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.
846
datasets available to search
ShareScore release 0.9.0
Dataset results
846 results for “homologs”
Homologous membrane protein structures (HOMEP) version 1
<p><strong>Table 1</strong> = List of membrane protein structures in the <strong>HOMEP</strong> data set (version 1).<br> From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 1)<br> <a href="https://www.ncbi.nlm.nih.gov/pubmed/16648166">https://www.ncbi.nlm.nih.gov/pubmed/16648166</a></p> <p>Contains the following columns:<br> PDB-Code Protein-Name Source Res-(Å) Length (Num-TM) Number-of-TM-domains Family</p> <p><strong>Table 2</strong> = List of pairs of membrane protein structures in the <strong>HOMEP</strong> data set (version 1).<br> From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 2)</p> <p>Contains the following columns:<br> Model Family Query Template ID(%) RMS(Å) GDT_TS(%) TM-ID(%) TM-RMS(Å) TM GDT_TS(%)</p> <p><strong>Table 3 </strong>= Manually-defined transmembrane regions in the <strong>HOMEP</strong> data set (version 1), listed for each family by transmembrane segment number. From Forrest, Tang & Honig 2006 Biophysical Journal (Supplementary Table 3).</p> <p>Contains the columns defined as follows:<br> Protein chain identifier, start (-s) and end (-e) residues for each PDB structure in the family</p>
Full-length and split homologs of human proteins in the gut microbiome
<p>These files were generated as part of the manuscript "Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome" (submitted).</p> <p>The .tar file contains .ipc files that are tables of full-length (full_humcover3.ipc) and split homologs (part_humcover3.ipc) of human proteins in the gut microbiome, organized by alignment coverage threshold. For example, the directory `HumanUPR_0.67_src_20000_70` contains results obtained at a 67% alignment coverage threshold for the bacterial protein, and 70% for the human protein. Note that our pipeline collapses full-length alignments to the same UHGP-90 protein family into a single entry per species, with the number of genomes reported in the column nGenomes. Split homologs are not collapsed because genomic context is used to define them, and this context may differ across individual genomes.</p> <p>These files are in Arrow <a href="https://arrow.apache.org/docs/python/ipc.html#ipc">IPC</a> format, which provides compression and fast I/O for large tables. We recommend reading them using <a href="https://pola.rs/">pola.rs</a> or the <a href="https://arrow.apache.org/docs/r/">R Arrow</a> package. In particular, because the full-length homolog table is large, you may wish to work with it without loading it into memory, which can be accomplished using <a href="https://docs.pola.rs/api/python/dev/reference/api/polars.scan_ipc.html">scan_ipc</a> in pola.rs or <a href="https://arrow.apache.org/docs/r/reference/open_dataset.html">open_dataset</a> in R Arrow.</p> <p>We also provide gzipped .csv format datasets of full-length (pgkb_FH_drugs.csv.gz) and split (pgkb_SH_drugs.csv.gz) homologs, at the default 67% alignment coverage threshold for bacterial and 70% for human proteins, organized by their <a href="https://www.pharmgkb.org/">PharmGKB</a> annotations. For each drug annotated in PharmGKB as being metabolized by a human protein with full-length or split homologs, we provide the human protein(s) responsible, its xenobiotic enzyme class, the bacterial protein homolog(s), length and percent identity of the alignment, and either the specific genome (g, split homologs only) or the number of genomes (nGenomes, full homologs only). Xenobiotic enzyme classes are defined as in Figure 4 of the manuscript, with the additional classes "nucl" (nucleobase-containing metabolic proteins not annotated to any other class), "redox" (oxidoreductases not annotated to any other class), and "other" (all remaining proteins).</p>
Probing center vortices and deconfinement in SU(2) lattice gauge theory with persistent homology — data release
