Find research datasets worth reusing

Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.

393

datasets available to search

ShareScore release 0.7.1

Dataset results

393 results for “Molecular dynamics simulations”

Learn how ShareScore rates datasets ↗

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% POPS with Na+ counterions using ff99 ions

System: Symmetric bilayer of anionic POPS (palmitoyl-oleoyl-phosphatidylserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of POPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion model: Amber ff99 [J Åqvist J. Phys. Chem. 94 8021 (1990)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 298 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

Molecular dynamics simulation trajectory of an anionic lipid bilayer: 100 mol% DOPS with Na+ counterions using Joung-Cheetham Ions

System: Symmetric bilayer of anionic DOPS (1,2-Dioleoyl-sn-glycero-3-phosphoserine 100 mol-%) lipids with sodium (Na+) counter ions. Number of DOPS: 128. Number of Na+-ions: 128. Number of waters: 4480. Lipid model: Amber Lipid 17 [IR Gould, AA Skjevik, CJ Dickson, BD Madej, RC Walker: "Lipid17: A Comprehensive AMBER Force Field for the Simulation of Zwitterionic and Anionic Lipids" in prep. (2018)]. Ion models: Joung–Cheatham [IS Joung, TE Cheatham III J. Phys. Chem. B 112 9020 (2008)]. Water model: TIP3P [WL Jorgensen, J Chandrasekhar, JD Madura, RW Impey, ML Klein J. Chem. Phys. 79 926 (1983)]. Simulation engine: Amber16 [DA Case et al. AMBER 2017 UCSF (2017)]. Number of independent repeats per setup: 2. Trajectory lengths per repeat: 400 ns + 100 ns. Previously equilibrated for: 100 ns. Sampling rate: every 10 ps. Time integration step: 2 fs. Thermodynamic ensemble: NpT.  Temperature coupling: 'Langevin' at T = 303 K. Pressure coupling: 'Berendsen' [J. Chem. Phys. 81 3684 (1984); J. Chem. Phys. 103 10252 (1995)] with xy and z coupled separately at p = 1.0 bar with no surface tension. Electrostatics: PME [J. Chem. Phys. 98 10089 (1993); J. Chem. Theory Comput. 9 3878 (2013)]. Van der Waals: Turned off between 1.0 nm and 1.5 nm. Constraints: Lengths of covalent bonds involving Hydrogens in lipids using SHAKE [J. Comput. Phys. 23 327 (1977)], in water using SETTLE [J. Comput. Chem. 13 952 (1992)]. Used in publications: OHS Ollila et al. "NMRlipids IV: Headgroup & glycerol backbone structures, and cation binding in bilayers with PS lipids" in prep (2018).

opencc-by-4.0Jan 2018View details →

zenodo44/100

Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling: Datasets.

Datasets related to the publication [1]. Including: <ul> <li>KRAS G12X mutations derived from COSMIC v.79 [http://cancer.sanger.ac.uk/cosmic/] (KRAS_G12X_mut_COSMICv79..xlsx)</li> <li>RMSFs (300-2000ns) of GDP-systems (300_2000rmsf_GDP_systems_RAW_AVG_SE.xlsx)</li> <li>RMSFs (300-2000ns) of GTP-systems (300_2000RMSF_GTP_systems_RAW_AVG_SE.xlsx)</li> <li>PyInteraph analysis data for salt-bridges and hydrophobic clusters (.dat files for each system in the PyInteraph_data.zip-file)</li> <li>Backbone trajectories for each system (residues 4-164; frames for every 1ns). Last number (e.g. _1) refers to the replica of the simulated system.</li> <li>backbone_4-164.gro/.pdb/.tpr -files (resid 4-164)  </li> </ul> [1] Pantsar T et al. Assessment of mutation probabilities of KRAS G12 missense mutants and their long-time scale dynamics by atomistic molecular simulations and Markov state modeling. PLoS Comput Biol Submitted (2018)

opencc-by-4.0Aug 2018View details →

zenodo44/100

Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 1-3)

Description of files in this dataset: MD_quadmut_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 5-6)

Description of files in this dataset: MD_mutR117A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with DHA (POSES 1-4)

Description of files in this dataset: MD_wt_CYP2J2_DHA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of docosahexaenoic acid (DHA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 3 and 4)

Description of files in this dataset: MD_wt_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 4 times, hence there are 4 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Sep 2019View details →

zenodo44/100

Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids

This is the "parent" repository for the Data Note : "Molecular dynamics simulations of the interaction of wild type and mutant human CYP2J2 with polyunsaturated fatty acids" by Abelak, Bishop-Bailey and Nobeli. It contains a document (Abelak_etal_Methods.pdf) describing the methods used to produce the data here and the data in all repositories supplementing it. It also contains a shell script (create_sim4_repeats.sh) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one. Finally, it contains the results of the homology modelling and docking simulations that formed the starting points for the molecular dynamics simulations in this study. Description of files in this dataset: C2J2_min3_mod_noH.pdb : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10. docking_wild_type_C2J2.zip : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2. Details of how this data was produced is available in the Abelak_etal_Methods.docx document.

opencc-by-4.0Sep 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 1 and 2)

opencc-by-4.0Sep 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with arachidonic acid (POSES 5 and 6)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of the double mutant human CYP2J2 (R117A and R111A) with arachidonic acid (POSES 1-3)

Description of files in this dataset: MD_mutR111A_R117A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the double R111A + R117A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R117A) with arachidonic acid (POSES 1-4)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of mutant human CYP2J2 (R111A) with arachidonic acid (POSES 4-6)

Description of files in this dataset: MD_mutR111A_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the R111A mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of wild type human CYP2J2 with EPA (POSES 1-4)

