Find research datasets worth reusing

opencc-by-4.0Jun 2020View details →

Diffraction images of a crystal of the F-BAR domain of PSTPIP1 (Proline-serine-threonine phosphatase-interacting protein 1) bound to the C-terminal homology (CTH) segment of the phosphatase LYP (PTPN22) (PDB entry 7AAM)

Diffraction images of a crystal of the F-BAR domain of human PSTPIP1 (residues 1-289, Uniprot reference O43586-1) in complex with the CTH of LYP (residues 787-807, Uniprot Q9Y2R2-1). Data were collected on a single crystal at the beamline i03 of the Diamond Light Source synchrotron (Didcot, UK) using radiation of 0.99987 Å wavelength and a PILATUS3 6M detector. The dataset consists of 3 groups, each containing of 1800 images (0.1 degree oscillation per image), collected at three different positions of the same crystal. Crystal belongs to the space group P2(1)2(1)2(1) with unit cell dimensions a=48.0 Å, b=72.0 Å, c=205.0 Å. The asymmetric unit contains an homodimer of the F-BAR domain bound to a LYP-CTH (~53% solvent content), which is the biological complex. Diffraction data was notably anisotropic. The lowest resolution limit was 4.05 Å in the direction b* and the highest limits were 2.11 Å and 2.10 in the directions a* and c*, respectively.   The structure derived form these data is published in: Manso, J.A., Marcos, T., Ruiz-Martín, V. Casas J, Alcón P, Sánchez Crespo M, Bayón Y, de Pereda JM, Alonso A PSTPIP1-LYP phosphatase interaction: structural basis and implications for autoinflammatory disorders. Cell. Mol. Life Sci. 79, 131 (2022). <a href="https://doi.org/10.1007/s00018-022-04173-w">https://doi.org/10.1007/s00018-022-04173-w</a> The structure is available at the PDB under the code 7AAM: <a href="https://www.ebi.ac.uk/pdbe/entry/pdb/7aam">https://www.ebi.ac.uk/pdbe/entry/pdb/7aam</a>

openmit-licenseMar 2022View details →

MATLAB code for 'Bounds on quantum evolution complexity via lattice cryptography'

We provide the MATLAB code and data to reproduce the numerical results presented in the paper https://arxiv.org/abs/2202.13924.

opencc-by-4.0Jan 2022View details →

Data for "Exemplifying parametric timed specifications over signals with bounded behavior"

Data for "Exemplifying parametric timed specifications over signals with bounded behavior" by Étienne André, Masaki Waga, Natuski Urabe, and Ichiro Hasuo, published in the proceedings of the 14th NASA Formal Methods Symposium (NFM 2022) See README.md in the zipped file for explanations and instructions for reproductibility.

opencc-by-4.0Aug 2021View details →

RvE1/Chemerin-9/αNETA bound to CMKLR1

All docking calculations were performed with the AutoDock Vina program. The crystal structures of human CMKLR1 was used as starting point. The PDB structures of 6os0.1. A was used as template for the predication of CMKLR1. All Molecular dynamics simulations (MD) simulations were performed with the pmemd module of Amber 18 software suite. Molecular mechanics generalized born surface area (MM/GBSA) was performed with mmpbsa.py program, enclosed in Amber 18 software, to estimate the binding free energy. The translational and rotational entropy was calculated with stardard statistical mechanics formulas. The vibrational entropy was computed from the frequencies of global motions by using normal mode analysis (N-mode) in mmpbsa.py program. The coordinates for these calculations are taken from the MD simulations trajectory. All docking calculations were performed with the AutoDock Vina program.

