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5,942 results for “Binding”
Example binding lifetime analysis: Kymographs and tracks
<p>Kymograph recorded on the LUMICKS C-Trap. LacI is labeled in green.</p> <p>The binding events on the kymograph were tracked using Pylake. The corresponding tracks are included in this dataset as tracks1.csv and tracks.csv.</p>
Self-Assembled Proteomimetic (SAP) with Antibody-like Binding from Short PNA-Peptide Conjugates
<p><span><span>Affinity proteins </span><span>based on </span><span>a </span><span>three-helix </span><span>bundle</span> <span>(</span><span>affibodies, </span><span>alphabodies</span><span> and computationally </span></span><span><span>de novo</span></span><span> <span>designed</span><span> ones)</span><span> have shown to be a general platform to discover binders with properties reminiscent of </span><span>antibodies</span><span>, combining </span><span>high </span><span>target </span><span>specificity</span><span> with </span><span>affinities reaching well below</span> <span>the </span><span>nanomolar</span><span>.</span> <span>Herein</span><span>,</span><span> we report a new strategy</span><span>, coined self-assembled proteomimetic (SAP)</span><span>,</span><span> to mimic </span><span>such</span><span> three-helix bundle</span><span> architecture with a hybridization-enforced two-helix </span><span>coiled</span> <span>coil</span><span> that is obtained by templated</span> <span>native chemical ligation (</span><span>T-</span><span>NCL) of PNA-peptide conjugates.</span> <span>This SAP </span><span>strategy</span> <span>stands out by</span><span> its</span><span> synthetic accessibility reducing the length on the longest </span><span>synthetic</span><span> peptide to </span><span>less than 30 amino acids, readily attainable by standard SPPS methodologies</span><span>. We show that the </span><span>T</span><span>-NCL dramatically accelerates the </span><span>ligation</span><span>, enabling this chemistry to </span><span>proceed</span> <span>in a combinatorial fashion </span><span>at</span><span> low</span> <span>micromolar</span><span> concentration</span><span>s</span><span>.</span> <span>We </span><span>demonstrate</span> <span>that small </span><span>combinatorial </span><span>libraries of </span><span>SAP</span><span>s</span><span> can be prepared in one operation and used directly in </span><span>affinity selection</span><span>s</span><span> against a target of interest </span><span>with an</span><span> LC-MS </span><span>analysis</span><span> of the fittest binders</span><span>.</span> <span>Moreover, we </span><span>show</span><span> that </span><span>the underlying</span> <span>design</span><span> paradigm</span><span> is functional for</span><span> SAPs based on structurally distinct three-helix peptides </span><span>aimed at</span><span> different </span><span>therapeutic </span><span>targets, namely</span> <span>HER2 </span><span>and</span><span> spike’s RBD</span><span>,</span></span> <span><span>reaching picomolar </span><span>affinities</span></span><span><span>. We further </span><span>illustrate </span><span>that the</span> <span>affinity </span><span>of the </span><span>S</span><span>AP</span><span> can be allosterically regulated using a toehold displacement</span><span> of the hybridizing PNAs</span><span> to disrupt the </span><span>coiled coil</span><span> stabilization.</span> <span>Finally, w</span><span>e show that </span><span>an RBD-targeting </span><span>SAP effectively inhibits viral </span><span>entry </span><span>of SARS-CoV-2</span> <span>with an IC</span></span><span><span>50</span></span><span><span> of </span><span>2.8</span> <span>nM</span><span>.</span></span><span> </span></p>
How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study
<p>The data necessary to independently reproduce the MD simulations and the first part of the simulation trajectories reported in the paper "<strong>How Binding Site Flexibility Promotes RNA Scanning in TbRGG2 RRM: A Molecular Dynamics Simulation Study</strong>", by Lemmens et al.</p> <p>Due to Zenodo data deposition limits, every 10th frame of the MD simulation trajectories is included. Due to Zenodo deposition limits, MD trajectory files for this paper are also available at 10.5281/zenodo.14260246.</p>
