cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7881097
title: MBC and ECBL Libraries: outstanding tools for drug discovery

description: <strong>UPDATE</strong>. New in this revision: python scripts to process DBs and calculate the percentage of molecules which pass the Veber and Ghose filters. Two new DBs were also added and considered for the analysis. Data and scripts to reproduce all the graphics reported in the Manuscript entitled: "MBC and ECBL Libraries: outstanding tools for drug discovery". <strong>List of analyzed DBs:</strong> MBC2016 (Total entries: 1,096 cmpds; 7.39% excluded from properties analysis - QikProp failure). MBC2022 (Total entries: 2,577 cmpds; 3.14% excluded from properties analysis - QikProp failure). ECBL (Total entries: 101,021 cmpds; 0.20% excluded from properties analysis - QikProp failure). ChEMBL v.31 (Total entries 1,908,325 cmpds; 2.97% excluded from properties analysis - QikProp failure). DrugBank v.5.0 (Total entries 10,981 cmpds; 4.13% excluded from properties analysis - QikProp failure). ZINC20 (Total entries 10,723,360 cmpds; 0.61% excluded from properties analysis - QikProp failure). NuBBE (Total entries 2,223 cmpds) - <strong>NEW</strong> Approved drugs (Total entries: 3,140 cmpds) - <strong>NEW</strong> <strong>Files:</strong> <em>QikProp_properties.docx</em>: doc file containing the full list of QikProp properties calculated for each analyzed DB. <em>DATA_comparison.xlsx</em>: excel file containing data used to reproduce plots in <strong>Figure 4</strong> of the MS. <em>Murcko_scaffold_percentages</em>: distribution (%) of the first 50 most populated Murcko scaffolds for MBC2016, MBC2022 and ECBL. <em>Murcko_scaffolds_comparison</em>: distribution (count) of the first 94 common Murcko scaffolds for MBC2016, MBC2022 and ECBL. QikProp properties for all the analyzed DBs (8 files; CSV format). SMILES codes for all the analyzed DBs (8 files; SMI format). <em>joinplots.py</em>: python script to generate the 2D plots in <strong>Figure 2</strong> of the MS. <em>fingerprint_similarity.py</em>: python script to run and generate the Tanimoto similarity plots in <strong>Figure 3</strong> of the MS. <em>calc_kde.py</em>: python script to run kernel density analysis reported in <strong>Figure 5 </strong>of the MS. <em>Veber_filter.py: python script to generate </em>data presented in <strong>Table 1 </strong>of the MS. <strong>(NEW)</strong> <em>Ghose filter.py: python script to generate </em>data presented in <strong>Table 1 </strong>of the MS. <strong>(NEW)</strong>
DOI: 10.17864/1947.000484
title: Dataset supporting the article 'Evaluation of empirical-dispersion-corrected, range-separated, double hybrid, and Meta-GGA density functional theory methods for interactions important in catecholic ligand/protein binding'

description: Complexation energies and structure descriptors for complexes of four catechols (catechol, dinitrocatechol, dopamine and DOPAC) with eight counter-molecules: Mg(EDA)2(H2O)^2+, Zn(EDA)2(H2O)^2+, methyl amine, methanol, benzene, indole, isobutane and methane thiol. Each complex is optimized and the complexation energy calculated with sixteen DFT methods (M062X, M06, MN15, MN12SX, SVWN, BLYP, B3LYP, CAM-B3LYP, B2PLYP, B97XD, wB97D, wPHEhPHE, LC-wHPBE, tHCTHhyb, LC-wPHE-D, and BMK) as well as HF, MP2 and CCSD, each with the cc-pVDZ basis set. All calculations performed using Gaussian 16. Raw data for manuscript 'Evaluation of empirical-dispersion-corrected, range-separated, double hybrid, and Meta-GGA density functional theory methods for interactions important in catecholic ligand/protein binding', by Harle and Cafiero.
DOI: 10.5281/zenodo.7709465
title: XPS and XANES spectra for Li doped MoS2 few-layer films

