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.
418
datasets available to search
ShareScore release 0.9.0
Dataset results
418 results for “Dimerization”
Amyloid-beta 16-22 peptide dimer simulation (150mM NaCl) with the CHARMM36m force field and Gromacs (Run 1)
<p>Amyloid-beta 16-22 peptide dimer simulation with the CHARMM36m force field. This directory contains first of the three independent trajectories and the simulation length is 1 microseconds. The system contains two amyloid-beta 16-22 monomers, 30 Na+, 30 Cl-, and 10564 TIP3P water.</p>
Simulations of Spontaneous TM Domain Dimer Formation
<p>Simulations of spontaneous dimer formation of 5 TM domain dimers in DLPC bilayers. Simulations are performed in the coarse-grained scheme using either standard Martini parametrization or its derivative in which the protein–protein interactions (Lennard-Jones epsilons) are downscaled by 10%. </p> <p>The tar files are named after the PDB codes of the corresponding dimers. Each tar contains 10 replicas (files numbered 1 to 10) for both scaled (S) and unscaled (U) force fields. The trajectory (.xtc, stored every 10ns, solvent omitted), energy file (.edr), and run input file (.tpr) for GROMACS are provided for each replica. The starting structures (.gro) shared by scaled and unscaled are also given. The index file (.ndx) is common for all simulations of the dimer, and the topology files (.top) are given separately for simulations using the scaled and unscaled force fields. The common simulation parameter file (.mdp) is provided. TOP.tar contains all topologies.</p> <p>The scaling is achieved by adding 'p' to the bead types in the proteins. The corresponding parameters are given in the "martini_v2.2_scaled.itp" file. Note that for uniform style, the unscaled parameters are given in a similar manner in a file "martini_v2.2_unscaled.itp".</p> <p>For a more thorough explanation of the purporse of the files and the simulation parameters, see the related publication:</p> <p>Javanainen M, Martinez-Seara H, Vattulainen I (2017) Excessive aggregation of membrane proteins in the Martini model. PLoS ONE 12(11): e0187936. https://doi.org/10.1371/journal.pone.0187936</p>
Umbrella Sampling Simulations of TM Domain Dimerization
<p>Umbrella sampling simulations of dimer formation of 2 TM domain dimers in DMPC/DLPC bilayers. Simulations are performed in the coarse-grained scheme using different force fields; normal Martini (N), Martini with all protein–protein interactions scaled (U) by 10% (U_10) or 20% (U_20), Martini with interactions among water-interacting beads scaled (W) either by 60% (W_60), 80% (W_80), or 90% (W_90), or the polarizable Martini (P). The original Martini is also repeated with an older set of 'common' simulation parameters (C).</p> <p>The tar files are named after the PDB codes of the corresponding dimer and the type of force field employed (see above). The tar files contain the run input files (.tpr) and the corresponding simulation parameter files (.mdp) for all umbrella windows; i.e. "EPHA_U_80_18.tpr" is the run input file for the EPHA dimer with all protein–protein interactions scaled down by 20% and with a protein–protein distance restrained to 18 Å by the umbrella potential. This tpr is generated from the simulation parameter file, the topology file (here EPHA_U_80.top), the index file (here EPHA.ndx), and the initial structure (here EPHA_start_18.gro, available in the EPHA-frames.tar). The index and initial structures for the polarizable model differ, and are provided in "EPHA-P.ndx" and "EPHA-frames-P.tar", respectively. All topologies (.itp) are provided in TOP.tar.</p> <p>The scaling is achieved by adding 'p' to the bead types in the proteins; either all types (scaling U) or to those more in contact with water than the membrane (scaling W) The corresponding parameters are given in the "martini_v2.2_scaled_X.itp" file. Note that for uniform style, the unscaled parameters are given in a similar manner in a file "martini_v2.2_unscaled.itp". Here, the .itp files follow the naming convention of the paper (see below) so that X=1 means downscaling of LJ epsilon by 10%, i.e. it corresponds to files with "_10".</p> <p>For a more thorough explanation of the purporse of the files and the simulation parameters, see the related publication:</p> <p>Javanainen M, Martinez-Seara H, Vattulainen I (2017) Excessive aggregation of membrane proteins in the Martini model. PLoS ONE 12(11): e0187936. https://doi.org/10.1371/journal.pone.0187936</p>