Double-stranded RNA structural elements holding the key to translational regulation in cancer: the case of editing in RNA Binding Motif Protein 8A
<p>Raw data supporting the manuscript</p> <p>Abukar, A.;Wipplinger, M.;<br> Hariharan, A.; Sun, S.; Ronner, M.;<br> Sculco, M.; Okonska, A.;<br> Kresoja-Rakic, J.; Rehrauer, H.; Qi, W.;<br> et al. Double-Stranded RNA<br> Structural Elements Holding the Key<br> to Translational Regulation in Cancer:<br> The Case of Editing in RNA-Binding<br> Motif Protein 8A. Cells 2021, 10, 3543.<br> https://doi.org/10.3390/<br> cells10123543</p>
Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations
<p>This dataset collects the unprocessed (= outputs from calculations) and processed (= plots, average values for orbital and ionization energies) results discussed in the paper titled "Predictive simulations of core electron binding energies of halogenated species adsorbed on ice surfaces from relativistic quantum embedding calculations" by Richard Asamoah Opoku, Céline Toubin, and André Severo Pereira Gomes.</p>
Predictions of the SARS-CoV-2 B.1.1.529 Variant Spike Protein Receptor Binding Domain Structure and Neutralizing Antibody Interactions
<p>Using AlphaFold2 and HADDOCK, we have generated a predicted structure for the SARS-CoV-2 B.1.1.529 variant's Spike receptor binding domain and then predicted the binding interaction with neutralizing antibodies. This was performed to understand the potential structural changes in the receptor binding domain of B.1.1.529 and how this may affect vaccine efficacy through antibody interaction.</p>
Polyphenols' Inflammation-mediated Deglucuronidation and Promiscuous-binding Behavior for Antiviral Assaying and Trialing
<p>Dataset based on EMSKE Phytochem's pre-existing library of more than 250 Pubchem compounds that supports the research work Polyphenols’ Inflammation-mediated Deglucuronidation and Promiscuous-binding Behavior for Antiviral Assaying and Trialing. It refers to Jasial et al. 2016's dataset uploaded to Zenodo, <br> <br> Jasial, S.; Hu, Y.; Bajorath, J. PubChem Compounds Tested in Primary and Confirmatory Assays, 2016<br> <br> located at https://doi.org/10.5281/zenodo.44593 , which itself supports their work Jasial et al 2017: <br> <br> Jasial, S.; Hu, Y.; Bajorath, J. Determining the Degree of Promiscuity of Extensively Assayed Compounds. PLOS ONE 2016, 11 (4), e0153873. https://doi.org/10.1371/journal.pone.0153873.</p>
Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?
<p>Datasets related to publication: </p> <p>Shevchenko E, Pantsar T: Regulatory spine RS3 residue of protein kinases: a lipophilic bystander or a decisive element in the small-molecule kinase inhibitor binding?. <em><em>Biochem Soc Trans</em></em> 28 February 2022; 50 (1): 633–648</p> <p>https://doi.org/10.1042/bst20210837</p> <p> </p> <p> </p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 20 Binding Site Data A
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 20 binding sites. Because this data set is too large to fit in one single repository we have split it up into parts. This is part A</p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 20 Binding Site Data C
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 20 binding sites. Because this data set is too large to fit in one single repository we have split it up into parts. This is part C.</p>
Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics: 20 Binding Site Data B
<p>This is the original data for the manuscript "Diffraction-Limited Molecular Cluster Quantification with Bayesian Nonparametrics" by J Bryan IV, I Sgouralis, and S Presse. This repository contains movies of DNA origami with 20 binding sites. Because this data set is too large to fit in one single repository we have split it up into parts. This is part B.</p>
Sodium binding stabilizes the outward-open state of SERT by limiting bundle domain motions
