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Different human linker histone (H1) variants are expected to have distinct binding modes to the nucleosome. The position and orientation of a number of different H1 globular domains on the nucleosome were investigated through molecular docking using MGLTools and HADDOCK. The nucleosome core and linker DNA in the GH5-chromatosome structure (PDB: 4QLC) were used as a docking template. GH5 (in PDB: 4QLC) was re-docked to this template to test the docking algorithm. Docked and re-docked GH5 compared well. The docking algorithm was further tested by docking the NMR solution structure of the globular domain of chicken H1 (GH1, PDB: 1GHC) to the nucleosome template. The position of docked GH1 on the nucleosome agreed with literature. 
The N-terminal - and globular domain H1x hybrid (NGH1x) was studied using solution NMR in both low (20 mM sodium phosphate, pH 7.0) and high (20 mM sodium phosphate, 1 M sodium perchlorate, pH 7.0) ionic strength conditions (de Wit, H., Vallet, A., Brutscher, B. et al. Biomol NMR Assign (2019) 13: 249. https://doi.org/10.1007/s12104-019-09886-x). These low and high ionic strength structures were docked to the nucleosome template. 
Homology (MODELLER) and ab initio modeling (CS-ROSETTA) were employed to model structures for other human H1 globular domains: GH1.0, GH1.4, GH1oo, and GH1t. The modeled structures were also docked to the nucleosome template.
 All the docking procedures listed above produced 100 models of different energies. In each case, the lowest energy docked model was chosen. The structures of all the H1 globular domains that were docked to the template are given as PDB files (1GHC_lowest_energy.pdb; 2LSO_lowest_energy.pdb; GH5_re-docked_position.pdb; NGH1x_high_salt_NTD.pdb; NGH1x_low_salt_NTD.pdb; modeled_GH1_0_lowest_energy.pdb; modeled_GH1_4_lowest_energy.pdb; modeled_GH1oo_lowest_energy.pdb; modelled_GH1t_lowest_energy.pdb) in the data file. The nucleosome template structure is also given in PDB file format (4QLC_nucleosome_without_GH5.pdb). Finally, the docked models are also given (GH5-chromatosome.pdb; 1GHC-chromatosome.pdb; 2LSO-chromatosome.pdb; GH1_0-chromatosome.pdb; GH1_4-chromatosome.pdb; GH1oo-chromatosome.pdb; GH1t-chromatosome.pdb; NGH1x_no_salt-chromatosome.pdb; NGH1x_salt-chromatosome.pdb). The files are compatible with most molecular graphics software. The file Dockings_modelling_test_and_results.pdf provides the modeling and docking results in figures and tables. A short description of each figure and table is given within the PDF file.
Data Types:
  • Sequencing Data
  • Dataset
  • Document
Variant call file of DENV2 16681 passage 1 in M3 iPSC cells (open with Microsoft Excel)
Data Types:
  • Sequencing Data
  • Dataset
The Indeterminate Domain (IDD) proteins are a plant specific subclass of C2H2 Zinc Finger transcription factors. Some of these transcription factors play roles in diverse aspects of plant metabolism and development; however the function of most of IDDs is unknown and its molecular evolution has not been explored. Here, Prochetto and Reinheimer reconstructed the evolution of IDDs during plant land conquest. They found that IDDs arose from the common ancestor of Streptophyta. Once in land, IDDs experienced a rapid radiation that accompanied key morphological, physiological and biochemical transitions required in plant terrestrialization. The authors present a solid phylogenetic framework of annotated IDD genes which links genetic and functional knowledge from model to non-model species.
Data Types:
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  • Sequencing Data
  • Tabular Data
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  • Text
Objective: To engage in a priority-setting exercise with both clinicians and consumers to determine systematic reviews of highest priority to update. Study Design & Setting: The US Satellite of the Cochrane Pregnancy & Childbirth Group (US-PCG) narrowed a list of over 600 review titles due for updating down to 97 review titles based on US relevance. The US-PCG then used the Delphi method to explore consensus on which titles to prioritize for updating. In Round 1, participants self-identified as a clinician/researcher or consumer, and then ranked titles into “high”, “medium”, and “low” priority groups. In Round 2, participants were given Round 1 results and asked to rank their top 5 titles. Results were analyzed within and between groups.
Data Types:
  • Slides
  • Tabular Data
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Data from: Bitomský M., Mládková P., Pakeman RJ, & Duchoslav M. (2020). Clade composition of a plant community indicates its phylogenetic diversity. Ecology and Evolution. doi: 10.1002/ece3.6170 Data summarises results from the case studies and simulations presented in our paper. In addition, we provide an R script for calculation of proposed phylogenetic diversity metrics (the clade indices). Brief description of each file: 1. Grasslands_DNA_markers_info.xls - Accession numbers of all DNA markers used for phylogeny inference in grasslands 2. Grasslands_DNA_alignment_BEFORE_GBlocks.fasta - DNA alignment matrix before utilisation of the GBlocks tool 3. Grasslands_DNA_alignment_AFTER_GBlocks.fasta - DNA alignment matrix after utilisation of the GBlocks tool 4. Grasslands_BEAST_file.xml - BEAST .xml file submitted to the CIPRES portal (www.phylo.org) 5. Grasslands_tree.txt - Dated MCC tree, grasslands (newick format) 6. Grasslands_tree.nex - Dated MCC tree, grasslands (nexus format) 7. Phyto-database_pruned_tree.txt - Pruned dated tree from the super tree of European flora (Durka & Michalski 2012, Ecology), phytosociological database (newick format) 8. Plot_data.slx - plot data of all case studies + species lists 9. Simulation_results.txt - Summary of R2 values (phylogeny-based metric ~ the clade index) for simulated phylogenies and community matrices (manipulated: phylogenetic scale, species pool size and species richness range) 10. Bitomsky2020EE_R_script_indices.R - An R script for computation of the clade indices (with notes and examples)
Data Types:
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  • Sequencing Data
  • Tabular Data
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  • Document
  • Text
Alignments for phylogenetic analyses
Data Types:
  • Sequencing Data
  • Dataset
Verifiable gender based Labor Participation Rate datasets from in North Cyprus are presented in the data pack in powerpoint (ppt). The North Cypriot datasets are derived from publicly accessible 'devplan.org' website. The specific location on the website for the data are expressed in the ppt display. Calculations to arrive at labor participation rate description are also detailed out in the presentation.
Data Types:
  • Slides
  • Dataset
There are two documents in the repository. The “MMCS_Summary.pdf” and “MMCS_nutsell.pptx”. The first is a summary of the main elements (graphic symbols) of the specification, and some examples. The second is a presentation to better understand some important characteristics of the specification. It is highly recommended to watch this presentation in full screen mode.
Data Types:
  • Slides
  • Dataset
  • Document
This dataset is the complete directory of all Trygve's web pages. The web page HTML code is found from its URL. For example, the HTML for http://folk.uio.no/trygver/themes/Personal/pp-index.html is in the file at themes/Personal/pp-index.html The University of Oslo is terminating its Web service after 25 years of operation. My gigabyte of web pages have been collected over the years and will no longer be accessible over the Net. The pages are stored in this dataset and it may be possible to transfer them to another service if required. It should in any case be possible to read the dataset with an HTML reader.
Data Types:
  • Other
  • Slides
  • Software/Code
  • Image
  • Video
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  • Document
  • Text
  • Audio
  • File Set
Raw data for Salmonella expresses foreign genes during infection by degrading their silencer
Data Types:
  • Slides
  • Dataset