description: <strong>Description</strong> Dataset for x-ray photoelectron (XPS) and absorption near-edge structure (XANES) spectra of Li doped MoS<sub>2</sub> nanofilms grown by one-zone sulfurization on c-plane sapphire substrate. <strong>XPS Data formats</strong> The same XPS datasets are saved into two different data formats. VAMAS (ASCII ISO 14976) Plain text column files: Double-column files (dat) and corresponding metadata files (txt) <strong>XANES Data formats</strong> XDI (XAS Data Interchange): raw XANES data PRJ (Athena Project File): normalized XANES data processed in ATHENA free software package.
description: Data were acquired at BACH beamline, Elettra synchrotron facility. Access was provided by IOM-CNR in Trieste (Italy) within the framework of the NFFA-Europe Pilot Transnational Access Activity, proposal ID101.
DOI: 10.5281/zenodo.7709466
title: XPS and XANES spectra for Li doped MoS2 few-layer films

description: <strong>Description</strong> Dataset for x-ray photoelectron (XPS) and absorption near-edge structure (XANES) spectra of Li doped MoS<sub>2</sub> nanofilms grown by one-zone sulfurization on c-plane sapphire substrate. <strong>XPS Data formats</strong> The same XPS datasets are saved into two different data formats. VAMAS (ASCII ISO 14976) Plain text column files: Double-column files (dat) and corresponding metadata files (txt) <strong>XANES Data formats</strong> XDI (XAS Data Interchange): raw XANES data PRJ (Athena Project File): normalized XANES data processed in ATHENA free software package.
description: Data were acquired at BACH beamline, Elettra synchrotron facility. Access was provided by IOM-CNR in Trieste (Italy) within the framework of the NFFA-Europe Pilot Transnational Access Activity, proposal ID101.
DOI: 10.5281/zenodo.7844566
title: Liquid-hexatic transition for soft disks

description: This dataset provides data files for the equation of state and equilibrium configurations of soft-disk models used in "Liquid-hexatic transition for soft disks" Physical Review E <strong>108</strong>, 024103 (2023) by Yoshihiko Nishikawa, Werner Krauth, and A. C. Maggs. The following directories are included. - equation_of_state: This directory includes two CSV files for the equation of state plotted in the paper. <br> - equilibrium_configuration: This directory includes equilibrium configurations of N = 1024^2 particles of the models studied in the paper. An equilibrium configuration is stored in start.h5, a HDF5 file, together with the parameters for the simulation. By using the CUDA code available at https://github.com/jellyfysh/SoftDisks, you can perform an equilibrium simulation starting from the configuration stored in start.h5.
DOI: 10.5281/zenodo.7844567
title: Liquid-hexatic transition for soft disks

description: This dataset provides data files for the equation of state and equilibrium configurations of soft-disk models used in "Liquid-hexatic transition for soft disks" Physical Review E <strong>108</strong>, 024103 (2023) by Yoshihiko Nishikawa, Werner Krauth, and A. C. Maggs. The following directories are included. - equation_of_state: This directory includes two CSV files for the equation of state plotted in the paper. <br> - equilibrium_configuration: This directory includes equilibrium configurations of N = 1024^2 particles of the models studied in the paper. An equilibrium configuration is stored in start.h5, a HDF5 file, together with the parameters for the simulation. By using the CUDA code available at https://github.com/jellyfysh/SoftDisks, you can perform an equilibrium simulation starting from the configuration stored in start.h5.
DOI: 10.18120/21bz-ef95
title: Differential Cortical Network Engagement During States of Un/Consciousness in Humans
DOI: 10.5281/zenodo.8210145
title: CRISPR-based engineering of RNA viruses

description: CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a new recombinant RNA technology with immediate applications for the facile engineering of RNA viruses. This dataset contains code for analyzing sequencing data and generating figures in the manuscript.
description: Link to the preprint https://doi.org/10.1101/2023.05.19.541219
DOI: 10.5281/zenodo.8210144
title: CRISPR-based engineering of RNA viruses

description: CRISPR RNA-guided endonucleases have enabled precise editing of DNA. However, options for editing RNA remain limited. Here, we combine sequence-specific RNA cleavage by CRISPR ribonucleases with programmable RNA repair to make precise deletions and insertions in RNA. This work establishes a new recombinant RNA technology with immediate applications for the facile engineering of RNA viruses. This dataset contains code for analyzing sequencing data and generating figures in the manuscript.
description: Link to the preprint https://doi.org/10.1101/2023.05.19.541219
DOI: 10.5519/qd.hjs80z8x
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (2295 records)
DOI: 10.17909/a5em-ga92
title: STIS FUV datasets from "Cycle of Alpha Centauri..."