<p>This release contains all data used to prepare the publication <a href="https://arxiv.org/abs/2207.13392">Probing center vortices and deconfinement in SU(2) lattice gauge theory with persistent homology</a>.</p> <p>Included are:</p> <ul> <li>The raw log output from the simulations and computed persistence images for the analysis in Section IV.B of the <a href="https://arxiv.org/abs/2207.13392">paper</a> in 'raw_data.zip'.</li> <li>The values of the action and Polyakov loop from the above logs, along with the persistence images restructured into netCDF4 format for convenience, in the files 'Nt=*_Ns=*_pis_actions_polyakovs.nc'.</li> <li>The values of the observable m_2 (as defined in the <a href="https://arxiv.org/abs/2207.13392">paper</a>) for configurations for the twisted boundary conditions analysis in netCDF4 format in 'Nt=4_Ns=12_16_20_m2.nc'.</li> <li>The example persistence diagrams used in the <a href="https://arxiv.org/abs/2207.13392">paper</a> in netCDF4 format in 'Nt=4_Ns=12_example_pds.nc'.</li> </ul>
Homologous membrane protein structures (HOMEP) dataset version v2
<p><strong>Protein structures from the dataset of Homologous MEmbrane Protein structures (HOMEP)</strong> version v2 created in 2010, published in 2013. A more automated version of HOMEP v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a><br> </p> <p><strong>Table 1</strong> = List of protein databank structure entries<br> From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 1, with the following entries:<br> Family grouping, Protein databank identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>Table 2</strong> = List of pairs of structures<br> From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary Table 2, with the following entries:<br> Family grouping, PDB code for first structure, Chain ID from PDB1, PDB for second structure, Chain ID from PDB2, protein structural difference (PSD), % sequence identity</p> <p> </p> <p><strong>File S2 HOMEP2 Dataset.tar.gz</strong> = Protein databank format files (PDB) are attached in the Dataset tar zipped file, organized by family. From Stamm et al, PLOS One 2013, <a href="https://www.ncbi.nlm.nih.gov/pubmed/23469223">https://www.ncbi.nlm.nih.gov/pubmed/23469223</a>, Supplementary dataset.</p>
Human Pleckstrin Homology domain Interacting Protein (PHIP); A Target Enabling Package
<p>SGC Oxford has expressed, purified and crystallized the second bromodomain of PHIP as part of the probe programme. Fragment screening and X-ray crystallography identified binders, some of which optimised to uM affinity. However, molecules with probe properties were not obtained. Consequently it has been decided to put the information generated into the public domain.</p>
Structural role for DNA ligase IV in promoting the fidelity of non-homologous end joining
<p>This repository contains the original, uncropped .tif files for gel images in Stinson et al., Nature Communications (2023). File names in the repository correspond to figure panels in the published manuscript.</p>
Evolution of Surface Tension and Hansen Parameters of Homologous Series of Imidazolium-Based Ionic Liquids
<p>This is the raw data for the manuscript:</p> <p>Evolution of Surface Tension and Hansen Parameters of Homologous Series of Imidazolium-Based Ionic Liquids</p> <p> </p> <p>All data are sorted according to their appearance in the figures of the main manuscript. All data is stored as .xslx format, the content of the colums can be found in the headlines and is following the nomenclature of the manuscript.</p> <p>doi journal article: <a title="DOI URL" href="https://doi.org/10.1021/acs.langmuir.4c00094">https://doi.org/10.1021/acs.langmuir.4c00094</a></p>
PSSH2 - database of protein sequence-to-structure homologies (including Sars-CoV-2 structures)
<p><strong>Protein sequence and structure data</strong></p> <p>This data set contains data from Uniprot (in the files called protein_sequence, protein_synonyms, protein_names, organism_synonyms) and PDB (in the files called PDB and PDB_chain) as used by the <a href="https://github.com/ODonoghueLab/Aquaria">Aquaria web resource</a> at the time of download (2022-02-08).</p> <p> </p> <p><strong>The PSSH2 data set</strong><br> <br> PSSH2 is a database of protein sequence-to-structure homologies based on HHblits, an alignment method employing iterative comparisons of hidden Markov models (HMMs). To ensure the highest possible final alignment quality for matches in Aquaria using HHblits, we first calculate HMM profiles for each unique PDB sequence (PDB_full) and also for each unique Swiss-Prot sequence. We generated PSSH2 using HHblits to find similarities between HMMs from PDB and HMMs from UniProt sequences.