ProtNAff: Protein-bound Nucleic Acid filters and fragment libraries

This archive contains data obtained by running the ProtNAff pipeline (<a href="https://github.com/isaureCdB/ProtNAff">https://github.com/isaureCdB/ProtNAff</a>) and used to perform the analyses described in the original ProtNAff paper. The input list of PDB IDs was obtained in October 2021 by searching all PDB structures that contain protein chains and RNA chains but no DNA, and where the resolution is less than 3 A or where the method is NMR. The ribosomes are removed from this database due to their size. The files provided are: - structures.json : the database containing metadata and parsing data for all the protein-RNA structures from the input list - fragments_clust.json : the list and description of all the trinucleotide fragments extracted from those structures - trinucl_clust1A_allatom: the all-atom coordinates of the trinucleotide fragment library , i.e. the centers of 1A clusters such that each initial fragment has a RMSD of less than 1A from at least one of those centers. - trinucl_clust1A_ATTRACT: the coordinates of the trinucleotide fragment library , but reduced into ATTRACT coarse-grained representation (Setny and Zacharias, NAR 2011).

Figure 2 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 2. Following John Ray's discovery of hermaphroditism in slugs and snails, Jan Swammerdam produced the first known image of copulating snails as part of the frontispiece of his 1667 doctoral thesis, De respiratione. Wellcome Images.

Figure 4 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 4. Colour plate from Jacob Christian Schäffer Der wunderbare und vieleicht in der Natur noch nie erschienene Eulenzwitter (1761) featuring Schäffer's hermaphrodite gypsy moth (Fig. IX in the image).

Figure 6 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 6. Without reference to Hunter's paper, the English physician and ornithologist John Latham, a co-founder of the Linnean Society, referred to the exhibit of Lady Tynte's extraordinary peahen in the Leverian Museum in A general synopsis of birds (1783), complete with this colour plate of the bird. Following a description of the white peacock, he wrote: 'I cannot close this account without mentioning a circumstance which now and then occurs in the females of this species, viz. having the external marks of the plumage of the male: two instances of which have occurred to me; the one belonging to a friend of mine in this county; the other now to be seen in the Leverian Museum. This last beautiful bird belonged to Lady Tynte, and had bred for some years; but after ceasing to lay eggs, began to put out the male eyed feathers; and at the time of its death appeared like a young male' (Latham, 1783, Vol. 2, Part 2: 672).

Figure 1 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 1. Remarkably, the drawing of a hermaphrodite rat, referred to by Johann Faber, still exists, rediscovered relatively recently in the collections of the Bibliothèque de l'Institut de France in Paris by art historian David Freedberg along with many other pictures of plants and animals produced by a scientific society known as the Academy of Linceans (or Lynxes) of which Theophilus Müller was a member (Freedberg, 2003: 243). Photo: RMN-Grand Palais (Institut de France)/René-Gabriel Ojeda.

Figure 5 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 5. The first known image of a female deer endowed with antlers, beautifully formed, was published in Miscellanea curiosa in 1684. It was submitted by German physician and alchemist Joel Langelott who wrote that the animal ('an amazing example of nature's abundance') had been captured in the area of Husamen (? perhaps Husum) in August 1597 and preserved in the hall of the Duke of Husum. A poet ('a pretty bad one') had added some verses in German to the illustration that was made from the exhibit. Upon hearing that the image was to be submitted for publication, prolific German scholar and poet Daniel Georg Morhof, an acquaintance of Langelott, took pity on the situation of the beast ('which Mother Nature in her great kindness had adorned in such a remarkable fashion') and decided that it deserved to be commended to posterity by means of a 'charming and elegant' elegy in Latin titled 'The stag speaks', which was also reproduced in Miscellanea curiosa alongside the picture. It begins: 'I was a female stag: look at me, sirs! do not believe that I was a stag: For as a female I bore antlers that should be given to males. A male neck was joined to a female body. See how that neck swells with adopted branches! Look how both sexes are mingled in a new shape And now a new shape makes a new androgyne.' (Langelott, 1680; transl. Carolinne White). Image: Bodleian library, University of Oxford.

