module of Maestro at neutral pH (LigPrep, Schrodinger v.2017). In<br> molecular docking, we used following protein structure: SARS-CoV2 Main Protease, (PDB, 6LU7). The protein<br> was prepared using Protein Preparation module of Maestro. PROPKA was used for<br> determination of protonation states of amino acid residues. Restrained minimization was<br> performed with OPLS3 force field for the protein using 0.3 Å heavy atom convergence.<br> Docking was performed with Glide/SP using default settings. Top-100 docking poses were provided.</p>
Large scale virtual screening for finding inhibitor against the main protease from herbal medicine for SARS-Cov2 therapy
<p>The pandemic COVID-19 caused by SARS-CoV-2 has raised global health concerns. However, there is still no targeted medicine available for treatment of this disease. It is reported that 3CLpro plays an important role for the life cycle of virus and this protein has also been proved as an effective drug target in the case of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Medicinal plantsare important resource for drug discovery. Therefore, we executed large scale virtual screening on the herbal medicine library and hoped to find a potential drug againstthe main protease. As a result, we obtained three available compounds derived from Chinese herbal medicines through the docking and binding free energy calculation.Then 100 ns molecular dynamic (MD) were employed to uncover the potential mechanisms which is helpful for further drug optimization.</p>
Large scale virtual screening for finding inhibitor against the main protease from herbal medicine for SARS-Cov2 therapy
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All Atom Molecular Dynamics Simulations of Ritonavir at the Binding Pocket of SARS-CoV2 Main Protease
<p>Data includes all of the trajectories (2000) of classical all-atom molecular dynamics (MD) simulations of ritonavir at the binding pocket of SARS-CoV2 main protease target. In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained by Glide/SP docking program. Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 500 ns production run was performed for the simulation.</p> <p> </p>
All Atom Molecular Dynamics Simulations of inhibitor N3 at the binding pocket of SARS-CoV2 Main Protease (PDB ID: 6LU7)
<p>Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of inhibitor N3 at the binding pocket of SARS-CoV2 main protease target (PDB ID: 6LU7). In order to decrease the size of the file only protein and ligand trajectories were provided. Simulation has been performed with Desmond. Protein–ligand complexes were obtained from RCSB PDB (PDB ID: 6LU7). Complex was placed in the cubic boxes with explicit TIP3P water models that have 10.0 Å thickness from surfaces of protein. The system is neutralized by adding counter ions, and salt solution of 0.15M NaCl was also used to adjust the concentration of the systems. The long-range electrostatic interactions were calculated by the particle mesh Ewald method. A cutoff<br> radius of 9.0 Å was used for both van der Waals and Coulombic interactions. The temperature was set as 310K initially, and Nose–Hoover thermostat was used for adjustment. Martyna–Tobias–Klein protocol was employed to control the pressure, which was set at 1.01325 bar. The time-step was assigned as 2.0 fs. The default values were used for minimization and equilibration steps, and finally 100 ns production run was performed for the simulations.</p>
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