<p>Measured distances, angles, RMSD, RMSF, vestibule diameters and principal components along with the structural representations in pymol pse files and the manuscript images. The measurements have a 1ns time resolution.</p> <p> </p> <p>DATA_sodium_stabilize_SERT.zip<br> ├── fig1<br> │ ├── fig1_v3.png<br> │ ├── occ_3ions_rmsf_TMH_fitted_250_500.xvg<br> │ ├── occ_Cl_rmsf_TMH_fitted_250_500.xvg<br> │ ├── occ_ionless_rmsf_TMH_fitted_250_500.xvg<br> │ ├── out_3ions_rmsf_TMH_fitted_250_500.xvg<br> │ ├── out_Cl_rmsf_TMH_fitted_250_500.xvg<br> │ └── out_ionles_rmsf_TMH_fitted_250_500.xvg<br> ├── fig2<br> │ ├── distances_n_angles_fig2.pse<br> │ ├── fig2_v2.png<br> │ ├── occ_apo_nosalt_3ions.rep1.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_3ions.rep1.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM1b-TM9up.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM1b-TM8down.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM1b-TM8down.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM1b-TM9up.dat<br> │ ├── out_apo_nosalt_ionless.rep5.TM1b-TM8down.dat<br> │ └── out_apo_nosalt_ionless.rep5.TM1b-TM9up.dat<br> ├── fig3<br> │ ├── fig3_v2.png<br> │ ├── occ_apo_nosalt_3ions.rep1.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep1.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep1.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep1.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM9-TM3-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM9-TM3-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM9-TM8-TM6a.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM9-TM8-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM9-TM3-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM9-TM3-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM9-TM8-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM9-TM8-TM6a.dat<br> │ ├── out_apo_nosalt_ionless.rep5.TM9-TM8-TM1b.dat<br> │ └── out_apo_nosalt_ionless.rep5.TM9-TM8-TM6a.dat<br> ├── fig4<br> │ ├── cluster_centr_250_500_concat_bundle-fit_bundle-measure_in_fig4.pse<br> │ ├── fig4_v2.png<br> │ ├── occ_apo_nosalt_3ions.rep1.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep1.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.TM6a-TM6b.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM1a-TM1b.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep1.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep2.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep3.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep4.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_3ions.rep5.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep1.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep2.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep3.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep4.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_Cl.rep5.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep1.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep2.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep3.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM1a-TM1b.dat<br> │ ├── out_apo_nosalt_ionless.rep4.TM6a-TM6b.dat<br> │ ├── out_apo_nosalt_ionless.rep5.TM1a-TM1b.dat<br> │ └── out_apo_nosalt_ionless.rep5.TM6a-TM6b.dat<br> ├── fig5<br> │ ├── concat_0_500_dt_RMSF_bundle_fit_bundle_measure_colored.pse<br> │ ├── fig5_v3.png<br> │ ├── occ_apo_nosalt_3ions.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── occ_apo_nosalt_3ions.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_3ions.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_3ions.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_3ions.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_3ions.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_Cl.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── occ_apo_nosalt_Cl.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_Cl.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_Cl.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_Cl.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_Cl.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_ionless.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── occ_apo_nosalt_ionless.