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474 results for “Molecular simulations”
Molecular Dynamics Simulation of SARS-CoV-2 Spike Protein
<p>Trajectory data corresponding to the manuscript, tentatively titled "Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein"</p> <p>Authors: Dhiman Ray, Ly Le, Ioan Andricioaei</p> <p>Affiliation: University of California Irvine, USA</p> <p>Description: Multiple unbiased simulations of 40 ns were performed for the SARS-CoV-2 spike protein. Frames are saved at 50 ps interval. The initial structures were generated from umbrella sampling simulation starting from PDB ID: 6VSB and 6VXX. The index at the end of filename stands for the umbrella sampling window from which the trajectory was initiated. The indices are not continuous as not all the umbrella sampling windows were used to start trajectories. Additionally 3 trajectories, each of length 80 ns, are included for the closed, partially open and fully open state. The topology is provided as a PDB file ("spike_dry.pdb").</p> <p>The trajectories are for the spike head only structure obtained from the CHARMM-GUI Covid-19 archive. No solvent or ions are included in the trajectory or the topology.</p> <p>Update: Additional trajectories and PDB files for D614G mutant added. Each trajectory is 40 ns long. The PDB files are named 6VXX_mutant_dry.pdb and 6VSB_mutant_dry.pdb for the closed and partially open state.</p> <p>Pre-print available: https://doi.org/10.1101/2020.12.07.415596</p>
Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments - DATA
<p>Specular reflectivities of the SoyPC bilayer stack measured at the vertical reflectometer MARIA at Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany.</p> <p>Offspecular reflectivity map (log scale) of the multilayer sample as a function of theangle of incidence (θi) and of the reflection angle (θi).</p> <p>Specular reflectivities of the Si/SiO<sub>2</sub>/DMPC/H2O at 4 different contrasts (H<sub>2</sub>O, D<sub>2</sub>O, SMW and 4MW)</p> <p>Small-angle neutron scattering of the unilamellar SoyPC</p>
Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form
<p>The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of<br> 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs); <br> 2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs); <br> SARS-CoV-2 E protein pentamer in a POPC bilayer.</p> <p>The trajectory of CG MD of system containing 2 pentamers in the membrane buckled in a single direction (BuckledMembrane_FeigLab_2xPentamerNoPTM_POPC_Martini3b: 1 μs).</p> <p>FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb<br> FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.</p>
Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation
<p>Data archive corresponding to the manuscript "Fine-Tuning of Colloidal Polymer Crystals by Molecular Simulation" by M. Herranz et al., Phys. Rev. E 107, 064605 (2023); DOI: 10.1103/PhysRevE.107.064605</p> <p>Please see README.txt for instructions on how to access and read the files from the crystallographic analysis based on the CCE norm descriptor.</p> <p>All snapshots have been generated and successively analyzed by the Simu-D software.</p>
TUK-FFDat - Data scheme and data format for transferable force fields for molecular simulation
<p>Online repository to suplement the following publication:</p> <p>G. Kanagalingam, S. Schmitt, F. Fleckenstein, S. Stephan: Data scheme and data format for transferable force fields for molecular simulation, Scientific Data, accepted (2023).</p>
Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis
<p>This dataset contains molecular dynamics simulations data generated using GROMACS for the upregulated biomarker 3UNF and its G210V mutant in the context of Experimental Autoimmune Encephalomyelitis (EAE). EAE is a widely studied animal model for multiple sclerosis, and investigating the behavior of biomarkers in this model is crucial for understanding disease progression and potential therapeutic interventions.</p> <p>The dataset includes trajectory files, coordinate files, and relevant parameters used in the simulations. These simulations provide valuable insights into the structural dynamics, conformational changes, and interactions of the PSMB8 biomarker 3UNF and its G210V mutant within the EAE system. The data offers researchers an opportunity to analyze and explore the behavior of these biomarkers at the atomic level, aiding in the identification of potential binding partners, functional sites, and mechanisms associated with disease progression.</p> <p>By sharing this dataset, we aim to contribute to the scientific community by providing a valuable resource for further analysis, validation, and comparison of the molecular behavior of the upregulated biomarker 3UNF and its G210V mutant in Experimental Autoimmune Encephalomyelitis.</p>
Molecular dynamics simulation data 1: Structure of the connexin-43 gap junction channel in a putative closed state
<p>Molecular dynamics data for the manuscript Qi C.*, Acosta-Gutierrez S.*, Lavriha P., Othman A., Lopez-Pigozzi D., Bayraktar E., Schuster D., Picotti P., Zamboni N., Bortolozzi M., Gervasio F.L., Korkhov V.M. Structure of the connexin-43 gap junction channel in a putative closed state. eLife (2023) <a href="https://doi.org/10.7554/eLife.87616.2">https://doi.org/10.7554/eLife.87616.2</a></p> <p>The dataset includes:</p> <p>1. The starting coordinates, topology, MD inputs</p> <p>2. Production run gromacs trajectories for the Cx43 gap junction channel</p>
Molecular dynamics simulation based analysis of celecoxib-polymer interactions
