cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5517/ccp6tym
title: CCDC 632181: Experimental Crystal Structure Determination

description: Related Article: G.Mansouri, A.R.Rezvani, H.Hadadzadeh, H.R.Khavasi, H.Saravani|2007|J.Organomet.Chem.|692|3810|doi:10.1016/j.jorganchem.2007.05.043
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpk007
title: CCDC 641948: Experimental Crystal Structure Determination

description: Related Article: M.M.Kubicki, P.Schwarz, W.Meier, J.Wachter, M.Zabel|2007|J.Organomet.Chem.|692|3931|doi:10.1016/j.jorganchem.2007.05.047
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/d71-svg-hp7
title: Crataegus kansuensis E. H. Wilson

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/y4k-bha-vw4
title: Galanthus nivalis L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/z70-e6w-nfw
title: Macleania smithiana Luteyn

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpbm6t
title: CCDC 635816: Experimental Crystal Structure Determination

description: Related Article: A.Malinowska, A.Kochel, T.Szymanska-Buzar|2007|J.Organomet.Chem.|692|3994|doi:10.1016/j.jorganchem.2007.06.013
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpkxfk
title: CCDC 642829: Experimental Crystal Structure Determination

description: Related Article: Chao-Yu Wang, Yi-Hong Liu, Shei-Ming Peng, Jwu-Ting Chen, Shiuh-Tzung Liu|2007|J.Organomet.Chem.|692|3976|doi:10.1016/j.jorganchem.2007.06.007
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/eml-4nn-1js
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/gef-gnb-8dg
title: Citrus aurantium L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/k43-2vy-ra2
title: Cochlearia aucheri Boiss.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccnq8yk
title: CCDC 617239: Experimental Crystal Structure Determination

description: Related Article: A.J.Deeming, C.S.Forth, G.Hogarth|2007|J.Organomet.Chem.|692|4000|doi:10.1016/j.jorganchem.2007.05.044
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccprg62
title: CCDC 648154: Experimental Crystal Structure Determination

description: Related Article: V.Vijaikanth, J.-F.Capon, F.Gloaguen, F.Y.Petillon, P.Schollhammer, J.Talarmin|2007|J.Organomet.Chem.|692|4177|doi:10.1016/j.jorganchem.2007.06.042
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/bb8-xe7-t21
title: Hieracium tephrosoma subsp. pseudoglandulosodentatum Rech. f. & Zahn

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/bx6-bxw-d8m
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5281/zenodo.17373117
title: Senotoxins target senescence via lipid binding specificity, ion imbalance and lipidome remodelling

description: OVERVIEW

This dataset contains molecular dynamics (MD) simulation data supporting Figure 10 of the manuscript. The simulations investigate the membrane-docking helix interactions of the StnIG (TVS1G) octameric pore-forming toxin with three different membrane systems:



Proliferating - Symmetric membrane with proliferating cell lipid composition

Senescent - Symmetric membrane with senescent cell lipid composition

Asymmetric - Asymmetric membrane with PE/PS restricted to inner leaflet




SIMULATION DETAILS

System Information:



Protein: StnIG octamer based on FraC crystal structure (PDB: 4TSY)

Replicates: n = 5 independent simulations per system (R1-R5)

Duration: 500 ns per replicate

Total sampling: 2.5 μs per system (7.5 μs total)

Force field: CHARMM36m

Temperature: 303.15 K

Ion concentration: 150 mM KCl

MD engine: GROMACS 2022.4


Key Residues Analyzed: GLN130, TYR133, GLU134, TYR137, TYR138 (α2 helix membrane-docking residues)



DATASET CONTENTS



Trajectories_Last_10ns/ - Last 10 ns trajectory segments used for Figure 10g RMSF analysis. Each system contains trajectory (.xtc), topology (.psf), and structure (.pdb) files.

Analysis_Data/ - Processed contact analysis and RMSF data including all protein-lipid contacts and phosphate RMSF values.

Analysis_Scripts/ - Python scripts to reproduce Figures 10B, 10C, 10E, 10F, and 10G.

CHARMM-GUI_Input_Files/ - Original CHARMM-GUI system setup files for all three membrane systems.


