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1,773 results for “package”
Human Dolichyl-Phosphate Alpha-N-Acetyl glucosaminyl transferase (DPAGT1); A Target Enabling Package
<p>The ER integral membrane enzyme dolichyl-phosphate alpha-N-acetyl glucosaminyl phosphotransferase (DPAGT1) catalyses the first step in the synthesis of the oligosaccharide-P-P-dolichol unit which provides the glycans structure for N-glycosylation of proteins. Mutations in DPAGT1 cause two muscle weakness conditions, limb-girdle congenital myasthenic syndrome (CMS) and congenital disorder of glycosylation type 1j (CDG1j). DPAGT1 overexpression has also been implicated in oral cancer. We have produced and solved structures of this integral membrane enzyme, DPAGT1 with the V264G mutation found in a patient with CMS, and complexes with a 50 nM inhibitor, tunicamycin. We have developed enzymatic activity and thermostability assays which have allowed us to assess the activity and stability of DPAGT1 mutants and the effect of small molecules. There are > 20 DPAGT1 associated missense variants in patients with CMS and CDG1j. We have mapped these mutations to the structure, and we will used the assays described here to assess how the activity and stability of DPAGT1 is affected by these missense variants.</p>
Human Hyperpolarization Activated Cyclic Nucleotide Gated Ion Channel 4 (HCN4); A Target Enabling Package
<p>HCN4 is one of four hyperpolarisation activated cyclic nucleotide gated ion channels. It is responsible for the pacemaker or funny (If) current in the heart and is required for maintenance of a stable heartbeat. Mutations in HCN4 lead to a number of arrhythmias. HCN4 is the target for the angina drug ivabradine, which reduces HCN4 activity. However, ivabradine is non-selective, affecting all of the four HCN channels. HCN4 is a close homologue of HCN2, which is a target for neuropathic and inflammatory pain treatment. We have solved the structure of HCN4 both in complex with cyclic AMP and without nucleotide. Comparison of our HCN4 structure with that of the related HCN1 channel (86% identity) allows us to suggest ways to design selectivity for small molecule inhibitors between these closely related channels. </p>
Human TWIK-related Acid-Sensitive K+ Channel 1 (TASK1): A Target Enabling Package
<p>The TWIK related acid-sensitive K<sup>+</sup> channel 1 (<a href="https://www.ncbi.nlm.nih.gov/gene/3777">TASK-1</a>) belongs to the family of two-pore domain potassium (K<sub>2P</sub>) channels. It regulates resting membrane potential and is expressed in cardiomyocytes, neurons and vascular smooth muscle cells. Loss of function mutations in TASK-1 lead to primary pulmonary hypertension type 4 (PPH4) which is often fatal in mid-life (1). We have produced TASK-1 and determined structures of this protein alone and in complex with two highly potent inhibitors, BAY 1000493 and BAY 2341237, with EC<sub>50</sub> values of 9.5 nM and 7.6 nM, respectively. We have used a two-electrode voltage clamp assay to measure the effect of mutations in TASK-1 and the effect of inhibitors. The native structure of TASK-1 also allowed us to map the six known disease mutations leading to PPH4.</p>
Replication package of https://doi.org/10.1088/1361-6595/abbae4
<p>This is the replication package of Plasma activation of N<sub>2</sub>, CH<sub>4</sub> and CO<sub>2</sub>: an assessment of the vibrational non-equilibrium time window, by A.W. van de Steeg et al.</p> <p>The zip file contains a general readme and all the required data on which the figures are based. </p> <p>Nearly all raw data is in .spe files, belonging to the Princeton Instruments camera used. The python library calibrate_fiber_pos can open the camera pictures.</p> <p> </p>
Artemis (DCLRE1C, SNM1C): A Target Enabling Package
<p>Currently several radio-sensitising and chemotherapeutic agents are used in conjunction with radiotherapy to enhance the efficacy of cancer treatment. DCLRE1C/Artemis is a major player in both programmed (V(D)J) recombination and non-programmed c-NHEJ DSB repair. This makes Artemis and other DSB repair enzymes an attractive pharmacological target for the radiosensitisation of tumours. This TEP includes expression and purification methods for producing the full-length (aa 1-692), and the catalytic domain (aa 1-362) of Artemis for high-throughput activity and inhibitor assays, and a robust crystallisation method that is able to generate reproducible crystals for small molecule compound soaking. We also present an Artemis structure in complex with the β-lactam anti-bacterial compound ceftriaxone.</p>