Code and data for Oxygen dimerization as a defect-driven process in bulk LiNiO2
<p>Data and code required to generate figures in the article "Oxygen dimerization as a defect-driven process in bulk LiNiO2".<br><br>Available as a preprint at 10.26434/chemrxiv-2024-lcmk</p>
Energies, forces, and Born effective charges for water and MAPbI3 + Born effective charges and polarization data for a water dimer
<p>Datasets containing energies, forces, and Born effective charges for water and MAPbI3 in the VASP format (ML_AB, OUTCAR, and POSCAR), polarization data and Born effective charges for a water dimer are also included.</p> <p><strong>Energies and forces:</strong><br>H2O/MLFF/RPBE-D3/ML_AB – 64 water molecules, 654 configurations.<br>H2O/MLFF/SCAN/ML_AB – 64 water molecules, 972 configurations.<br>MAPbI3/MLFF/ML_AB – 8(MAPbI3), 1414 configurations, tetragonal and orthorhombic phase, SCAN.</p> <p><strong>Born effective charges:</strong><br>dimer/BEC/ – 2 water molecules, 150 configurations.<br>H2O/BEC/ – 64 water molecules, 100 configurations.<br>MAPbI3/BEC/ – 8(MAPbI3), 300 configurations, tetragonal, orthorhombic, and cubic phase.</p> <p><strong>Polarization:<br></strong>dimer/P/ – 2 water molecules, 1000 configurations.</p> <p>See preprint for more details: </p> <table> <tbody> <tr> <td><a href="https://doi.org/10.48550/arXiv.2404.19674">https://doi.org/10.48550/arXiv.2404.19674</a></td> </tr> </tbody> </table>
Electronic Energy Singularities of Weakly H-bonded Ammonium Dimer
<p><strong><u>Background: </u></strong></p> <p>Following set of data has been provided as a proof of general hypothesis for weak H-bonded and also VDW dimers. The methods of quantum mechanics have been applied are Hartree-Fock, Møller-Plesset, Density Functional Theory with state-of-art quantum chemistry software. And for this specific case results from NH3 dimer has been reported.</p> <p>[A]. The general hypothesis first proposed in a paper published online in 2020 and in archive in 2021 [1] with explicit mention of hypothesis that torsional electronic energy has singularities for weak H-Bonds contrast to force field results of energy continuum.</p> <p>[B]. This energy singularities are associated with quantum geometrical criticality of weak H-bonded or VDW dimers. Any QM energy computation method with reasonable basis set must reveal electronic energy singularities unlike smooth force field or molecular mechanics based dihedral energy continuum for weak H-bonded or VDW dimers. Also for weak H-bonded atoms if separated by a distance beyond bond length; internal rotation must show energy singularities; or equivalently geometry must show criticality feature in all QM energy computations.</p> <p>[C]. These QM computational results cannot be explained by classical reasoning because of no stearic clashes among atoms; molecular mechanics/force field always predict finite energy beyond bond-length. </p> <p><strong><u>Hypothesis Tested: </u></strong></p> <p>All conformational geometry in weak H-bonded or VDW molecules cannot be allowed as per QM contrast to MM even though no stearic clashes of atoms do exist; bond-breaking involves two aspects: <I> sudden jumps in energy <II> breaking of molecular geometry. The energy singularities results are indicative of geometry break-up or in other words bond breaking. </p> <p><strong><u>References: </u></strong></p> <p>[1] Ali, M Rejwan and Mezei M. 2021. “Observation of Quantum Signature in Rivastigmine Chemical Bond Break-up and Quantum Energetics, Spectral Studies of Anti-Alzheimer Inhibitors.” Journal of Biomolecular Structure and Dynamics 39 (1): 118–28. https://doi.org/10.1080/07391102.2019.1708462.