</p> <p> </p> <p><strong>Calculating PSSH2</strong></p> <p>The Swissprot and PDB data was downloaded in November 2021.<br> Generating PSSH2: We used <a href="https://gwdu111.gwdg.de/~compbiol/uniclust/2021_03/UniRef30_2021_03.tar.gz">UniRef30_2021_03</a> (originally called UniRef30_2021_06) from HH-suite, a database of non-redundant UniProt sequence clusters in which the highest pairwise sequence identity between clusters was 30%. The HHblits code and the code for running the calculations was retrieved from git (https://github.com/soedinglab/hh-suite.git and https://github.com/aschafu/PSSH2.git respectively) at the respective time of calculation in the timeframe until December 2021. <br> </p> <p><strong>PDB based sequence-to-structure alignments</strong></p> <p>In addition to the PSSH2 data, new PDB structures were retrieved based on the primary accession of the proteins, by querying for all chains in all PDB entries with exact matches using the sequence cross references records given in PDB. Sequence-to-structure alignments were then created, again based on information provided in each PDB entry. These are contained in the PDBchain data.</p> <p>This data covers sequences and PDB structures in the timeframe until February 2022. </p> <p> </p> <p><strong>Evaluating PSSH2</strong></p> <p>The resulting alignment data was analysed using CATH domain assignments downloaded from /cath/releases/all-releases/v4_2_0/cath-classification-data/ to define correct hits and false hits: </p> <ul> <li>The set of query sequences is defined by the CATH non-redundant S40_overlap_60 dataset (ftp://orengoftp.biochem.ucl.ac.uk/cath/releases/all-releases/v4_2_0/non-redundant-data-sets/)</li> <li>The set of all expected hits are all pdb structures containing a domain with the same CATH code if contained in the set of processed sequences (-> all) or only if also contained in the set of non redundant sequences (-> nr40).</li> <li>The set of true positives is defined by sharing the same CATH code up to the level of homology ("CATH") or up to the level of topology ("CAT").</li> </ul> <p>The data was evaluated with respect to false discovery rate (FDR) and recall (true positive rate TPR) by cumulatively considering all hits with an E-value below the threshold ("C") or in bins with an E-value between the threshold and one tenth of the threshold ("B"). This evaluation was carried out for the data obtained in November 2021 (202111) as well as previous data from October 2020 (202010), February 2020 (202002) and September 2017 (201709). The results are collected in <a href="https://zenodo.org/api/files/445add84-fcf1-4dfe-b8a1-63dc55f378ee/PSSH%20CATH%20validation.csv?versionId=a5df7473-6efd-442b-b422-3944e9452003">PSSH CATH validation.csv</a>. </p> <p> </p> <p><strong>Known errors</strong></p> <p>Due to processing error, the profile of pdb structure 5fia A / B (sequence md5 052667679fc644184f40063c7602c9e1) is incomplete in the pdb_full hhblits database which led to further errors in generating sequence based alignments for sequences for 1vtm P (sequence md5 c844aff103449363cb8489c78c58ebf1) and 434t A / B (sequence md5 d67aa1c3a36492c719cb48b5e7ecc624).<br> <br> </p>
Homologous membrane protein structures (HOMEP) version 3
<p><strong>Homologous membrane protein structures (HOMEP)</strong> version 3 (created 2013)<br> An updated version of v2 <a href="https://doi.org/10.5281/zenodo.2646539">10.5281/zenodo.2646539</a> and v1: <a href="https://doi.org/10.5281/zenodo.2646534">10.5281/zenodo.2646534</a></p> <p><strong>Table 1</strong> = Alpha-helical membrane protein structures in the HOMEP3 data set (2013), listed by family<br> From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 1):<a href="http://https://www.ncbi.nlm.nih.gov/pubmed/26178143"> https://www.ncbi.nlm.nih.gov/pubmed/26178143</a> </p> <p>Contains the following columns:<br> Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>Table 2</strong> = Beta-barrel membrane protein structures in the HOMEP3 data set (2013), listed by family<br> From Stamm M, Forrest LR, Proteins 2015 (Supplementary Table 2)</p> <p>Contains the following columns:<br> Protein family, Protein databank identifier, Chain identifier, Name, Source organism, Resolution (Å)</p> <p> </p> <p><strong>HOMEP3_pairs_alpha.txt</strong><br> List of all pairs of protein structure chains of alpha-helical proteins</p> <p> </p> <p><strong>HOMEP3_pairs_beta.txt</strong><br> List of all pairs of protein structure chains of beta-barrel proteins</p> <p> </p> <p><strong>HOMEP3_pdbs.tar.gz</strong><br> All pdb files for individual chains in both alpha-helical and beta-barrel subsets</p>