Full documentation including usage examples and detailed file descriptions is provided in the README.md file within the dataset.
DOI: 10.5517/ccpdxfd
title: CCDC 638024: Experimental Crystal Structure Determination

description: Related Article: B.Machura, R.Kruszynski|2007|J.Organomet.Chem.|692|4161|doi:10.1016/j.jorganchem.2007.06.036
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpm98v
title: CCDC 644157: Experimental Crystal Structure Determination

description: Related Article: Yu.A.Min'ko, N.V.Belina, V.V.Sushev, G.K.Fukin, M.P.Bubnov, A.N.Kornev|2007|J.Organomet.Chem.|692|4157|doi:10.1016/j.jorganchem.2007.06.025
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/bxt-xmb-fz1
title: Tortula subulata Hedw.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/dws-0fy-fnj
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/pl6-al0-dvg
title: Coelogyne corniculata Rchb. f.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccq4cbj
title: CCDC 659597: Experimental Crystal Structure Determination

description: Related Article: H.Hanaoka, T.Hino, H.Souda, K.Yanagi, Y.Oda, A.Imai|2007|J.Organomet.Chem.|692|4059|doi:10.1016/j.jorganchem.2007.06.006
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/g7f-nqt-gxc
title: Linaria aeruginea subsp. aeruginea (Gouan) Cav.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/lht-aaa-nkr
title: Crataegus aronia (L.) Bosc

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5281/zenodo.17373116
title: Senotoxins target senescence via lipid binding specificity, ion imbalance and lipidome remodelling

description: OVERVIEW

This dataset contains molecular dynamics (MD) simulation data supporting Figure 10 of the manuscript. The simulations investigate the membrane-docking helix interactions of the StnIG (TVS1G) octameric pore-forming toxin with three different membrane systems:



Proliferating - Symmetric membrane with proliferating cell lipid composition

Senescent - Symmetric membrane with senescent cell lipid composition

Asymmetric - Asymmetric membrane with PE/PS restricted to inner leaflet




SIMULATION DETAILS

System Information:



Protein: StnIG octamer based on FraC crystal structure (PDB: 4TSY)

Replicates: n = 5 independent simulations per system (R1-R5)

Duration: 500 ns per replicate

Total sampling: 2.5 μs per system (7.5 μs total)

Force field: CHARMM36m

Temperature: 303.15 K

Ion concentration: 150 mM KCl

MD engine: GROMACS 2022.4


Key Residues Analyzed: GLN130, TYR133, GLU134, TYR137, TYR138 (α2 helix membrane-docking residues)



DATASET CONTENTS



Trajectories_Last_10ns/ - Last 10 ns trajectory segments used for Figure 10g RMSF analysis. Each system contains trajectory (.xtc), topology (.psf), and structure (.pdb) files.

Analysis_Data/ - Processed contact analysis and RMSF data including all protein-lipid contacts and phosphate RMSF values.

Analysis_Scripts/ - Python scripts to reproduce Figures 10B, 10C, 10E, 10F, and 10G.

CHARMM-GUI_Input_Files/ - Original CHARMM-GUI system setup files for all three membrane systems.


Full documentation including usage examples and detailed file descriptions is provided in the README.md file within the dataset.
DOI: 10.5517/ccpkqyw
title: CCDC 642659: Experimental Crystal Structure Determination

description: Related Article: A.Semioshkin, E.Nizhnik, I.Godovikov, Z.Starikova, V.Bregadze|2007|J.Organomet.Chem.|692|4020|doi:10.1016/j.jorganchem.2007.06.001
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpngxp
title: CCDC 645293: Experimental Crystal Structure Determination

description: Related Article: H.Caldwell, S.Isseponi, P.S.Pregosin, A.Albinati, S.Rizzato|2007|J.Organomet.Chem.|692|4043|doi:10.1016/j.jorganchem.2007.06.003
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/g45-qn4-hws
title: Crataegus jozana C. K. Schneid.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/km1-3vc-paj
title: Crataegus rhipidophylla Gand.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccnm23f
title: CCDC 614144: Experimental Crystal Structure Determination

description: Related Article: A.Szorcsik, L.Nagy, I.Kokeny, A.Deak, M.Scopelliti, T.Fiore, L.Pellerito|2007|J.Organomet.Chem.|692|3409|doi:10.1016/j.jorganchem.2007.04.003
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccp8g9p
title: CCDC 633742: Experimental Crystal Structure Determination

description: Related Article: R.M.Ceder, C.Garcia, A.Grabulosa, F.Karipcin, G.Muller, M.Rocamora, M.Font-Bardia, X.Solans|2007|J.Organomet.Chem.|692|4005|doi:10.1016/j.jorganchem.2007.02.020
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/8e4-dj7-m1e
title: Tournefortiopsis crispiflora subsp. discolor (Rusby) A. C. Berger & C. M. Taylor