Figure 3 in REVIEW Bounds of diversity: queer zoology in Europe from Aristotle to John Hunter

Figure 3. Hermaphrodite lobster, dissected by Frank Nicholls. Philosophical Transactions (May 1730). Reproduced with permission of the Royal Society Library.

opencc-by-4.0Aug 2017View details →

Raw diffraction images of endothelin ETB receptor bound to clinical antagonist bosentan and its analog

Diffraction images of endothelin ETB receptor bound to bosentan (PDB code 5XPR) and K-8794 (5X93). Bosentan is an oral medication approved for the treatment of pulmonary arterial hypertension. K-8794 is the ETB-selective high-affinity analog of bosentan. Two datasets of 5X93 were collected with helical method, while for 5XPR 16 small-wedge (10°/crystal) datasets were collected automatically using ZOO system. In both cases the diffraction images were collected from loop-harvested microcrystals using MX225HS CCD detector at a wavelength of 1 Å on BL32XU, SPring-8. For 5XPR, 14 datasets were merged at 3.6 Å resolution in the published result (Shihoya et al. NSMB 2017) using KAMO; see processing note: https://github.com/keitaroyam/yamtbx/wiki/Processing-ETBR-bonsentan-data-(5XPR) NOTE <ul> <li> Most frames have (relatively weak) lipid rings. </li> </ul> <ul> <li> There is the indexing ambiguity problem in 5XPR (space group P3221) that should be resolved before merging. </li> <li> 5xpr_bosentan/bosentan-1425-01/multi_002_000019.img.bz2 is missing (probably due to a detector problem) </li> </ul>

opencc-by-4.0Dec 2017View details →

Raw diffraction images of human orexin 2 receptor bound to the subtype-selective antagonist EMPA

Human orexin 2 receptor (OX2R) is a member of G protein-coupled receptors (GPCR). OX2R plays important roles in modulating feeding behavior and regulating the sleep-wake cycle. 805 small-wedge (1-6°/crystal) datasets collected from loop-harvested microcrystals using MX225HS CCD detector at a wavelength of 1 Å on BL32XU, SPring-8. The crystals belonged to space group C2 with unit cell parameters a=94.1, b=75.5, c=95.9 Å, β=111.4°. 631 datasets were merged at 1.96 Å resolution in the published result (Suno et al. Structure 2017; PDB code: 5WQC) using KAMO; see https://github.com/keitaroyam/yamtbx/wiki/Processing-OX2R-data-(5WQC) Note <ul> <li>Most frames have lipid rings.</li> <li>One dataset (not included in the published result) was lost for some reason (so 804 datasets are available).</li> </ul>

opencc-by-4.0Jun 2024View details →

Theoretical simulations data for "Experimental observation of repulsively bound magnons"

The files contain the data obtained from the theoretical simulations depicted in the figures of the article "Experimental observation of repulsively bound magnons" Nature (2024). The format of the data and to which figure it corresponds is described in the file "read_me_metadata.txt".

opencc-by-4.0Apr 2024View details →

Drag, lift, and torque correlations for axi-symmetric rod-like non-spherical particles in linear wall-bounded shear flow

Data linked to the manuscript:  Drag, lift, and torque coefficients of fixed axi-symmetric rod-like particles in linear wall-bounded shear flow Authors: Victor Cheron, Berend van Wachem Corresponding author: Berend.van.Wachem@gmail.com Files Temporally averaged drag, lift and torque coefficients are written in .txt files stored in the folder ResultsCoefficients. Python scripts used to plot the correlations are stored in the folder PythonScript. Two simulation results are provided in the folder SimulationResults. Results and Coefficients The .txt files are split per coefficient, aspect ratio and shear rate, which can be identified by the name of the .txt file. The results obtained for the torque coefficient of the particle of aspect ratio 2.5 for a uniform flow configuration are given in the file: Uniform-Torque-Angles-Size2-5.txt The results obtained for the lift coefficient of the particle of aspect  ratio 10 for a shear rate 0.2 configuration are given in the file: Shear02-Lift-Angles-Size10.txt In the files, the results are ordered per orientation angle and particle Reynolds number.  PythonScripts The python scripts are split among three files: - Getter.py: this script reads the .txt files storing the coefficients. - ManuscriptCorrelations.py : this script returns the functions to read plot the correlations for the drag, lift and torque coefficients. - generalmain.py : calls the functions The scripts Getter.py and ManuscriptCorrelations.py are called from the script generalmain.py file.  This will return a 1D column vector ordering the variables used to derive the correlations: - Coefficients - Reynolds number - Orientation Angle - Dimensionless distance to the wall - Aspect ratio Simulation Results A simulation result is provided: - Aspect ratio 5, particle Reynolds number 100, orientation angles 30 and 150,   dimensionless distance 1. The data of all fields (pressure, velocity, source terms from the particles) are stored in .h-files. A .xmf reader is provided to read the simulation results in Paraview. Data for one converged simulation time are provided due to storage limits.   Acknowledgments This research was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 448292913 and by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) - Project-ID 422037413 - TRR 287.

