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5 results for “Protein Structure Initiative”
Protein Structure Initiative Publications, 2000-2016
<p>These files contain the full list of the 2313 publications and book chapters written as part of the Protein Structure Initiative, from 2000-2016. This data was collected from PubMed and by manual entry by the PSI Structural Biology Knowledgebase's Publication Portal, managed by Wladek Minor at University of Virginia. These files were created at the end of the PSI project on June 30, 2017.</p> <p>The references are provided as lists in two formats:</p> <ul> <li>in CSV (comma-separated variables) format that can be read in Excel or other spreadsheet application, or</li> <li>an Endnote Library Import file (store-endnote-pubs). To import this library into Endnote, select File --> Import... and then under Options, select the Import Option "Endnote Library Import". Then this text file will be processed and loaded into the library.</li> </ul> <p>--created by the Structural Biology Knowledgebase, July 5, 2017. (sbkb.org)</p>
Initial Structures of PKM1/M2 proteins for AMOEBA Molecular Dynamics studies (xyz Tinker format)
<p>Here are presented our initial structures of PKM1/M2 (solvated and neutralized) for the different states to initiate molecular dynamics in AMOEBA force field.</p> <p>Those are represented in xyz Tinker format and come from their respectives PDB crystal structure after extraction of the unwanted ligands :</p> <p>3SRF for PKM1,</p> <p>1ZJH for monomer PKM2,</p> <p>6B6U for dimer PKM2,</p> <p>3SRH for free-tetramer PKM2,</p> <p>3SRD for tetramer PKM2 bound to FBP,</p> <p>3U2Z for tetramer PKM2 bound to TEPP-46.</p>
Protein Structure Initiative - TargetTrack 2000-2017 - all data files
<p><strong>Protein Structure Initiative - TargetTrack protein target registration database (795 MB, gzipped tarball)</strong></p> <p>The Protein Structure Initiative was a high-throughput structural genomics effort from 2000-2015 focused on developing technologies to enable greater coverage of protein structure space. Over its 15-year tenure, over 100 investigators at 35 centers (see ContributingCenters.xls) declared over 350,000 protein sequences (targets) that they would study using state-of-the-art protein production and structure determination methods. Many of these targets were selected through bioinformatics-based methods to serve as representatives for sequence and structure clusters. </p> <p>From 2003-2010, these selected sequences and some basic identifying metadata were kept in a database called TargetDB, created at the Research Collaboratory for Structural Bioinformatics at Rutgers University. In 2008, a second database named PepcDB was created to track detailed experimental trial history and the standard protocols used by the PSI centers. These two databases became the principal structural genomics target databases, and were rolled into the <strong>PSI Structural Biology Knowledgebase</strong> in 2008. </p> <p>As part of the third phase of the PSI, TargetDB and PepcDB were merged into a single resource, <strong>TargetTrack</strong>, to facilitate one-stop access to the data as well as expanding the schema to include new required data items. Participating centers deposited the latest status on their active targets and the protocols that were used (along with any deviations) on a weekly or quarterly basis. TargetTrack provided a variety of pre-computed data downloads on a weekly basis as well. </p> <p>In July 2017, the Structural Biology Knowledgebase ceased operations. The files provided in this tarball represent the final datafiles generated by TargetTrack (timestamp June 30, 2017). <strong>Please read the README included in this dataset for descriptions of each file. </strong></p> <p><strong>The entire TargetTrack datafile in XML format can be found in /TargetTrack XML files/tt.xml.gz</strong></p> <p>Key documentation can be found in the /Documentation folder.<br> TargetTrack schema: targetTrack-v1.4.1.pdf<br> Spreadsheet with TargetTrack enumerations for relevant fields: targetTrackEnumeratedDataItems-v1.4.1-1.xls<br> Image depicted the XML data schema: targetTrack-v1.4.1.jpg</p> <p>These files are 868 MB in total size, uncompressed. <br> To open the tarball, use the command 'tar -zxvf TargetTrack-1Jul2017.tar.gz'</p> <p>-- created by the PSI Structural Biology Knowledgebase, July 5, 2017</p>
Initial structures of macrocyclic Gαq protein inhibitors bound to the Gq heterotrimer
<p>Initial PDB structures of the Gq heterotrimer in its apo form or bound to either ym2 or fr9 inhibitors. These structures were used in the molecular dynamics simulations described in the manuscript below: </p> <p><strong>Unraveling binding mechanism and kinetics of macrocyclic Gαq protein inhibitors</strong> (under review)<br> <em>Jan H. Voss<sup>1</sup>, Jessica Nagel<sup>1</sup>, Muhammad Rafehi<sup>1</sup>, Ramon Guixà-González<sup>2,5</sup>, Davide Malfacini<sup>3</sup>, Julian Patt<sup>3</sup>, Stefan Kehraus<sup>3</sup>, Asuka Inoue<sup>4</sup>, Gabriele M. König<sup>3</sup>, Evi Kostenis<sup>3</sup>, Xavier Deupi<sup>2,5</sup>, Vigneshwaran Namasivayam<sup>1</sup>, and Christa E. Müller<sup>1</sup></em></p> <p><em><sup>1</sup>PharmaCenter Bonn, Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany<br> <sup>2</sup>Condensed Matter Theory Group, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland<br> <sup>3</sup>Institute of Pharmaceutical Biology, University of Bonn, Nussallee 6, 53113 Bonn, Germany<br> <sup>4</sup>Tohoku University, Graduate School of Pharmaceutical Sciences, Sendai, Miyagi, 980-8578 Japan<br> <sup>5</sup>Laboratory of Biomolecular Research, Paul Scherrer Institute, Forschungsstrasse 111, 5232 Villigen PSI, Switzerland</em></p>
Initial and final MD simulation coordinates for "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization"
<p>Initial and final coordinates for all MD simulations performed for the manuscript: "Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization."</p> <p>File uploaded is a ZIP folder, containing sub-folders for each capsid construct (wild type and mutants). Additionally, a README file is given in the top-level folder, which contains a description of the file contents.</p>
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