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/vsd-x05-9zx
title: Tortula subulata Hedw.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/zda-8bx-xmz
title: Crataegus linnaeana Pojark.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpbqd3
title: CCDC 635915: Experimental Crystal Structure Determination

description: Related Article: A.Scrivanti, F.Benetollo, A.Venzo, M.Bertoldini, V.Beghetto, U.Matteoli|2007|J.Organomet.Chem.|692|3577|doi:10.1016/j.jorganchem.2007.04.021
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpg61c
title: CCDC 639252: Experimental Crystal Structure Determination

description: Related Article: R.E.White, T.P.Hanusa, B.E.Kucera|2007|J.Organomet.Chem.|692|3479|doi:10.1016/j.jorganchem.2007.04.016
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/td8-5zs-4fx
title: Digitalis parviflora Jacq.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/y9p-3qm-4j7
title: Zonaria isselii Picc. & Grunow

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccphjnb
title: CCDC 640542: Experimental Crystal Structure Determination

description: Related Article: J.A.Cabeza, I.del Rio, P.Garcia-Alvarez, D.Miguel|2007|J.Organomet.Chem.|692|3583|doi:10.1016/j.jorganchem.2007.04.023
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.30312.52488
title: R Code: Ration Formulation using Linear Optimization (R Mosek) - Dr. VL Daley 2019
DOI: 10.3535/90w-sj2-87s
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/jg5-083-plk
title: Digitalis parviflora Jacq.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpfsb6
title: CCDC 638858: Experimental Crystal Structure Determination

description: Related Article: P.Ovejero, M.J.Mayoral, M.Cano, J.A.Campo, J.V.Heras, E.Pinilla, M.R.Torres|2007|J.Organomet.Chem.|692|4093|doi:10.1016/j.jorganchem.2007.06.015
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccpfsc7
title: CCDC 638859: Experimental Crystal Structure Determination

description: Related Article: P.Ovejero, M.J.Mayoral, M.Cano, J.A.Campo, J.V.Heras, E.Pinilla, M.R.Torres|2007|J.Organomet.Chem.|692|4093|doi:10.1016/j.jorganchem.2007.06.015
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/fzb-79f-ryq
title: Crataegus aronia (L.) Bosc

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/l7z-a0z-a5b
title: Crataegus aronia (L.) Bosc

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/myd-5gk-jat
title: Tortula subulata Hedw.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccpfsd8
title: CCDC 638860: Experimental Crystal Structure Determination

description: Related Article: P.Ovejero, M.J.Mayoral, M.Cano, J.A.Campo, J.V.Heras, E.Pinilla, M.R.Torres|2007|J.Organomet.Chem.|692|4093|doi:10.1016/j.jorganchem.2007.06.015
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccq4nk1
title: CCDC 659883: Experimental Crystal Structure Determination

description: Related Article: S.P.Green, C.Jones, D.P.Mills, A.Stasch|2007|Organometallics|26|3424|doi:10.1021/om700345m
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/az7-gbl-6r8
title: Allium ochroleucum Waldst. & Kit.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/he5-2q8-23g
title: Macleania smithiana Luteyn

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccq4nl2
title: CCDC 659884: Experimental Crystal Structure Determination

description: Related Article: S.P.Green, C.Jones, D.P.Mills, A.Stasch|2007|Organometallics|26|3424|doi:10.1021/om700345m
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccq4nm3
title: CCDC 659885: Experimental Crystal Structure Determination

description: Related Article: S.P.Green, C.Jones, D.P.Mills, A.Stasch|2007|Organometallics|26|3424|doi:10.1021/om700345m
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/gec-868-vab
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/v8n-y1p-4vq
title: Crataegus linnaeana Pojark.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccq4nn4
title: CCDC 659886: Experimental Crystal Structure Determination

description: Related Article: S.P.Green, C.Jones, D.P.Mills, A.Stasch|2007|Organometallics|26|3424|doi:10.1021/om700345m
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.13140/rg.2.2.11097.36964
title: Identification and Analysis of Galaxies with Signatures of Extraplanar Gas in the MaNGA Survey
DOI: 10.3535/b3a-hy6-7w1
title: Crataegus laevigata (Poir.) DC.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/nd7-3pn-s60
title: Crataegus azarolus subsp. azarolus L.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.5517/ccq4np5
title: CCDC 659887: Experimental Crystal Structure Determination

description: Related Article: S.P.Green, C.Jones, D.P.Mills, A.Stasch|2007|Organometallics|26|3424|doi:10.1021/om700345m
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.3535/0hn-s47-s2s
title: Polygala major Jacq.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.
DOI: 10.3535/f1m-267-m6v
title: Allium ochroleucum Waldst. & Kit.

description: Digital Specimen for the physical specimen hosted at Natural History Museum Vienna.