description: STIS E140M and E140H spectra of Alpha Cen A+B, Procyon, and two reference red giants: Alpha Boo and Gamma Cru.
DOI: 10.6084/m9.figshare.23834670
title: filtered.zip

description: The zip archive contains <code>cellranger count</code> filtered output for 11 BLCA samples from Zhaohui Chen <i>et al.</i> paper published in Nature Communications 11, Article number: 5077 (2020). The cohort consisted of eight primary bladder tumor tissues (2 low-grade bladder urothelial tumors, six high-grade bladder urothelial tumors) along with 3 adjacent normal mucosae. In SRA datasets are under BioProject PRJNA662018 and SRA-explorer can be used to download the data.
DOI: 10.6084/m9.figshare.23837601
title: <b>699Maqam_dataset</b>

description: Dataset number 1 of Maqam Classification of Quranic Recitations using Deep Learning article, By Faisal Omari.699 audio samples of Quranic recitations, including 4 reciteres and 8 maqams.
DOI: 10.15472/hxxkei
title: Listado de las especies de Anamorphidae (Coleoptera: Coccinelloidea) de Colombia

description: Este recurso presenta el listado de las especies de la familia Anamorphidae (Coleoptera: Coccinelloidea) con ocurrencia conocida para el territorio colombiano. Se lista un género con tres especies. Una de las especies se considera endémica del país. La información ha sido recopilada a partir de los principales catálogos que tratan el grupo y en literatura reciente. Se incluyen las referencias de todas las descripciones originales y de los trabajos de revisión taxonómica.
DOI: 10.5517/ccdc.csd.cc2c01t8
title: CCDC 2174799: Experimental Crystal Structure Determination

description: Related Article: Haiyang Shu, YuLu Liu, Liang Chen, Zhiqiang Cheng, Xin Wang, Xiaofu Wu, Hui Tong, Lixiang Wang|2023|J.Mater.Chem.C|11|10398|doi:10.1039/D3TC01124K
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/ccdc.csd.cc2c059w
title: CCDC 2174907: Experimental Crystal Structure Determination

description: Related Article: Haiyang Shu, YuLu Liu, Liang Chen, Zhiqiang Cheng, Xin Wang, Xiaofu Wu, Hui Tong, Lixiang Wang|2023|J.Mater.Chem.C|11|10398|doi:10.1039/D3TC01124K
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/ccdc.csd.cc2chcr0
title: CCDC 2189522: Experimental Crystal Structure Determination

description: Related Article: Yaru Song, Jie Dong, Jiangyan Yuan, Xinyu Zhang, Guoling Wu, Enbing Zhang, Guangyuan Feng, Lingli Wu, Shengbin Lei, Wenping Hu|2023|J.Mater.Chem.C|11|10230|doi:10.1039/D3TC01475D
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/ccdc.csd.cc2chcs1
title: CCDC 2189523: Experimental Crystal Structure Determination

description: Related Article: Yaru Song, Jie Dong, Jiangyan Yuan, Xinyu Zhang, Guoling Wu, Enbing Zhang, Guangyuan Feng, Lingli Wu, Shengbin Lei, Wenping Hu|2023|J.Mater.Chem.C|11|10230|doi:10.1039/D3TC01475D
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/ccdc.csd.cc2f9ztk
title: CCDC 2243929: Experimental Crystal Structure Determination

description: Related Article: Rahul Ghosh, Surajit Panda, Ashutosh MahaKhuda, Ratnakar Saha, Bidraha Bagh|2023|RSC Sustainability|1|1223|doi:10.1039/D3SU00114H
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: 10.26030/hdr2-2940
title: Evaluating the effect of spaceflight on the host-pathogen interaction between human intestinal epithelial cells and Salmonella Typhimurium

description: Spaceflight uniquely alters the physiology of both human cells and microbial pathogens, stimulating cellular and molecular changes directly relevant to infectious disease. However, the influence of this environment on host-pathogen interactions remains poorly understood. Here we report our results from the STL-IMMUNE study flown aboard Space Shuttle mission STS-131, which investigated multi-omic responses (transcriptomic, proteomic) of human intestinal epithelial cells to infection with Salmonella Typhimurium when both host and pathogen were simultaneously exposed to spaceflight. To our knowledge, this was the first in-flight infection and dual RNA-seq analysis using human cells. Additionally, it is the first global transcriptomic and proteomic profiling of human intestinal epithelial cultures during spaceflight (either infected or uninfected).
DOI: 10.25345/c5m61c09f
title: MassIVE MSV000092587 - QC mix; quality control mix of 6 compounds trial2
title: This is another test QC mix to learn about molecular networking.
DOI: 10.21227/e2gy-vw70
title: InGaN Quantum Well PL emission in Tamm cavity