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_ionless.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_ionless.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_ionless.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── occ_apo_nosalt_ionless.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_3ions.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── out_apo_nosalt_3ions.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_3ions.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_3ions.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_3ions.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_3ions.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_Cl.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── out_apo_nosalt_Cl.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_Cl.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_Cl.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_Cl.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_Cl.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_ionless.concatenated_trajectories.rmsf_bundle_fitted_0_500_concat_protein.xvg<br> │ ├── out_apo_nosalt_ionless.rep1.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_ionless.rep2.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_ionless.rep3.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ ├── out_apo_nosalt_ionless.rep4.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> │ └── out_apo_nosalt_ionless.rep5.RMSD_fit-boundle_CA_measure-boundle_CA_preEQreference.xvg<br> ├── fig6<br> │ ├── fig6_v5.png<br> │ ├── occ_3ions_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ ├── occ_Cl_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ ├── occ_ionless_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ ├── out_3ions_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ ├── out_Cl_extreme_scaffoldFIT_bundleMEASURE1.pdb<br> │ ├── out_Cl_extreme_scaffoldFIT_bundleMEASURE2.pdb<br> │ ├── out_Cl_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ ├── out_ionless_projected_scaffoldFIT_bundleMEASURE.xvg<br> │ └── scaffoldFIT_bundleMEASURE_global_covar_extrame1.pse<br> ├── fig7<br> │ ├── fig7_v2.png<br> │ ├── occ_apo_nosalt_3ions.rep1.radii_refitted.dat<br> │ ├── occ_apo_nosalt_3ions.rep2.radii_refitted.dat<br> │ ├── occ_apo_nosalt_3ions.rep3.radii_refitted.dat<br> │ ├── occ_apo_nosalt_3ions.rep4.radii_refitted.dat<br> │ ├── occ_apo_nosalt_3ions.rep5.radii_refitted.dat<br> │ ├── occ_apo_nosalt_Cl.rep1.radii_refitted.dat<br> │ ├── occ_apo_nosalt_Cl.rep2.radii_refitted.dat<br> │ ├── occ_apo_nosalt_Cl.rep3.radii_refitted.dat<br> │ ├── occ_apo_nosalt_Cl.rep4.radii_refitted.dat<br> │ ├── occ_apo_nosalt_Cl.rep5.radii_refitted.dat<br> │ ├── occ_apo_nosalt_ionless.rep1.radii_refitted.dat<br> │ ├── occ_apo_nosalt_ionless.rep2.radii_refitted.dat<br> │ ├── occ_apo_nosalt_ionless.rep3.radii_refitted.dat<br> │ ├── occ_apo_nosalt_ionless.rep4.radii_refitted.dat<br> │ ├── occ_apo_nosalt_ionless.rep5.radii_refitted.dat<br> │ ├── out_apo_nosalt_3ions.rep1.radii_refitted.dat<br> │ ├── out_apo_nosalt_3ions.rep2.radii_refitted.dat<br> │ ├── out_apo_nosalt_3ions.rep3.radii_refitted.dat<br> │ ├── out_apo_nosalt_3ions.rep4.radii_refitted.dat<br> │ ├── out_apo_nosalt_3ions.rep5.radii_refitted.dat<br> │ ├── out_apo_nosalt_Cl.rep1.radii_refitted.dat<br> │ ├── out_apo_nosalt_Cl.rep2.radii_refitted.dat<br> │ ├── out_apo_nosalt_Cl.rep3.radii_refitted.dat<br> │ ├── out_apo_nosalt_Cl.rep4.radii_refitted.dat<br> │ ├── out_apo_nosalt_Cl.rep5.radii_refitted.dat<br> │ ├── out_apo_nosalt_ionless.rep1.radii_refitted.dat<br> │ ├── out_apo_nosalt_ionless.rep2.radii_refitted.dat<br> │ ├── out_apo_nosalt_ionless.rep3.radii_refitted.dat<br> │ ├── out_apo_nosalt_ionless.rep4.radii_refitted.dat<br> │ └── out_apo_nosalt_ionless.rep5.radii_refitted.dat<br> └── Sfig1<br> ├── distances_n_angles_fig2.pse<br> ├── occ_apo_nosalt_3ions.rep1.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_3ions.rep1.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_3ions.rep2.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_3ions.rep2.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_3ions.rep3.