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605 simulations
Spike mutation A222V; cryo-em simple
Miłosz Wieczór, Tiziana Ginex
The structural background of emergence and success of the A222V Spike mutation
OpenPDB 6VXX, 6VSBCC BY 4.0Published 1 Dec 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; oleic acid; open
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 28 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; dexamethasone; open
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 28 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; cholesterol; open
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 28 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; apo; open
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 28 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; oleic acid; closed
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 28 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; dexamethasone; closed
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 27 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; cholesterol; closed
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 27 Sept 2021MD simulations of trimeric SARS-Cov2 spike protein ectodomain in explicit solvent; apo; closed
Deborah K Shoemark
The CryoEM stuctures of the apo and linoleic acid bound SARS-Cov2 spike protein trimer (residues 15/25 to 1139) were used to build complete atomistic models. Other putative ligands, including cholesterol and vitamins, retinoids and steroids identified by docking with BUDE, were simulated in both open and closed states. The closed and open structures have 42 and 43 disulfide bonds respectively. Simulations were performed with GROMACS 2019.x.
OpenPDB 6ZB5CC BY 4.0Published 13 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C4 popc
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 22 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C4 mix
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 22 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C3 popc
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 21 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C3 mix
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 21 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C2 popc
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 21 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C2 mix
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 22 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C1 popc
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 20 Sept 2021All-atom molecular dynamics simulations of SARS-CoV-2 envelope protein E in the monomeric form, C1 mix
Alexander Kuzmin, Philipp Orekhov, Roman Astashkin, et al.
The trajectories of all-atom MD simulations were obtained based on 4 starting representative conformations from the CG simulation. For each starting structure, there are six trajectories of the E protein: 3 with the protein embedded in the membrane containing POPC, and 3 with the membrane mimicking the natural ERGIC membrane (Mix: 50% POPC, 25% POPE, 10% POPI, 5% POPS, 10% cholesterol).
OpenNo structureCC BY 4.0Published 20 Sept 2021This trajectory is from a 300 ns atomic MD simulation of the SARS-CoV-2 RdRp apo-protein model. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 400 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
OpenPDB 6M71CC BY 4.0Published 4 Feb 2021Gromacs 100 ns MD of SARS-CoV-2 RdRp + RNA template-primer + ATP model, All Atom model (100 ns)
Vaibhav Modi
This trajectory is from a 100 ns atomic MD simulation of the SARS-CoV-2 RdRp-RNA-ATP-complex protein. The protein was solvated in a 16 x 16 x 16 nm box of solvent containing water and 0.15 M NaCl. The simulation was performed with Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Amber14sb-OL15 force field. The interval between frames is 100 ps. The simulation was conducted in the NPT ensemble (1 bar and 300K).
OpenPDB 6M71CC BY 4.0Published 4 Feb 2021This trajectory is from a 60 ns MD simulation of the SARS-CoV-2 spike protein. The proteinwas solvated in a 20 x 20 x 20 nm water box containing 0.1 M NaCl. The simulation was performedwith Gromacs 2018.8 on the Puhti cluster located at the CSC-IT using the Charmm27 force field. The interval between frames is 80 ps. The simulation was conducted in the NPT ensemble (1 bar). This trajectory is all atom.
OpenPDB 6VXXCC BY 4.0Published 30 Apr 2020