description: In this work we present a study of micro-photoluminescence (PL) emission from a novel InGaN quantum well (QW) emitting structure with integrated micro-cavity, which can be used for VCSEL applications. The micro-cavity exhibiting Tamm plasmon optical states is formed by porous GaN distributed Bragg reflector (DBR) bottom mirror and top plasmonic silver metal mirror. Results of PL, Fourier imaging spectroscopy and finite-difference time-domain simulations are presented and discussed. An estimated 8.5 times enhancement of QW PL intensity at around 480-500 nm and a red-shift of QW peak emission is attributed to the Tamm plasmon resonance in the cavity at around 514 nm.
DOI: 10.6084/m9.figshare.23838153
title: <b>Effects of tefluthrin and guadipyr on midgut bacteria of adult </b><i><b>Apis mellifera</b></i>

description: This study aims to analyze whether heptafluthrin and pentylpyrazine affect the gut microbes’ structure and metabolism of adult Apis mellifera ligustica, enrich the mechanism of insecticide action, and have practical significance for bee protection. [Methods] In this study, <i>Apis mellifera </i>were fed with 1) control sugar water, 2) tefluthrin sugar water or 3) guadipyr sugar water. After 10 days, the genomic DNA of gut bacteria were extracted. We use high-throughput sequencing to determine whether tefluthrin and guadipyr treated would influence the diversity and abundance of gut bacteria. 【Results】There were 20 species of gut bacteria in <i>A. mellifera</i>, which belonged to 5 phyla, 6 classes, 11 orders, 11 families and 15 genera. The dominant phyla of the gut bacteria are Proteobacteria and Bacteroides. Compared with the control group, the structure of the bacteria flora in the deltamethrin-treated group and tefluthrin-treated group changed. At the phylum level, the relative abundance of Cyanobacteria decreased significantly (<i>P</i> &lt; 0.05). At the genus level, the relative abundance of the <i>Bartonella</i> and <i>Serratia</i> in the tefluthrin group increased significantly (<i>P</i> &lt; 0.05). The relative abundance of <i>Gilliamella</i> and <i>Frischella</i> increased significantly (<i>P</i> &lt; 0.05) in the guadipyr-treated group, and the relative abundance of <i>norank_o_Chloroplast </i>and <i>Enterobacteria</i> decreased significantly (<i>P</i> &lt; 0.05). The prediction of COG function showed that the metabolism of gut microbes changed after tefluthrin treatment, but there was no change after guadipyr treatment.【Conclusion】Exposure of bees to tefluthrin and guadipyr can change the structure and function of gut bacteria of <i>A. mellifera</i>. The effect of tefluthrin on gut bacteria of <i>A. mellifera</i> is greater than that of guadipyr.
DOI: 10.6084/m9.figshare.23838153.v1
title: <b>Effects of tefluthrin and guadipyr on midgut bacteria of adult </b><i><b>Apis mellifera</b></i>

description: This study aims to analyze whether heptafluthrin and pentylpyrazine affect the gut microbes’ structure and metabolism of adult Apis mellifera ligustica, enrich the mechanism of insecticide action, and have practical significance for bee protection. [Methods] In this study, <i>Apis mellifera </i>were fed with 1) control sugar water, 2) tefluthrin sugar water or 3) guadipyr sugar water. After 10 days, the genomic DNA of gut bacteria were extracted. We use high-throughput sequencing to determine whether tefluthrin and guadipyr treated would influence the diversity and abundance of gut bacteria. 【Results】There were 20 species of gut bacteria in <i>A. mellifera</i>, which belonged to 5 phyla, 6 classes, 11 orders, 11 families and 15 genera. The dominant phyla of the gut bacteria are Proteobacteria and Bacteroides. Compared with the control group, the structure of the bacteria flora in the deltamethrin-treated group and tefluthrin-treated group changed. At the phylum level, the relative abundance of Cyanobacteria decreased significantly (<i>P</i> &lt; 0.05). At the genus level, the relative abundance of the <i>Bartonella</i> and <i>Serratia</i> in the tefluthrin group increased significantly (<i>P</i> &lt; 0.05). The relative abundance of <i>Gilliamella</i> and <i>Frischella</i> increased significantly (<i>P</i> &lt; 0.05) in the guadipyr-treated group, and the relative abundance of <i>norank_o_Chloroplast </i>and <i>Enterobacteria</i> decreased significantly (<i>P</i> &lt; 0.05). The prediction of COG function showed that the metabolism of gut microbes changed after tefluthrin treatment, but there was no change after guadipyr treatment.【Conclusion】Exposure of bees to tefluthrin and guadipyr can change the structure and function of gut bacteria of <i>A. mellifera</i>. The effect of tefluthrin on gut bacteria of <i>A. mellifera</i> is greater than that of guadipyr.
DOI: 10.5517/ccdc.csd.cc2f6cyz
title: CCDC 2240461: Experimental Crystal Structure Determination