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_3ions.rep3.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_3ions.rep4.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_3ions.rep4.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_3ions.rep5.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_3ions.rep5.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_Cl.rep1.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_Cl.rep1.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_Cl.rep2.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_Cl.rep2.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_Cl.rep3.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_Cl.rep3.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_Cl.rep4.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_Cl.rep4.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_Cl.rep5.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_Cl.rep5.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_ionless.rep1.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_ionless.rep1.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_ionless.rep2.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_ionless.rep2.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_ionless.rep3.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_ionless.rep3.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_ionless.rep4.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_ionless.rep4.TM6a-TM9up.dat<br> ├── occ_apo_nosalt_ionless.rep5.TM6a-TM8down.dat<br> ├── occ_apo_nosalt_ionless.rep5.TM6a-TM9up.dat<br> ├── out_apo_nosalt_3ions.rep1.TM6a-TM8down.dat<br> ├── out_apo_nosalt_3ions.rep1.TM6a-TM9up.dat<br> ├── out_apo_nosalt_3ions.rep2.TM6a-TM8down.dat<br> ├── out_apo_nosalt_3ions.rep2.TM6a-TM9up.dat<br> ├── out_apo_nosalt_3ions.rep3.TM6a-TM8down.dat<br> ├── out_apo_nosalt_3ions.rep3.TM6a-TM9up.dat<br> ├── out_apo_nosalt_3ions.rep4.TM6a-TM8down.dat<br> ├── out_apo_nosalt_3ions.rep4.TM6a-TM9up.dat<br> ├── out_apo_nosalt_3ions.rep5.TM6a-TM8down.dat<br> ├── out_apo_nosalt_3ions.rep5.TM6a-TM9up.dat<br> ├── out_apo_nosalt_Cl.rep1.TM6a-TM8down.dat<br> ├── out_apo_nosalt_Cl.rep1.TM6a-TM9up.dat<br> ├── out_apo_nosalt_Cl.rep2.TM6a-TM8down.dat<br> ├── out_apo_nosalt_Cl.rep2.TM6a-TM9up.dat<br> ├── out_apo_nosalt_Cl.rep3.TM6a-TM8down.dat<br> ├── out_apo_nosalt_Cl.rep3.TM6a-TM9up.dat<br> ├── out_apo_nosalt_Cl.rep4.TM6a-TM8down.dat<br> ├── out_apo_nosalt_Cl.rep4.TM6a-TM9up.dat<br> ├── out_apo_nosalt_Cl.rep5.TM6a-TM8down.dat<br> ├── out_apo_nosalt_Cl.rep5.TM6a-TM9up.dat<br> ├── out_apo_nosalt_ionless.rep1.TM6a-TM8down.dat<br> ├── out_apo_nosalt_ionless.rep1.TM6a-TM9up.dat<br> ├── out_apo_nosalt_ionless.rep2.TM6a-TM8down.dat<br> ├── out_apo_nosalt_ionless.rep2.TM6a-TM9up.dat<br> ├── out_apo_nosalt_ionless.rep3.TM6a-TM8down.dat<br> ├── out_apo_nosalt_ionless.rep3.TM6a-TM9up.dat<br> ├── out_apo_nosalt_ionless.rep4.TM6a-TM8down.dat<br> ├── out_apo_nosalt_ionless.rep4.TM6a-TM9up.dat<br> ├── out_apo_nosalt_ionless.rep5.TM6a-TM8down.dat<br> ├── out_apo_nosalt_ionless.rep5.TM6a-TM9up.dat<br> └── Sfig1_v2.png</p> <p> </p>
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (1/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>Cneg</td> <td>RNASEQ-AVF1</td> <td>RNASEQ-AVF1_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF1_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF2</td> <td>RNASEQ-AVF2_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF2_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF3</td> <td>RNASEQ-AVF3_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF3_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF4</td> <td>RNASEQ-AVF4_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF4_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF5</td> <td>RNASEQ-AVF5_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF5_S5_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA A</td> <td>RNASEQ-AVF6</td> <td>RNASEQ-AVF6_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF6_S6_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA B</td> <td>RNASEQ-AVF7</td> <td>RNASEQ-AVF7_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF7_S7_R2_001.fastq.gz</td> </tr> <tr> <td>TDP-43 siRNA C</td> <td>RNASEQ-AVF8</td> <td>RNASEQ-AVF8_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF8_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