Homology modelling, molecular docking and molecular dynamics simulations of wild type and mutant human CYP2J2 with three polyunsaturated fatty acids
<p>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.</p> <p>It contains a document (<strong>Abelak_etal_Methods.pdf</strong>) describing the methods used to produce the data here and the data in all repositories supplementing it.</p> <p>It also contains a shell script (<strong>create_sim4_repeats.sh</strong>) that is typical of those used to set up the molecular dynamics simulations in the repositories supplementing this one.</p> <p>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.</p> <p>Description of files in this dataset:</p> <p><strong>C2J2_min3_mod_noH.pdb</strong> : Homology model of the wild type CYP2J2 built from an alignment of templates with PDB ids: 1SUO, 2P85, 3EBS and 1Z10.</p> <p><strong>docking_wild_type_C2J2.zip</strong> : Nine docked poses of arachidonic acid docked to the homology model of the wild type CYP2J2.</p> <p>Details of how this data was produced is available in the Abelak_etal_Methods.docx document.</p>
Light and confocal micrographs on the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, the accumulation of lipid droplets, and the heterologous expression and localisation of signature LD protein homologs to tobacco pollen tubes
<p>These micrographs accompany the work "Environmental gradients reveal stress hubs predating plant terrestrialization", posted as a pre-print on bioRxiv https://doi.org/10.1101/2022.10.17.512551 </p> <p>The light and confocal micrographs show the response of Mesotaenium endlicherianum SAG 12.97 to a bifactorial environmental gradient, especially their accumulation of lipid droplets (LDs); in confocal micrographs, LDs appeared as distinct structures upon staining with BODIPY.</p> <p>Further confocal micrographs show the heterologous expression and localisation of signature LD protein homologs detected in Mesotaenium endlicherianum SAG 12.97; heterologous expression was carried out in tobacco pollen tubes were also stained with BODIPY and proteins were tagged with mCherry.</p>
FIG. 10 in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 10. — Scanning electron micrographs of Monchenkocyclops mehmetadami n. sp., paratype ♂: A, antennule, ventral view; B, C, inset showing detail of modified seta on segment 11 (ancestral segment (XVI) and 12 (ancestral segment XVII), ventral view; D, segment 14 (ancestral segment (XIX-XX), ventral view; E, segment 15 (ancestral segment (XXI-XXIII), ventral view; F, segments 16 and 17, ventral view; G, segment 17, posterior view. Scale bars: A, 10 µm; B, C, 1 µm; D, F, G, 2 µm; E, 4 µm.
FIG. 6. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 6. — Monchenkocyclops mehmetadami n. sp., holotype ♀: A, urosome, ventral view; B, urosome, dorsal view; C, P6, lateral view; D, furcal ramus, ventral view. Roman numerals indicating terminology proposed by Huys et al. (1996). Symbol: *, indicating insert of seta IV and V. Scale bars: A, B, 100 µm; C, 25 µm, D, 50 µm.
FIG. 1. — Monchenkocyclops mehmetadami n in A new hyporheic Monchenkocyclops Karanovic, Yoo & Lee, 2012 (Crustacea: Copepoda) from Turkey with special emphasis on antennulary homology
FIG. 1. — Monchenkocyclops mehmetadami n. sp.: A, holotype ♀, habitus, dorsal view; B, allotype ♂, habitus, dorsal view; C, holotype ♀, anal somite and furca, dorsal view, setae are indicated by Roman numerals, following Huys et al. (1996). Not all integumental pore and sensilla of the prosomites are drawn as they are extremely difficult to observe even under 100 × magnification, but in general similar to that of M. changi Karanovic, Yoo & Lee, 2012. Scale bars: 50 µm.