description: Related Article: Alexander A. Fadeev, Martin Kotora|2023|Org.Biomol.Chem.|21|6174|doi:10.1039/D3OB00636K
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/ccdc.csd.cc2f6cz0
title: CCDC 2240462: Experimental Crystal Structure Determination

description: Related Article: Alexander A. Fadeev, Martin Kotora|2023|Org.Biomol.Chem.|21|6174|doi:10.1039/D3OB00636K
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: 10.5281/zenodo.6394810
title: LMW Binding Affinity Screen for TBXT

description: Uploaded excel spreadsheets contain the raw data for a SPR campaign targeting TBXT. The data was collected by HDBioscience and is made public by UNC-SGC, The Chordoma Foundation, The Mark Foundation for Cancer Research. If prompted "HDB" is the password for any Excel file. The "ID with Smiles" spreadsheet contains the corresponding SMILES for all the compounds screened. ----- More SPR data has been uploaded from 20230103. This dataset has a tab with the SMILES.
DOI: 10.5281/zenodo.6394811
title: LMW Binding Affinity Screen for TBXT

description: Uploaded excel spreadsheets contain the raw data for a SPR campaign targeting TBXT. The data was collected by HDBioscience and is made public by UNC-SGC, The Chordoma Foundation, The Mark Foundation for Cancer Research. If prompted "HDB" is the password for any Excel file. The "ID with Smiles" spreadsheet contains the corresponding SMILES for all the compounds screened.
DOI: 10.5281/zenodo.8212611
title: LMW Binding Affinity Screen for TBXT

description: Uploaded excel spreadsheets contain the raw data for a SPR campaign targeting TBXT. The data was collected by HDBioscience and is made public by UNC-SGC, The Chordoma Foundation, The Mark Foundation for Cancer Research. If prompted "HDB" is the password for any Excel file. The "ID with Smiles" spreadsheet contains the corresponding SMILES for all the compounds screened. ----- More SPR data has been uploaded from 20230103. This dataset has a tab with the SMILES.
DOI: 10.25345/c5gf0n659
title: MassIVE MSV000092588 - Proteomic Analysis of Fbp1F/F and Fbp1 in mouse livers
title: Comparison of liver tissue from mice deficient of Fbp1 reveal Fbp1 and NRF2 as important protein regulators.
DOI: 10.5519/qd.h9il1ol3
title: Query on the Natural History Museum Data Portal (data.nhm.ac.uk) (504 records)
DOI: 10.5281/zenodo.8212215
title: COVID Moonshot X-ray Data

description: X-ray crystal structures determined at the XChem facility at Diamond Light Source as part of the COVID Moonshot Consortium
DOI: 10.5281/zenodo.8212214
title: COVID Moonshot X-ray Data

description: X-ray crystal structures determined at the XChem facility at Diamond Light Source as part of the COVID Moonshot Consortium
DOI: 10.6084/m9.figshare.23839929
title: 20230804_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6084/m9.figshare.23839929.v1
title: 20230804_starrydata2

description: All data on Starrydata2, a database of experimental properties in the field of inorganic materials
DOI: 10.6073/pasta/37cf0ded54b059cd46eb25ee529af511
title: Mycorrhizal Fungi of Native Red Pine Stands in the Forests of the Huron Mountains (1996-2015).

description: This data includes mycorrhizal fungi population data in Michigan’s Huron Mountains from 1996-2015 collected by Dana Ritcher. Seven stands consisting of primarily pine forests were surveyed for two separate sampling periods annually during the study period.
DOI: 10.6084/m9.figshare.23692005
title: Supplementary information file.docx

description: Supplementary information file
DOI: 10.6084/m9.figshare.23692005.v1
title: Supplementary information file.docx

description: Supplementary information file