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1,321 results for “HIV-1”
Simulation and analysis data set for apo-conformational kinetics and gated ligand binding to HIV-1 protease
<p>The data set provided here accompanies a study described in the manuscript:</p> <p>S. Kashif Sadiq, Abraham Muñiz Chicharro, Patrick Friedrich, Rebecca Wade, A multiscale approach for computing gated ligand binding from molecular dynamics and Brownian dynamics simulations. (2021) Preprint available: https://doi.org/10.1101/2021.06.22.449380</p> <p>This study combines molecular dynamics MD simulations and associated conformational analyses and Markov state models (MSMs) with Brownian dynamics (BD) simulations to compute conformation gated ligand association kinetics to HIV-1 protease.</p> <p>To download the data, go to a directory where you would like to download the files. Then for each of the provided tar files enter the following command:</p> <p>tar xvf $X.tar</p> <p>where $X is the name prefix of the corresponding tar file.</p> <p>The unpacked data set creates a ./data sub-directory which itself contains two further sub-directories: MD and BD. Please see README.txt files within these sub directories for further instructions on the software tools and scripts that have been provided therein for using and reproducing the data set. The MD README.txt is found within: data_MD_MSM_analysis.tar, the BD README.txt is found within: data_BD_examples.tar.</p> <p>Please note, the python Jupyter notebook and associated module for further analysis of the MSM from the pre-defined feature set calculated in the study as well as other analyses can also be found at:</p> <p>https://github.com/kashifsadiq/hiv1pr-msm/</p> <p>MD trajectory files are provided for further analysis but are not required to reproduce the MSM and conformational analyses reported in the study. To facilitate overview, MSM analysis has been stored in several object files. To exactly reproduce the reported MD/MSM analyses, untar only the 1) data_MD_MSM_analysis.tar and 2) data_MD_MSMobj.tar files and work through the python Jupyter notebook.</p> <p> </p>
Data from: HIV-1 capsid stability enables inositol phosphate-independent infection of target cells and promotes integration into genes
<p>The mature HIV-1 capsid is stabilized by host and viral determinants. The capsid protein CA binds to the cellular metabolites inositol hexakisphosphate (IP6) and its precursor inositol (1, 3, 4, 5, 6) pentakisphosphate (IP5) to stabilize the mature capsid. In target cells, capsid destabilization by the antiviral compounds lenacapavir and PF74 reveals an HIV-1 infectivity defect due to IP5/IP6 (IP5/6) depletion. To test whether intrinsic HIV-1 capsid stability and/ or host factor binding determines HIV-1 insensitivity to IP5/6 depletion, a panel of CA mutants was assayed for infection of IP5/6-depleted T cells and wildtype cells. Four CA mutants with unstable capsids exhibited dependence on host IP5/6 for infection and reverse transcription (RTN). Adaptation of one such mutant, Q219A, by spread in culture resulted in Vpu truncation and a capsid three-fold interface mutation, T200I. T200I increased intrinsic capsid stability as determined by <em>in vitro</em> uncoating of purified cores and partially reversed the IP5/6-dependence in target cells for each of the four CA mutants. T200I further rescued the changes to lenacapavir sensitivity associated with the parental mutation. The premature dissolution of the capsid caused by the IP5/6-dependent mutations imparted a unique defect in integration targeting that was rescued by T200I. Collectively, these results demonstrate that T200I restored other capsid functions after RTN for the panel of mutants. Thus, the hyperstable T200I mutation stabilized the instability defects imparted by the parental IP5/6-dependent CA mutation. The contribution of Vpu truncation to mutant adaptation was linked to BST-2 antagonization, suggesting that cell-to-cell transfer promoted replication of the mutants. We conclude that interactions at the three-fold interface are adaptable, key mediators of capsid stability in target cells and are able to antagonize even severe capsid instability to promote infection.</p>
Figure S1: Phylogenetic tree of HIV-1 subtype D
<p>Figure S1: Phylogenetic tree of HIV-1 subtype D, branches with Brazilian sequences are highlighted: (a) Maximum likelihood tree of 1945 HIV-1 subtype D sequences; (b) Highlighted branch with Brazilian sequences from Rio Grande do Sul; (c) Highlighted branch with a Brazilian sequence from Pará; (d) Highlighted branch with a Brazilian sequence from Goiás; (e) Highlighted branch with a Brazilian sequence from São Paulo; (f) Highlighted branch with another Brazilian sequence from Pará; (g) Highlighted branch with Brazilian sequences from Rio de Janeiro; (h) Highlighted branch with a Brazilian sequence from Rio de Janeiro; (i) Highlighted branch of the major Brazilian clade; (j) Highlighted branch with another Brazilian sequence from Pará.</p>
Clinical Study of TUTI-16 in HIV-1 Infected and Uninfected Subjects
ClinicalTrials.gov study NCT01144026. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Pharmacokinetics of Atazanavir/Ritonavir in HIV-1 Infected Pregnant Women
ClinicalTrials.gov study NCT00326716. IPD Sharing: Not stated. Countries: 3. Publications: 3.