RNAseq sequences of the study "Transactive response DNA-binding Protein (TARDBP/TDP-43) regulates early HIV-1 entry and infection" (2/2)
<p>Each pair of FASTQ files corresponds to a specific sample condition:</p> <table> <thead> <tr> <th scope="col">Condition</th> <th scope="col">Sample</th> <th scope="col">FASTQ name R1</th> <th scope="col">FASTQ name R2</th> </tr> </thead> <tbody> <tr> <td>TDP-43 siRNA D</td> <td>RNASEQ-AVF9</td> <td>RNASEQ-AVF9_S1_R1_001.fastq.gz</td> <td>RNASEQ-AVF9_S1_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF10</td> <td>RNASEQ-AVF10_S2_R1_001.fastq.gz</td> <td>RNASEQ-AVF10_S2_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-wt-TDP-43</td> <td>RNASEQ-AVF11</td> <td>RNASEQ-AVF11_S3_R1_001.fastq.gz</td> <td>RNASEQ-AVF11_S3_R2_001.fastq.gz</td> </tr> <tr> <td>Flag-NLS-mut-TDP-43</td> <td>RNASEQ-AVF12</td> <td>RNASEQ-AVF12_S4_R1_001.fastq.gz</td> <td>RNASEQ-AVF12_S4_R2_001.fastq.gz</td> </tr> <tr> <td>Cneg</td> <td>RNASEQ-AVF13</td> <td>RNASEQ-AVF13_S5_R1_001.fastq.gz</td> <td>RNASEQ-AVF13_S5_R2_001.fastq.gz</td> </tr> <tr> <td>Scramble</td> <td>RNASEQ-AVF14</td> <td>RNASEQ-AVF14_S6_R1_001.fastq.gz</td> <td>RNASEQ-AVF14_S6_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos B+C</td> <td>RNASEQ-AVF15</td> <td>RNASEQ-AVF15_S7_R1_001.fastq.gz</td> <td>RNASEQ-AVF15_S7_R2_001.fastq.gz</td> </tr> <tr> <td>Oligos A+B+C</td> <td>RNASEQ-AVF16</td> <td>RNASEQ-AVF16_S8_R1_001.fastq.gz</td> <td>RNASEQ-AVF16_S8_R2_001.fastq.gz</td> </tr> </tbody> </table> <p> </p>
Dataset related to article. "Nonphosphorylated tau slows down Aβ1–42 aggregation, binds to Aβ1–42 oligomers, and reduces Aβ1–42 toxicity"
<p>Figures presented in the paper and their data can be found in the corresponding prism files (www.graphpad.com).<br> The raw data and the picture files for most of the figures can be found in the folder with the corresponding figure name.</p>
Supporting data files for "A consistent picture of phosphate-divalent cations binding from models with implicit and explicit electronic polarization"
<p>Additional supporting data for the paper "A consistent picture of phosphate-divalent cations binding from models with implicit and explicit electronic polarization". Includes parameter files, as well as typical input files and analysis scripts to reproduce the simulations.</p>
To what extent naringenin binding and membrane depolarization shape mitoBK channel gating - a machine learning approach (code and dataset)
<p>The dataset consists of dwell-time series (sampling frequency 100 kHz) of the mitoBK ion channel activation modulated by the naringenin binding and membrane<br> depolarization. It also contains the code written in Python, with the use of tslearn and scikit-learn packages, classifying the dwell-time subseries into right categories.</p> <p>The dataset is organized as follows. The mitoBK_ML.zip directory consists of two directories:</p> <ol> <li><strong>dwell times </strong>containing 5 subdirectories comprising groups of dwell-time subseries obtained at different pipette potentials and naringenin concentration. First number in the name od directory stands for the applied voltage in mV, whilst the second one denotes the naringenin concentration in µmol. For instance, directory named 20_3 means that the obtained dwell-times series were obtained at 20 mV (value of pipette potential) and 3 µmol (concentration of naringenin). These subdirectories are named as follows:</li> </ol> <ul> <li><strong>1group </strong>comprising dwell time series <strong>20_3, 40_1, 60_0</strong></li> <li><strong>2group</strong> comprising dwell-time series <strong>20_10, 60_1</strong></li> <li><strong>3group</strong> comprising dwell-time series <strong>40_10</strong>, <strong>60_3</strong></li> <li><strong>naringenina</strong> comprising dwell-time series <strong>60_0, 60_10</strong></li> <li><strong>voltage</strong> comprising dwell-time series <strong>20_10, 60_10</strong></li> </ul> <p><strong>1group, 2group and 3group</strong> contain the dwell-time series with approximately the same value of open-state probability of the ion channel.