</p> <p>[2] Ali, Md R. 2022 “Quantum Signature of Anisotropic Singularities in Hydrogen Bond Breaking of Water Dimer” (12th Triennial Congress of the World Association of Theoretical and Computational Chemists (WATOC), Vancouver, Canada)</p> <p>[3] Ali, M Rejwan 2025, “Electronic Energy Singularities of Weakly H-bonded Ammonium Dimer" </p> <p>Journal of Micromechanics and Molecular Physics https://doi.org/10.1142/S2424913025500079</p> <p>Preprint: https://arxiv.org/abs/2504.17107 </p> <p><strong><u>Description of Files: </u></strong></p> <p>File Folder Explanation: All the results have been obtained via SPARTAN-20 version software. Both MM and QM methods have been used to compute torsion angle based electronic energy of NH3 dimer. The files have corresponding extension name for methods used as also listed below: </p> <p>NH3-dimer_MM: </p> <p>1. MMFF</p> <p>2. SYBYL</p> <p> NH3-dimer_QM</p> <p>1. HF/6-311G*</p> <p>2. MP2/CC-PVDz</p> <p>3. B3LYP/6-311G* (Both forward and reverse torsion electronic energy scan)</p> <p><strong><u> </u></strong></p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p> <p> </p>
STAT5B N642H Dimer
<p>The final 75 ns of the 1 µs trajectory for the STAT5B<sup>N642H</sup> dimer (system 1). The color scheme is identical to Supplementary Video 1 with H642 highlighted in green. A smoothing window of 5 frames was applied using VMD, and the protein was aligned to the conformation obtained after the equilibration simulations. Water and ions are not shown for clarity. As can be seen in the movie, in contrast to the wild type STAT5B dimer, STAT5B<sup>N642H</sup> dimer remains stable for the entirety of the simulation.</p>
STAT5B WT Dimer
<p>The simulation trajectory for the STAT5B dimer (system 3) over 75 ns. The CCD (cyan), DBD (blue), linker domain (purple) and SH2 domain (orange) are all shown with residue N642 highlighted in green. A smoothing window of 5 frames was applied using VMD, and the protein was aligned to the conformation obtained after the equilibration simulations. Water and ions are not shown for clarity. As can be seen in the movie, the inter-monomer contacts are lost at ~75 ns, resulting in dissociation and dimer separation.</p>
Input files for MD simulations of VP40 matrix protein dimer-dimer structure for WT, G198R, and G201R
<p>For AA simulations, the inp files need to have the path for the toppar folder and the corresponding pdb/psf files need to be renamed.</p>
FIGURE 1 in Paepalanthus modestus (Eriocaulaceae), a new dimerous species from Goiás, Brazil, with notes on leaf and scape anatomy
FIGURE 1. Holotype of Paepalanthus modestus collected in Alto Paraíso de Goiás (Goiás–Brazil) (M.L.O. Trovó & A.L. Silva 646– RB).
FIGURE 2. Paepalanthus modestus. A. Habitat. B. Stem and rosette before fire. C. Stem and rosette after fire. D. Leaf apex. E. Spathe detail. F. Spathe detail. G. Young scape detail. H. Old scape detail. I. Mature capitulum. J. Young capitulum highlighting the involucral bracts. K. Capitulum with abnormal involucral bracts. L. Floral bract abaxial surface. M. Staminate flower. N. Pistillate flower. O. Gynoecium. P in Paepalanthus modestus (Eriocaulaceae), a new dimerous species from Goiás, Brazil, with notes on leaf and scape anatomy
FIGURE 2. Paepalanthus modestus. A. Habitat. B. Stem and rosette before fire. C. Stem and rosette after fire. D. Leaf apex. E. Spathe detail. F. Spathe detail. G. Young scape detail. H. Old scape detail. I. Mature capitulum. J. Young capitulum highlighting the involucral bracts. K. Capitulum with abnormal involucral bracts. L. Floral bract abaxial surface. M. Staminate flower. N. Pistillate flower. O. Gynoecium. P. Fruit releasing the seeds. (M.L.O. Trovó & A.L. Silva 646–RB).