Description of files in this dataset: MD_wt_CYP2J2_EPA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of eicosapentaenoic acid (EPA) in the active site of wild type CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 4 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage 005.md : Production stage 006.analysis : Basic energy graphs 007.cpptraj: Contains only the file strip.md.nc (Amber trajectories stripped of water in netCDF format)

opencc-by-4.0Oct 2019View details →

zenodo44/100

Molecular dynamics simulations of the interaction of the quadruple mutant human CYP2J2 (R111A + R117A + R382A + R446A) with arachidonic acid (POSES 4-6)

Description of files in this dataset: MD_quadmut_CYP2J2_AA_StateX_repeatY.zip : Series of zipped directories for molecular dynamics simulations of arachidonic acid in the active site of the quadruple (R111A + R117A+R382A+R446A) mutant CYP2J2. X is the docking pose number that constitutes the starting point of the simulation (the 6 lowest-energy poses from docking were selected as the starting points of the simulations - this dataset is State(pose) 1). Y is the repeat (each simulation was repeated 3 times, hence there are 3 repeats per pose).   Each directory contains the following sub-directories: 001.leap : Amber parameter and coordinate files; PDBs; ligands; leap commands 002.min : Minimisation stage 003.heat : Heating stage 004.equil: Equilibration stage

opencc-by-4.0Oct 2019View details →

zenodo44/100

Evaluating Changes in the Local Protein Physicochemical En-vironment induced by Molecular Dynamics Simulation

Mutation of a single amino acid residue may significantly affect the structure and function of an entire protein. The effect of single amino acid substitutions can be assessed by examining the physicochemical environment surrounding the amino acid of interest, an emerging form of quantification of which is multidimensional tensors. However, the effect with respect to a protein variant’s inherent dynamics in tensor space is rarely assessed despite the potential importance of this form of analysis in revealing local physicochemical properties of the protein and response to mutation. Using the wild-type and 936 mutant structures of the protein domain 1pga, the present research evaluated the effects of local protein context and single amino acid substitutions on molecular dynamics simulation-derived structural distributions via the use of tensors capturing a range of biochemical properties. It was observed that the extent of simulated physicochemical variation local to a substituted amino acid is positively associated with local mechanical stiffness, loss of protein thermostability and decreased local hydrophobicity. In addition, it was observed that the largest tensor variation occurs in densely-packed, hydrophobic core-associated regions of protein structures. In summary, the pattern of tensor change aligns with prior knowledge about protein stability and physicochemical properties.

opencc-by-4.0Sep 2024View details →

zenodo44/100

Molecular Dynamics Simulation of SARS-CoV-2 Spike Protein

Trajectory data corresponding to the manuscript, tentatively titled "Distant Residues Modulate the Conformational Opening in SARS-CoV-2 Spike Protein" Authors: Dhiman Ray, Ly Le, Ioan Andricioaei Affiliation: University of California Irvine, USA 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"). 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. 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. Pre-print available: https://doi.org/10.1101/2020.12.07.415596

opencc-by-4.0Dec 2020View details →

zenodo44/100

Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments - DATA

Specular reflectivities of the SoyPC bilayer stack measured at the vertical reflectometer MARIA  at Heinz Maier-Leibnitz Zentrum (MLZ) in Garching, Germany. Offspecular reflectivity map (log scale) of the multilayer sample as a function of theangle of incidence (θi) and of the reflection angle (θi). Specular reflectivities of the Si/SiO2/DMPC/H2O at 4 different contrasts (H2O, D2O, SMW and 4MW) Small-angle neutron scattering of the unilamellar  SoyPC

opencc-by-4.0May 2021View details →

zenodo44/100

Coarse-grained molecular dynamics simulations of SARS-CoV-2 envelope protein E in the pentameric form

The trajectories of coarse-grained (CG) molecular dynamics (MD) simulations of 1) unmodified (FeigLab_NMR; FeigLab_PentamerNoPTM_POPC_Martini3b: 5 μs; 5 μs);  2) palmitoylated (FeigLab_PentamerCYSP43; PentamerCYSP44_POPC_Martini3b: 5 μs; 5 μs);  SARS-CoV-2 E protein pentamer in a POPC bilayer. 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). FeigLab_Pentamer: https://github.com/feiglab/sars-cov-2-proteins/blob/master/Membrane/E_protein.pdb FeigLab_NMR_Pentamer is assembled based on the transmembrane domain determined by NMR (PDB ID: 7K3G) and FeigLab model for the rest.

opencc-by-4.0Aug 2021View details →

zenodo44/100

Dataset of Molecular Dynamics Simulations for the Upregulated Biomarker PSMB8: 3UNF and its G210V Mutant in Experimental Autoimmune Encephalomyelitis

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. 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. 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.

opencc-by-4.0Jun 2023View details →

ScienceDex guides

Understand access before you commit

These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.

Compare curated datasets

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.

allen-brain-atlas

neuroscienceopenDocumentation, web resources, and API references are available online.

Last verified 2026-04-30Open record

Annotated Behaviour and Observability Dataset (ABODe)

ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.

abode-home-cage

behavioral-neuroscienceopenThe DataShare record exposes download links for annotations, documentation, license text, and the zipped per-snippet data directory.

Last verified 2026-04-30Open record

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.

dandi-nwb

electrophysiologyopenPublished Dandiset metadata and archive endpoints are available through the production DANDI API.

Last verified 2026-04-30Open record

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.

ibl

behavioral-neuroscienceopenPublic sessions can be searched and loaded from the IBL public data server through ONE.

Last verified 2026-04-29Open record

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.

openneuro

neuroscienceopenPublished datasets are available on demand over the internet.

Last verified 2026-04-29Open record