</p> <p>The <strong>naringenina</strong> contains the dwell-time series with the same value of potential (60 mV) and different values of naringenin concentration (0 µmol and 10 µmol). </p> <p>The <strong>voltage </strong>contains the dwell-time series with the same value of naringenin concentration (10 µmol) and different values of applied voltage (20 mV and 60 mV).</p> <p> 2. <strong>rslt </strong>is organized analogously to <strong>dwell times. </strong>The subdirectories are empty, but they will be filled with the results after launching the Python scripts placed in the <strong>knn_ion_channel.ipynb</strong> or <strong>shapelet_ion_channel.ipynb </strong>files.</p> <p>The Python code is placed in two files:</p> <ol> <li><strong>knn_ion_channel.ipynb </strong>containing kNN (<em>k-Nearest Neighbors</em>) algorithm classifying dwell-time series belonging to one of 5 different categories enumerated above: <strong>1group, 2group, 3group, naringenina, voltage</strong>. More detailed description of the code can be found inside uploaded Jupyter notebook.</li> <li><strong>shapelet_ion_channel.ipynb </strong>containing <em>shapelet-learning algorithm</em> classifying dwell-time series belonging to one of 5 different categories enumerated above. <strong>1group, 2group, 3group, naringenina, voltage. </strong>More detailed description of the code can be found inside uploaded Jupyter notebook.</li> </ol> <p> </p> <p> </p> <p> </p>
Structural basis for Parkinson's Disease-linked LRRK2's binding to microtubules
<p>This dataset includes all of the tabular data used in the figures in the article. Original article is available at: https://doi.org/10.1101/2022.01.21.477284</p> <p>Leucine Rich Repeat Kinase 2 (<em>LRRK2</em>) is one of the most commonly mutated genes in familial Parkinson’s Disease (PD). Under some circumstances, LRRK2 co-localizes with microtubules in cells, an association enhanced by PD mutations. We report a cryo-electron microscopy structure of the catalytic half of LRRK2, containing its kinase, which is in a closed conformation, and GTPase domains, bound to microtubules. We also report a structure of the catalytic half of LRRK1, which is closely related to LRRK2, but is not linked to PD. LRRK1’s structure is similar to LRRK2, but LRRK1 does not interact with microtubules. Guided by these structures, we identify amino acids in LRRK2’s GTPase domain that mediate microtubule binding; mutating them disrupts microtubule binding in vitro and in cells, without affecting LRRK2’s kinase activity. Our results have implications for the design of therapeutic LRRK2 kinase inhibitors.</p>
Simulation of Receptor Binding Domain of SARS-CoV-2 spike protein (WT and variants) in complex with neutralizing antibodies.
<p>This repository contains the molecular dynamics trajectories of the SARS-CoV-2 Spike RBD bound to BD23 and B38 monoclonal antibodies. The simulations for the RBD only systems are also provided. The trajectories are available for the WT spike protein as well as for four different variants (alpha, beta, kappa and delta). The simulations of the RBD only system are propagated for 300 ns and for the RBD-Antibody complex for 500 ns. The trajectories are saved at 100 ps interval. The Steered MD simulation trajectories (WT_RBD_B38_SMD_1.dcd etc.) and collective variables files are also included (WT_RBD_B38_SMD_1.colvars.traj etc.). There are 5 SMD trajectories for each RBD antibody pair. The details of the simulation can be obtained from the preprint: https://doi.org/10.1101/2021.08.13.456317</p>
Screening routine for integrative dynamic structural biology using SAXS and intramolecular FRET and DEER-EPR on hGBP1 (human guanalyte binding protein 1)
<p>Initial and selected ensemble for major and minor species of the human guanalyte binding protein 1 with scripts for the reading routine to combine and analyse jointly SAXS, EPR and FRET data.</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.