Elongation of very long chain fatty acids protein 7 (ELOVL7); A Target Enabling Package
<p>The long-chain fatty acid elongases (ELOVL) catalyse the first rate-limiting step in the two carbon elongation of the acyl chains of fatty acids (FAs) greater than 12 carbons in length. Defects in these ELOVL elongases cause severe genetic diseases, such as Stargardt disease-3 and several ataxias, and knockout studies suggest roles in insulin resistance and hepatic steatosis. This TEP provides the first structural information for this family of enzymes which, coupled with mutagenesis and biophysical studies, demonstrates how substrates and products bind within the active site.</p>
SH2-containing-inositol-5-phosphatases (INPP5D); A Target Enabling Package
<p>SH2-containing-inositol-5-phosphatases (SHIP1 and SHIP2, coded for by genes <em>INPP5D</em> and <em>INPPL1</em>, respectively) dephosphorylate phosphatidylinositol-3,4,5-trisphosphate (PI(3,4,5)P<sub>3</sub>) to produce phosphatidylinositol-3,4-bisphosphate (PI(3,4)P<sub>2</sub>). This is an important part of the PI3K/AKT/mTOR signalling pathway. The SHIPs have been linked to a range of conditions, including cancer, diabetes, hypertension, and graft versus host disease. A link has also been demonstrated by GWAS between a non-coding mutation in the <em>INPP5D</em> (SHIP1) gene and increased risk of late-onset Alzheimer’s disease. The role of SHIP1 in Alzheimer’s disease is believed to be mediated through inflammatory processes such as the regulation of microglia and cytokine release. The distinction between the effects of SHIP1 and SHIP2 on these processes is not fully understood. In this TEP we present an apo structure of the phosphatase and C2 domains of SHIP1 and a structure with a magnesium ion and a phosphate ion bound to the active site. We also present 91 fragment bound structures that may act as starting points for the modulation of SHIP1. We are also able to crystallise an equivalent construct of SHIP2 and purify a range of other inositol-5-phosphatases to serve as a selectivity panel for the development of specific compounds. An assay has also been developed.</p>
MSN (Moesin); A Target Enabling Package
<p>Moesin (MSN; membrane-organizing extension spike protein) contains a FERM domain (Four-point-1, Ezrin, Radixin, Moesin) that links transmembrane receptors such as CD44 to the actin cytoskeleton, in a manner regulated by phosphorylation and PIP2. A proteomic, post-mortem analysis of >400 brains identified a protein co-expression module that is highly correlated with pathological and cognitive measures of Alzheimer’s disease (AD). Moesin and CD44 have emerged as key drivers in the module. MSN is highly expressed in microglia and brain endothelium (as well as several non-brain tissues). This TEP targets the CD44-MSN interaction, to test the hypothesis that inhibiting the CD44-MSN interaction would reverse harmful activities of microglia and provide beneficial outcomes for AD patients.</p>
Fibrinogen-like globe domain of human Tenascin-C (hFBG-C); A Target Enabling Package
<p>Chronic activation of the innate immune system by the damage-associated molecular pattern FBG-C (C-terminal fibrinogen-like globe domain of Tenascin-C) contributes to a variety of inflammatory diseases including arthritis, systemic sclerosis, and cancer. This TEP summarizes the first reported efforts to develop small-molecule FBG-C binders, with the aim to disrupt FBG-C-mediated pro-inflammatory protein-protein interactions (PPIs). We present the soluble expression of disulphide-containing human FBG-C (hFBG-C) in <em>E. coli</em>, the novel structure of hFBG-C, and preliminary chemical matter against hFBG-C derived from a crystallographic fragment screen. Finally, we introduce two robustly validated cellular assays, in either immortalized monocytes or primary human macrophages, which provide a route to development of small molecules which inhibit hFBG-C-activated inflammation.</p>
EPB41L3; A Target Enabling Package