FIGURE 3 in Paepalanthus modestus (Eriocaulaceae), a new dimerous species from Goiás, Brazil, with notes on leaf and scape anatomy
FIGURE 3. Anatomical sections of leaves and scapes of Paepalanthus modestus (M.L.O. Trovó & A.L. Silva 646–RB). A. Transverse section of the leaf. B. Paradermal view of the abaxial leaf surface. C. Detail of the abaxial leaf surface. D. Detail of a vascular bundle. E. Transverse section of the scape. (Scale bars: A, E= 200μm; B–D= 50μm).
The effect of S427F mutation on RXRα activity depends on its dimeric partner
<p>Simulations for RXRa-RARa can be found at: https://repo.vi-seem.eu/handle/21.15102/VISEEM-169 </p> <p>Below are the datasets of the MD simulations RXRα-RXRα and RXRα-PPARγ for the paper:</p> <p>"The effect of S427F mutation on RXRα activity depends on its dimeric partner", Galdadas et al, 2021, Chemical Science.</p> <p>RXRs are nuclear receptors acting as transcription regulators that control key cellular processes in all tissues. All type II nuclear receptors require RXRs for transcriptional activity by forming heterodimeric complexes. Recent whole-exome sequencing studies have identified the RXRα S427F hotspot mutation in 5% of the bladder cancer patients, which is always located at the interface of RXRα with its obligatory dimerization partners. Here, we show that mutation of S427 deregulates transcriptional activity of RXRα dimers, albeit with diverse allosteric mechanisms of action depending on its dimeric partner. S427F acts by allosteric mechanisms, which range from inducing the collapse of the binding pocket to allosteric stabilization of active co-activator competent RXRα states. Unexpectedly, RXR S427F heterodimerization leads to either loss- or gain-of-function complexes, in both cases likely compromising its tumor suppressor activity. This is the first report of a cancer-associated single amino acid substitution that affects the function of the mutant protein variably depending on its dimerization partner.</p>
Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details
<p>The system construction and dynamic simulation data of paper "Dimerization the ACE-2 with Different RBD Mounts: A Dynamic Simulation Perspective on SARS-Cov-2 Infecting Details"(manuscript, ci-2023-00041c) are prepared.</p>
Dataset for computational study of the ALS mutation G335D modulating the dimerization of TDP-43 amyloidogenic core peptide
<p>This dataset consist the following contents:</p> <p>1. The data used to generate MD/RSET2 trajectories for WT and G335D systems, including initial structures, parameter files and topology files;</p> <p>2. The final structures and representative conformations of intermediates for WT and G335D systems in MD simulations;</p> <p>3. Representative conformations of the top eight clusters for WT and G335D systems in REST2 simulations.</p>
Ultrafast formation dynamics of D3+ from the light-driven bimolecular reaction of the D2-D2 dimer
<p>All the raw data for the main figures of our literature of "Ultrafast formation dynamics of D<sub>3</sub><sup>+</sup> from the light-driven bimolecular reaction of the D<sub>2</sub>-D<sub>2</sub> dimer". Molecular dynamics trajectories and the initial configurations are supplied.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor dimer simulation - 80 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Bicelle size and lipid/surfactant ratio screening - Gwalp tail anchor dimer simulation - 60 Lipids - q0.38 - PBS neutralized - CHARMM36m - 310K - OPC water model
<p>Bicelle size and lipid to surfactant ratio screening to investigate the influence on spin relaxation data with monomers of a given peptide.</p>
Micelle size screening - Gwalp tail anchor dimer simulation - 45 SDS - Na neutralized - CHARMM36m - 310K - OPC water model
<p>Micelle size screening by varying the amount of SDS to investigate the influence on spin relaxation data with dimers of a given peptide.</p>
Micelle size screening - yFis1 tail anchor dimer simulation - 50SDS - Na neutralized - CHARMM36m - 310K - OPC water model
<p>Micelle size screening by varying the amount of SDS to investigate the influence on spin relaxation data with dimers of a given peptide.</p>
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research 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.
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.
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.