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opencc-by-4.0Mar 2020View details →

Molecular dynamics trajectories for "Structure and chemistry of graphene oxide in liquid water from first principles"

This dataset contains molecular dynamics (MD) trajectories from the paper <a href="https://doi.org/10.1038/s41467-020-15381-y">“Structure and chemistry of graphene oxide in liquid water from first principles”, F. Mouhat, F.-X. Coudert and M.-L. Bocquet, Nature Commun., 2020, 11, 1566, 10.1038/s41467-020-15381-y</a>

All Atom Molecular Dynamics Simulations of Lopinavir at the Binding Pocket of SARS-CoV2 Main Protease

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 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.

Molecular dynamics simulation data of designed cyclic peptide (ligand-only)

Trajectories of ligand-only simulation and simulation set-up files of designed cyclic peptide as MDM2 binders.  The original paper of these designed cyclic peptide: Danelius, E., Pettersson, M., Bred, M., Min, J., Waddell, M. B., Guy, R. K., et al. (2016). Flexibility is important for inhibition of the MDM2/p53 protein–protein interaction by cyclic β-hairpins. Org. Biomol. Chem., 14(44), 10386–10393. http://doi.org/10.1039/C6OB01510G

Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH)

Raw data of molecular dynamics simulations of regulatory ACT domain dimer. binding.zip: simulation starting from 21 dimer conformations with 19 Phe ligand  bound.zip: simulation starting from dimer with bound Phe ligand dimer.zip: simulation starting from 21 dimer conformations simulation Simulation setup files are also included in each folder. Details can be found in this paper: Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532">Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</a> J. Biol. Chem., 2018, 293(51), pp 19532-19543

Molecular dynamics simulation data of regulatory ACT domain monomer of human phenylalanine hydroxylase (PAH)

Raw data of molecular dynamics simulations of regulatory ACT domain monomer. binding.zip: simulation starting from 21 monomer conformations with 19 Phe ligand  bound.zip: simulation starting from monomer with bound Phe ligand monomer_only.zip: simulation starting from 21 monomer conformations simulation Simulation setup files are also included in each folder. Adaptive sampling data are also included in monomer and binding simulations. Details can be found in this paper: Yunhui Ge, Elias Borne, Shannon Stewart, Michael R. Hansen, Emilia C. Arturo, Eileen K. Jaffe and Vincent A. Voelz. <a href="http://www.jbc.org/content/293/51/19532">Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</a> J. Biol. Chem., 2018, 293(51), pp 19532-19543

Molecular dynamics simulation data of designed β-hairpins

Raw simulations data (protein only) and simulation set-up files of designed β-hairpins. More details can be found in this paper:  Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132">Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620

Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff96)

Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff96 and implicit solvent model is used. More details can be found in this paper:  Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132">Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620

Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn)

Raw REMD simulation data (protein only) of designed β-hairpins. AMBER ff99SB-ildn and implicit solvent model is used. More details can be found in this paper:  Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132">Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620

Molecular dynamics trajectories for SARS-CoV-2 Mpro with 7 HIV inhibitors

Raw trajectory data (GROMACS format) of all atom molecular dynamics simulation of COVID-19 related SARS-CoV-2 dimeric main protease (based on PDB 6LU7) with 7 kinds of HIV inhibitors (darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir) were calculated on massively parallel supercomputer HOKUSAI Big Waterfall at RIKEN ISC, and a special-purpose computer, MDGRAPE-4A, at RIKEN BDR, JAPAN. For each ligand, 200ns length 28 trajectories were calculated. Some of these trajectories were calculated further longer. We can observe formation of encounter complex and investigate potential binding sites on the surface of the dimeric protease. We hope that these raw data are valuable for further drug repurposing/development research targeting the SARS-CoV-2 main protease. We will submit analysis of these data to refereed journal. Molecular dynamics simulations were performed under NVT at 310K, with the time step 2.5fs. The starting structure was prepared based on PDB 6LU7, with amber14sb force field in about 10nm cubic box with periodic boundary conditions. The ligands were initially placed apart from the active sites of the dimeric main protease. We have also already deposited 10 microseconds trajectories of the dimeric protease without ligand (with amber99sb-ildn force field) in the repository https://data.mendeley.com/datasets/vpps4vhryg/1 (DOI:10.17632/vpps4vhryg.1). Files: <ul> <li>LIG_28traj200ns_every200ps.zip    (28trajectories for each ligand) <ul> <li>traj200ns_every200ps/LIG/a/traj200ns_every200ps_LIG-a-n.xtc <ul> <li>(trajectory in GROMACS XTC)</li> </ul> </li> <li>traj200ns_every200ps/LIG/a/conf.gro <ul> <li>(initial condition in GROMACS GRO)</li> </ul> </li> <li>traj200ns_every200ps/LIG/topology/ <ul> <li>(contains topology files)</li> </ul> </li> <li>traj200ns_every200ps/LIG/mdp/ <ul> <li>(contains run paramter files)</li> </ul> </li> </ul> </li> <li>ZZZ_20traj1us_every200ps.zip               (20trajectories extended to 1microsecond) <ul> <li>traj1us_every200ps/traj1us_every200ps_LIG-a-n.xtc <ul> <li>DAR-C-06, DAR-D-07</li> <li>IND-C-05, IND-C-06, IND-D-06</li> <li>LOP-A-02, LOP-D-03</li> <li>NEL-B-01, NEL-C-07, NEL-D-02</li> <li>RIT-B-07, RIT-C-07</li> <li>SAQ-B-01, SAQ-C-04, SAQ-D-03</li> <li>TPR-A-07, TPR-B-04, TPR-B-06, TPR-C-05, TPR-D-02</li> </ul> </li> </ul> </li> <li>ZZZ_3traj6us_every1ns.zip                 (3trajectories extended to 6microseconds or more) <ul> <li>traj6us_every1ns/traj6us_every1ns_LIG-a-n.xtc <ul> <li>IND-D-06, NEL-B-01, TPR-B-04</li> </ul> </li> </ul> </li> </ul>   <ul> <li>ZZZ_LigandBindingPosePDBs.zip        (pickup 3 snapshots for each ligand) <ul> <li>LigandBindingPosePDBs/LIG-a-n_frame.pdb</li> </ul> </li> </ul>   <ul> <li>movies_overlooking_28traj200ns.zip     (7x2movies) <ul> <li>movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewA.mp4 <ul> <li>inspecting 28traj at once</li> </ul> </li> <li>movies_28traj200ns/movie_overlooking_LIG_28traj200ns-viewB.mp4 <ul> <li>from the opposite angle</li> </ul> </li> </ul> </li> <li>movies_1us.zip          (17movies) <ul> <li>movies_1us/movie_LIG-a-n_1us.mp4</li> </ul> </li> <li>movies_6us.zip          (3movies) <ul> <li>movies_6us/movie_LIG-a-n_6us.mp4</li> </ul> </li> </ul>         where              LIG={DAR,IND,LOP,NEL,RIT,SAQ,TPR}                  DAR:darunavir                  IND:indinavir                  NEL:nelfinavir                  RIT:ritonavir                  SAQ:saquinavir                  TPR:tipranavir              a={A,B,C,D}              n={01,02,03,04,05,06,07}   <ul> <li>ZZZz_3traj1us_every200ps_unbinding.zip      (3trajectories extended to 1microsecond exhibiting unbinding)</li> <li>ZZZz_56traj200ns_every200ps_negative_control.zip    (56trajectories as a negative control)</li> <li>ZZZz_LigandBindingPosePDBsRevised.zip                    (pickuped 3 snapshots for each ligand)</li> </ul>