<p>EPB41L3 is, with moesin (MSN), a member of the FERM family, which is highly expressed in brain as well as in other tissues (kidney, intestine, and testis). Similar to MSN, it binds to the C-terminus of CD44 and transmits signals to the cytoskeleton. EPB41L3 is inversely correlated with markers of Alzheimer’s Disease (AD). We have chosen to pursue the EPB41L3-CD44 interaction as a potential key driver in AD, and as a selectivity target for FERM proteins. This TEP includes expression constructs and methods for purification of the FERM domain from recombinant <em>E. coli</em>; Fluorescence-based assays for binding its ligand; a peptide from the cytoplasmic tail of CD44; crystal structures and a soakable crystallization system; and small molecules identified from a crystal-based fragment screen. We have also expressed several related FERM domains which can be used as a selectivity panel when developing new ligands. In follow-up work, we plan to expand the fragment hits to generate chemical tools for both EPB41L3 and moesin.</p>
SLC12A4/SLC12A6; A Target Enabling Package
<p>KCC1 (SLC12A4) and KCC3 (SLC12A6) are co-transporters of potassium and chloride, and members of cation-chloride co-transporter (CCC; or Solute Carrier 12) family. They regulate chloride level and cell volume via export of potassium and chloride ions. KCC1 plays an important role in sickle cell diseases, where its activity leads to sickling of red blood cells, a key pathological feature of the disease. Hence, symptoms of this common genetic disorder can be significantly reduced by inactivation of KCC1. KCC3 is highly expressed in neurones, where its inherited defect can lead to a rare form of peripheral neuropathy, Andermann Syndrome. This TEP presents the structures of KCC1 and KCC3 in both wild-type and inactivated states, revealing structural mechanisms for their regulation. From these structures, we have identified ligands ATP and magnesium ion, and have subsequently used biophysical assay and mass spectrometry to characterise them. These can be exploited to develop small molecule modulators to treat sickle cell diseases, one of the most common genetic disorders with unmet needs, as well as neurological disorders.</p>
Activin A receptor, type I (ACVR1); A Target Enabling Package
<p>Germline gain of function mutations in the gene <em>ACVR1</em> encoding the BMP receptor ALK2 lead to the rare congenital syndrome FOP in which aberrant signalling through the BMP signalling pathway leads to progressive heterotopic ossification in muscle and connective tissue. Identical somatic mutations have been identified in 25% of cases of the childhood brain tumour DIPG. Both conditions affect young children and have no approved therapies. Highly selective ALK2 kinase inhibitors are therefore desirable to achieve chronic treatment of children with safety. We prepared recombinant ALK2 kinase domain and solved structures of ALK2 in complex with new ATP-competitive inhibitors. We identified a novel allosteric pocket in the ALK2 kinase domain and took advantage of these structures to perform crystallographic fragment screening (XChem) using both a standard poised fragment library and a new mini-fragment library. This work identified a poised fragment for development as an allosteric ALK2 inhibitor, as well as mini-fragments exploiting new areas of the ATP and substrate binding pockets. <em>In vitro</em> and cellular assays are available to advance these compounds for drug development in collaboration with patient groups.</p>
SARS-CoV-2 NSP13; A Target Enabling Package
<p>To contribute towards the development of novel anti-viral therapeutics targeting the current and future emerging coronavirus threats, the Gileadi lab at the University of Oxford, together with the XChem team at Diamond Light Source, have teamed up to perform a crystallographic fragment screen against SARS-CoV-2 NSP13 helicase. NSP13 is believed to act in concert with the replication-transcription complex (NSP7/NSP8<sub>2</sub>/NSP12), possibly being involved in either disrupting downstream RNA secondary structures or template switching, and plays an essential role in the life cycle of SARS-CoV-2.</p> <p>This TEP includes expression clones and methods for producing the full length NSP13, and fluorescence-based activity assays suitable for compound screening. We provide a crystallisation system that produces reproducible crystals that diffract to high resolution, and have performed a crystallographic fragment screen revealing 63 fragment hits across 51 datasets. The fragment hits include several hits in pockets predicted to be of functional importance, including the nucleotide and nucleic acid binding sites, opening the way to development of novel antiviral agents.</p>
SARS-CoV-2 Nidoviral RNA Uridylate‐Specific Endoribonuclease (NSP15); A Target Enabling Package