Fig. 5 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 5. Neophyllobius tepoztlanensis sp. nov., ♀, holotype. A. Palp. B. Subcapitulum. C. Dorsal idiosoma. D. Ventral idiosoma. E. Trochanter–tibia of leg I. F. Tarsus I.
Fig. 4 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 4. Schematic tarsal setations of Neophyllobius cibyci sp. nov. A–D. ♀, holotype. A. Tarsus I. B. Tarsus II. C. Tarsus III. D. Tarsus IV. E–H. ♁, paratype (CNAC009238). E. Tarsus I. F. Tarsus II. G. Tarsus III. H. Tarsus IV. I–L. Protonymph, paratype (CNAC009241). I. Tarsus I. J. Tarsus II. K. Tarsus III. L. Tarsus IV. M–O. Larva, paratype (CNAC009242). M. Tarsus I. N. Tarsus II. O. Tarsus III.
Fig. 1 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 1. Neophyllobius cibyci sp. nov., ♀, holotype. A. Palp. B. Subcapitulum. C. Dorsal idiosoma. D. Ventral idiosoma. E. Trochanter–tibia of leg I. F. Tarsus I.
Fig. 2 in Camerobiid mites (Acariformes: Raphignathina: Camerobiidae) inhabiting epiphytic bromeliads and soil litter of tropical dry forest with analysis of setal homology in the genus Neophyllobius
Fig. 2. Neophyllobius cibyci sp. nov. A–B. ♁, paratype (CNAC009238). A. Dorsal idiosoma. B. Ventral idiosoma. C–D. Protonymph, paratype (CNAC009241). C. Dorsal idiosoma. D. Ventral idiosoma. E–F. Larva, paratype (CNAC009242). E. Dorsal idiosoma. F. Ventral idiosoma.
Structure of the Nt domain of mouse NBCe1 by homology modeling
<p>For the generation of the Nt model for NBCe1, a pair-wise alignment of the Nt region (residues 82-381) of mouse NBCe1-B (NCBI accession NP_061230.2) and the homologous portion of human NDCBE Nt (NCBI accession AAY79176) was generated by SWISS-MODEL. The overall identity is 54.55% between the two sequences. The alignment was used for structural modeling with the crystal structure of human NDCBE Nt (PDB ID: 5JHO) as the template. Structural assessment shows that the simulated model of NBCe1 Nt had QMEAN value −3.25, Cβ value −3.11, solvation value −0.62, torsion value −2.54, and scored 1.86 by using a MolProbity approach.</p>
FIGURES 10 – 15 in Mature larva of Stenichnus godarti (Latreille) (Coleoptera: Staphylinidae, Scydmaeninae): redescription, hypothesis of displaced epicranial suture and alternative interpretation of homology between chaetotaxic structures
FIGURES 10 – 15. Larva of Stenichnus godarti. Head in dorsal (10) and ventral (11) views; left (12) and right (13) antenna in dorsal view; right (14) and left (15) maxilla in ventral view. Abbreviations: Ag, antennal gland; An 1 – 3, antennomere I – III; Cd, cardo; Da, dorsoanterior seta; De, dorsoepicranial seta; Df, dorsofrontal seta; Dl, dorsolateral seta; Dp, dorsoposterior seta; Es, frontal arm of epicranial suture; Est, epicranial stem; L, lateral seta; l, lentiform structure; La, labral anterior seta; Ma, mala; Md. mandible; MdS, mandibular seta; Mn, mentum; Mxp 1 – 3, maxillary palpomere II – III; Ptp, posterior tentorial pit; SA, sensory appendage; Smn, submentum; sol, solenidion; St, stemma; Stp, stipes; V, ventral seta; Va, ventroanterior seta; Vl, ventrolateral seta.
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.