opencc-by-4.0Mar 2020View details →

The Complex Geometry and Dynamical Role of Stellar Wind Bubbles in Turbulent Molecular Clouds

Research Data Management Package for paper in Monthly Notices of the Royal Astronomical Society with same title and author list

All-atom Molecular Dynamics Simulations of SARS-CoV-2 Spike Receptor-binding Domain bound with ACE2

Data includes all of the trajectories (1000) of classical all-atom molecular dynamics (MD) simulations of of SARS-CoV2 Spike Protein/ACE2 complex (PDB ID: 6M0J). In order to decrease the size of the file only protein rajectories were provided.  Simulation has been performed with Desmond.  Protein 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 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 simulation.

opencc-zeroJul 2015View details →

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 13C-1H solid-state NMR and molecular dynamics simulations"

Simulation trajectories for the article "Molecular conformation and bilayer pores in a nonionic surfactant lamellar phase studies with 1H-13C solid-state NMR and molecular dynamics simulations" Langmuir 2014, 30 (2), pp 461–469 http://dx.doi.org/10.1021/la404684r System: 80 wt% C12E5, T=298K Other files available: http://dx.doi.org/10.6084/m9.figshare.861071

Molecular dynamic trajectory of magnesium binding wild type for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"

ATP synthase molecular dynamics simulations files for wild type of the beta subunit binding magnesium: 50ns trajectory (ATPsynth_woh2o_Mg_wt.dcd) and corresponding psf file (ATPsynth_mg_wt.psf)

Molecular dynamic trajectory of calcium binding T163S mutant for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"

ATP synthase molecular dynamics simulations files for T163S mutants of the beta subunit binding calcium: 50ns trajectory (ATPsynth_woh2o_Ca_mut.dcd) and corresponding psf file (ATPsynth_ca_mut.psf)

Molecular dynamic trajectory of calcium binding wild type for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"

ATP synthase molecular dynamics simulations files for wild type of the beta subunit binding calcium: 50ns trajectory (ATPsynth_woh2o_Ca_wt.dcd) and corresponding psf file (ATPsynth_ca_wt.psf)

Molecular dynamic trajectory of magnesium binding T163S mutant for the article "Ca 2+ binding to F-ATP synthase β subunit triggers the mitochondrial permeability transition"

ATP synthase molecular dynamics simulations files for T163S mutants of the beta subunit binding magnesium: 50ns trajectory (ATPsynth_woh2o_Mg_mut.dcd) and corresponding psf file (ATPsynth_mg_mut.psf)

opencc-by-4.0Oct 2023View details →

Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer

Gaussian-accelerated Molecular Dynamics simulations of the CCR8-CCL1-Gprotein complex in a POPC lipid bilayer. Simulation system was prepared with OpenMM v7.7 and simulations were performed using the GaMD-OpenMM package (https://github.com/MiaoLab20/gamd-openmm) with a modification to include the MDTraj h5 file formate reporter as the output file format. These simulations were then converted to pdb topologies and dcd trajectories using MDTraj. Files include:CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topologyCCL1_CCR8_config.xml : config for running GaMD-OpenMMCCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structureCCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file Simulations can be loaded in python using MDTraj:import mdtrajtrj = mdtraj.load(<dcd file>, top=<pdb file>)