<p>The non-structural protein 15 (NSP15, NendoU<sup>SARS-CoV-2</sup>) from severe acute respiratory syndrome 2 virus (SARS-CoV-2) is an uridylate-specific endoribonuclease, likely responsible in the viral immune evasion mechanism. This TEP provides a set of reagents for further interrogation of the molecular function of NSP15. We have established a purification protocol for the active protein for biochemical and structural studies. Moreover, we have crystallised the protein and performed a crystallographic fragment screen which yielded several hits. Data generated here will be used for the development of enzyme inhibitors that would illuminate the biological role of the gene product, and eventually point the way to new antiviral therapies.</p>
Chemicals associated with plastics packaging (CPPdb) for MS-FIDNER
<p>The original chemicals associated with plastic packaging database (CPPdb) was compiled by Ksenia J. Groh, etc., and is downloadable in https://zenodo.org/record/1287773. To make the use of this database for structural elucidation in MS-FINDER, the CPPdb is re-organized to the form that is compatible with MS-FINDER. Vital information, e.g., smiles and InChIKey, which are vital for in-silico fragmentation, are added to the CPPdb. Hope this re-formed database would be helpful for anyone who wants to use it for MS-FINDER.</p>
Dehydrogenase E1 and transketolase domain-containing protein 1 (DHTKD1); A Target Enabling Package
<p>Inherited mutations of the <em>GCDH </em>gene for glutaryl-CoA dehydrogenase, catalysing the sixth enzymatic step in lysine catabolism, lead to the rare neurometabolic disorder Glutaric Aciduria type 1 (GA1). There is a rationale that inhibition of the fifth lysine catabolising step, catalysed by the DHTKD1 enzyme, could provide therapeutic benefit for GA1 by means of substrate reduction. This TEP provides early tools to develop DHTKD1 inhibitors, including recombinant protein, structure, biophysical (activity and stability) assays and fragment hits of human DHTKD1. This work also reports the interaction of DHTKD1 with its functional partner DLST as a binary complex, and an EM reconstruction of the DLST catalytic core.</p>
Präzi: From Package-based to Call-based Dependency Networks
<p>The data is originally derived from commit 6c550c8 of <a href="https://web.archive.org/web/20210129124622/https://github.com/rust-lang/crates.io-index">https://github.com/rust-lang/crates.io-index</a>. The dataset includes the following files:</p> <ul> <li><a href="/api/files/0386399e-bc22-4e16-a2e3-2d331696e1de/releases.csv?versionId=0fbac7f6-820c-4411-80ee-26967eda0652">releases.csv</a>: extracted package releases.</li> <li><a href="/api/files/0386399e-bc22-4e16-a2e3-2d331696e1de/docsrs.csv?versionId=b61f6277-0f19-4c21-bb54-04dcb19f8d43">docsrs.csv</a>: build status and compile toolchain of package releases scrapped from <a href="https://web.archive.org/web/20210118074327/https://docs.rs/">Docs.rs</a>.</li> <li><a href="/api/files/0386399e-bc22-4e16-a2e3-2d331696e1de/rustcg-corpus.tar.xz?versionId=914e7e03-0509-443f-8841-a76408f329d3">rustcg-corpus.tar.xz</a>: call graphs and type hierarchies corpus of <a href="https://web.archive.org/web/20210125175834if_/https://crates.io/">crates.io</a> in JSON format. Constructed using <a href="https://web.archive.org/web/20210129130825/https://github.com/ktrianta/rust-callgraphs">rust-callgraphs</a>.</li> <li><a href="/api/files/0386399e-bc22-4e16-a2e3-2d331696e1de/CDN.tar.xz?versionId=9e0d7baa-32c8-4594-b8b9-fb486eee7d11">CDN.tar.xz</a>: static call-based dependency network (CDN) and package-based dependency network (PDN) in JSON format. </li> </ul>
A Non-galvanic D-band MMIC-to-Waveguide Transition Using eWLB Packaging Technology-dataset
<p>This paper presents a novel D-band interconnect implemented in a low-cost embedded Wafer Ball Grid Array (eWLB) commercial process. The transition is realized through a patch slot antenna directly radiating to a standard waveguide opening. The interconnect achieves low insertion loss and good bandwidth. The measured minimum Insertion Loss (IL) is 2 dB and the average is 3 dB across a bandwidth of 22% covering the frequency range 110-138 GHz. In addition, the structure is easy to integrate as it does not require any special assembly nor any galvanic contacts. Adopting the low-cost eWLB process and standard waveguides makes the transition an attractive solution for interconnects beyond 100 GHz.</p>
Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches (Replication Package Part 3: OpenSSL dataset)