opencc-by-4.0Apr 2019View details →

Data set for Sicoli et al. - Conformational tuning of a DNA-bound transcription factor

The data set contains NMR, EPR and MD data. The NMR folder contains 1H-15N correlation NMR data of DNA-bound MAX with a paramagnetic MTSL spin label at position 5, with a chemically reduced, diamagnetic spin label, respectively. The EPR folder contains DEER data of MAX for three difference labeling positions R5C, G35C and R55C, with and without bound DNA. The MD folder contains MD trajecrories at three different temperatures, 310 K, 320 K and 330 K. Further details can be found in the readme.txt files in the respective folders.

Text-fig. 19. Geological position of the flora of Roudníky in the cores Ru 43 and Ru 60 and radiometric dating (from Bellon et al. 1998, adapted). 1 – xenolites intercalated with claystone, 2 – claystone, 3 – pyroclastite, 4 – tuffaceous claystone, 5 – olivine basalt, 6 – Quaternary cover. in Mid-Latitude Palaeogene Floras Of Eurasia Bound To Volcanic Settings And Palaeoclimatic Events - Experience Obtained From The Far East Of Russia (Sikhote-Alin') And Central Europe (Bohemian Massif)

Text-fig. 19. Geological position of the flora of Roudníky in the cores Ru 43 and Ru 60 and radiometric dating (from Bellon et al. 1998, adapted). 1 – xenolites intercalated with claystone, 2 – claystone, 3 – pyroclastite, 4 – tuffaceous claystone, 5 – olivine basalt, 6 – Quaternary cover.

Text-fig. 18. Geographical position of the main palaeobotanical localities in the České středohoří Mountains. in Mid-Latitude Palaeogene Floras Of Eurasia Bound To Volcanic Settings And Palaeoclimatic Events - Experience Obtained From The Far East Of Russia (Sikhote-Alin') And Central Europe (Bohemian Massif)

Text-fig. 18. Geographical position of the main palaeobotanical localities in the České středohoří Mountains.

Text-fig. 17. Ohře (Eger) rift in Central Europe with main magmatic structures (from Cajz et al. 1999, adapted). in Mid-Latitude Palaeogene Floras Of Eurasia Bound To Volcanic Settings And Palaeoclimatic Events - Experience Obtained From The Far East Of Russia (Sikhote-Alin') And Central Europe (Bohemian Massif)

Text-fig. 17. Ohře (Eger) rift in Central Europe with main magmatic structures (from Cajz et al. 1999, adapted).

Text-fig. 10. Typical elements of the flora of Sjurkum. 1 – Myrica vyvenkensis AKHMETIEV, leaf, × 0.7; 2 – Rhododendron lancifolium AKHMETIEV, leaf, × 0.7; 3, 4 – cf. Vaccinium sp., leaves, × 0.8 and 1; 5 – Salix sp. (ex gr. S. glauca L.), leaf, × 0.7; 6 – Carpinus sp., involucre, × 1 (coll. Geol. Inst. RAS Moscow). in Mid-Latitude Palaeogene Floras Of Eurasia Bound To Volcanic Settings And Palaeoclimatic Events - Experience Obtained From The Far East Of Russia (Sikhote-Alin') And Central Europe (Bohemian Massif)

Text-fig. 10. Typical elements of the flora of Sjurkum. 1 – Myrica vyvenkensis AKHMETIEV, leaf, × 0.7; 2 – Rhododendron lancifolium AKHMETIEV, leaf, × 0.7; 3, 4 – cf. Vaccinium sp., leaves, × 0.8 and 1; 5 – Salix sp. (ex gr. S. glauca L.), leaf, × 0.7; 6 – Carpinus sp., involucre, × 1 (coll. Geol. Inst. RAS Moscow).