<p>This dataset contains scripts and coordinate files for running and analysing molecular dynamics simulations to investigate celecoxib-polymer interactions in aqueous solution. Trajectory files (stripped of water and ions) are included.</p> <p>The associated study is described in:</p> <p>" Comparative analysis of drug-salt-polymer interactions by experiment and molecular simulation improves biopharmaceutical performance", Sumit Mukesh, Goutam Mukherjee, Ridhima Singh, Nathan Steenbuck, Carolina Demidova, Prachi Joshi, Abhay T. Sangamwar, Rebecca C. Wade, submitted.</p>
Molecular dynamics simulations PksD AH
<p>This data set includes topology files, trajectories and force field parameters for non-standard residues for the molecular dynamics simulations discussed in the accompanying manuscript "<strong>Basis for controlled acyl chain hydrolysis in <em>trans</em>-AT polyketide synthases</strong>"</p>
Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations"
<p>Dataset from "Deciphering the Catalytic Mechanism of Virginiamycin B Lyase with Multiscale Methods and Molecular Dynamics Simulations", containing the most relevant simulation output trajectories ran with GROMACS 2021:</p> <p>1) apo simulations, including wildtype, Y28F, and H228A;<br> 2) holo simulations, including the two tested protonation states for the antibiotic;<br> 3) mutant simulations, including Y18F, H228A, E268Q, and E284Q.</p> <p>All folders contain the topology file (.top), restraint files (.itp), the initial coordinates file (.gro), and the coordinates after the first minimization (em1.gro). The output trajectories of all replicas (per system) have been concatenated in a single compressed file (.xtc).</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>
Molecular dynamics simulation data of designed cyclic peptide (ligand-only)
<p>Trajectories of <strong>ligand-only </strong>simulation and simulation set-up files of designed cyclic peptide as MDM2 binders. <br> 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. <em>Org. Biomol. Chem.</em>, <em>14</em>(44), 10386–10393. http://doi.org/10.1039/C6OB01510G</p>
Molecular dynamics simulation data of regulatory ACT domain dimer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain dimer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 dimer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from dimer with bound Phe ligand</p> <p><strong>dimer.zip</strong>: simulation starting from 21 dimer conformations simulation</p> <p>Simulation setup files are also included in each folder.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, 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"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular dynamics simulation data of regulatory ACT domain monomer of human phenylalanine hydroxylase (PAH)
<p>Raw data of molecular dynamics simulations of regulatory ACT domain monomer.</p> <p><strong>binding.zip</strong>: simulation starting from 21 monomer conformations with 19 Phe ligand </p> <p><strong>bound.zip</strong>: simulation starting from monomer with bound Phe ligand</p> <p><strong>monomer_only.zip</strong>: simulation starting from 21 monomer conformations simulation</p> <p>Simulation setup files are also included in each folder. Adaptive sampling data are also included in <strong>monomer </strong>and <strong>binding</strong> simulations.</p> <p>Details can be found in this paper:</p> <p><strong>Yunhui Ge</strong>, 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"><em>Simulation of the regulatory ACT domain of human PAH unveil the mechanism of phenylalanine binding.</em></a> J. Biol. Chem., 2018, 293(51), pp 19532-19543</p>
Molecular dynamics simulation data of designed β-hairpins
<p>Raw simulations data (protein only) and simulation set-up files of designed β-hairpins. More details can be found in this paper: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff96)
<p>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: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
Replica exchange molecular dynamics simulation data of designed β-hairpins (implicit solvent, AMBER ff99SB-ildn)
<p>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: </p> <p>Yunhui Ge, Brandon Kier, Niels H. Andersen and Vincent A. Voelz. <a href="https://pubs.acs.org/doi/10.1021/acs.jcim.7b00132"><em>Computational and experimental evaluation of designed beta-cap hairpins using molecular simulations and kinetic network models.</em></a> J. Chem. Inf. Model., 2017, 57 (7), pp 1609–1620</p>
All-atom Molecular Dynamics Simulations of SARS-CoV-2 Spike Receptor-binding Domain bound with ACE2
<p>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.</p>
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"
<p>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</p> <p>System: 80 wt% C12E5, T=298K</p> <p>Other files available: http://dx.doi.org/10.6084/m9.figshare.861071</p>
Gaussian-accelerated Molecular Dynamics simulations of CCR8-CCL1-Gprotein complex in a POPC lipid bilayer
<p>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. </p><p>Files include:</p><p>CCL1_CCR8_noSer23_oriented_repaired1_system.pdb : system topology</p><p>CCL1_CCR8_config.xml : config for running GaMD-OpenMM</p><p>CCL1_CCR8_N_1ns_imaged_structure.pdb : initial topology/structure</p><p>CCL1_CCR8_N_1ns_imaged_trajectory.dcd : trajectory file</p><p> </p><p>Simulations can be loaded in python using MDTraj:</p><p>import mdtraj</p><p>trj = mdtraj.load(<dcd file>, top=<pdb file>)</p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.