<h1><strong>The Replication Package of</strong></h1> <h1><strong>"Today's cat is tomorrow's dog: accounting for time-based changes in the labels of ML vulnerability detection approaches"</strong></h1> <h3><strong>Part 3 (OPENSSL Dataset)</strong></h3> <div> <div>This repository includes:</div> <ol> <li><em><strong>Code.zip</strong></em> that contains the codes to replicate some parts of this study:<br>a. <em>1_generate_datasets</em> implements our methodology to generate the datasets.<br>b. <em>2_run_models</em> runs the ML models during the evaluation.<br>c. <em>3_result_replication </em>generates charts presented in the paper from the ML evaluation results.</li> <li><em><strong>Datasets.zip</strong></em> that contain 2 folders:<br>a. <em>original</em> datasets: 1 from <a href="https://github.com/CGCL-codes/VulDeePecker" target="_blank" rel="noopener">NVD Vuldeepecker</a> and 3 extracted from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a>.<br> <div> <div>b. <em>OPENSSL</em> datasets: train, validation, test sets for each time of observation extracted using our methodology from <a href="https://github.com/ZeoVan/MSR_20_Code_vulnerability_CSV_Dataset" target="_blank" rel="noopener">BigVul</a> dataset for project <em>openssl</em>.</div> </div> </li> <li><em><strong>Pretrained-models.zip</strong></em> that we generated during our evaluation (3 test results for each time point in the timeline [2013-2019]).</li> <li><em><strong>Results.zip</strong></em> of our evaluation, the folder <em>ALL</em> contains the overall results and other folders are results by model.</li> </ol> <p><strong>UPDATED version 5<br></strong>- added a GLOBAL_README.md which contains the 3 stages and how they are connected to each other<br>- updated LineVul.ipynb: import AdamW from torch.optim instead of transformers<br>- updated README.md in Code2Vec with the prerequisites of Java to run gradlew for astmine</p> <p><strong>UPDATED version 6<br></strong>- updated CodeBert.ipynb: import AdamW from torch.optim instead of transformers</p> <p>Documentations</p> <ol> <li><em><strong>INSTALL.pdf </strong></em>: how to install the codes</li> <li><em><strong>README.pdf</strong></em>: readme file</li> <li><em><strong>REQUIREMENTS.pdf</strong></em>: hardware and software requirements</li> <li><em><strong>STATUS.pdf</strong></em> : status for artifact submission</li> <li><em><strong>LICENSE.pdf</strong></em>: the license of this artifact</li> <li><em><strong>PAPER.pdf</strong></em>: the camera-ready version of the paper</li> </ol> </div> <div> <div>Please refer to the following repositories for the other datasets and pre-trained models:</div> <div>- Part 1 NVD Vuldeeepecker : <a href="https://doi.org/10.5281/zenodo.8207883" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.8207883</a></div> - Part 2 LINUX : <a href="https://doi.org/10.5281/zenodo.10960662" target="_blank" rel="noopener">https://doi.org/10.5281/zenodo.10960662</a><br> <div>- Part 4 POPPLER : <a href="https://doi.org/10.5281/zenodo.14713143">https://doi.org/10.5281/zenodo.14713143</a></div> <div> </div> <div>This work was partly funded by the EU under the H2020 Program AssureMOSS (Grant n. 952647) and the Horizon Europe Program Sec4AI4Sec (Grant n. 101120393), by the Italian Ministry of University and Research (MUR) under the P.N.R.R. – NextGenerationEU grant n.\ PE00000014 (SERICS subproject COVERT), and by the Dutch Research Council (NWO) under the grant NWA.1215.18.006 (Theseus) and grant KIC1.VE01.20.004 (HEWSTI). </div> </div>
Community Package Lasry Dataset
<p>The Community package (<a href="https://github.com/SoloveyMaria/community">https://github.com/SoloveyMaria/community</a>) is an R package designed for the analysis of single-cell RNA sequencing data, specifically for inferring interactions between different cell types. The dataset provided here is compatible with the Community tool, allowing for direct utilization. </p><p>The dataset associated with this research has undergone peer review and has been published in the journal Nature Cancer. The publication can be accessed via the following link: <a href="https://doi.org/10.1038/s43018-022-00480-0">https://doi.org/10.1038/s43018-022-00480-0</a>. For access to the raw data, please visit: <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185381">https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185381</a>. It's important to note that the data in this repository has undergone batch correction and normalization, and the corresponding metadata has been appropriately adjusted. This processed data serves as the input for the Community tool.</p>
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.