Switch Study to Evaluate F/TAF in HIV-1 Infected Adults Who Are Virologically Suppressed on Regimens Containing ABC/3TC
ClinicalTrials.gov study NCT02469246. IPD Sharing: YES. Countries: 12. Publications: 2.
Safety of and Immune Response to Dolutegravir in HIV-1 Infected Infants, Children, and Adolescents
ClinicalTrials.gov study NCT01302847. IPD Sharing: Not stated. Countries: 8. Publications: 6.
Cobicistat-containing Highly Active Antiretroviral Regimens in HIV-1 Infected Patients With Mild to Moderate Renal Impairment
ClinicalTrials.gov study NCT01363011. IPD Sharing: Not stated. Countries: 9. Publications: 2.
A Study of Heterologous Vaccine Regimen of Adenovirus Serotype 26 Mosaic4 Human Immunodeficiency Virus(Ad26.Mos4.HIV), Adjuvanted Clade C gp140 and Mosaic gp140 to Prevent HIV-1 Infection Among Cis-ge
ClinicalTrials.gov study NCT03964415. IPD Sharing: YES. Countries: 9. Publications: 1.
Pharmacodynamics, Safety and Pharmacokinetics of BMS-663068, an HIV Attachment Inhibitor, in HIV-1
ClinicalTrials.gov study NCT01009814. IPD Sharing: Not stated. Countries: 1. Publications: 3.
HIV-1 Infection Study of Once a Day Versus Twice a Day Protease Inhibitor in Antiretroviral Treatment Naive Adults
ClinicalTrials.gov study NCT00450580. IPD Sharing: Not stated. Countries: 9. Publications: 2.
Oral Islatravir (MK-8591) Once-Monthly as Preexposure Prophylaxis (PrEP) in Men and Transgender Women Who Are at High Risk for HIV-1 Infection (MK-8591-024)
ClinicalTrials.gov study NCT04652700. IPD Sharing: YES. Countries: 7. Publications: 0.
Study to Evaluate the Safety and Efficacy of Bictegravir/Emtricitabine/Tenofovir Alafenamide Versus Abacavir/Dolutegravir/Lamivudine in Human Immunodeficiency Virus-1 (HIV-1) Infected, Antiretroviral
ClinicalTrials.gov study NCT02607930. IPD Sharing: YES. Countries: 10. Publications: 9.
Switch Study to Evaluate the Safety and Efficacy of Emtricitabine/Rilpivirine/Tenofovir Alafenamide (FTC/RPV/TAF) Fixed Dose Combination (FDC) in HIV-1 Positive Adults Who Are Virologically Suppressed
ClinicalTrials.gov study NCT02345252. IPD Sharing: YES. Countries: 12. Publications: 2.
Maraviroc Plus Darunavir/Ritonavir for Treatment-Naïve Patients Infected With R5-tropic HIV-1
ClinicalTrials.gov study NCT00993148. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Dolutegravir Plus Lamivudine Dual Therapy in Treatment Naïve HIV-1 Patients
ClinicalTrials.gov study NCT02582684. IPD Sharing: Not stated. Countries: 2. Publications: 2.
Antiviral Activity of Peg-IFN-Alpha-2A in Chronic HIV-1 Infection
ClinicalTrials.gov study NCT00594880. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Safety and Efficacy of E/C/F/TAF (Genvoya®) Versus E/C/F/TDF (Stribild®) in HIV-1 Infected, Antiretroviral Treatment-Naive Adults
ClinicalTrials.gov study NCT01497899. IPD Sharing: YES. Countries: 2. Publications: 1.
Evaluating the Safety and Pharmacokinetics of PC-1005 Administered Rectally to HIV-1 Seronegative Adults
ClinicalTrials.gov study NCT03408899. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Changes in Cerebral Function in Treatment Naive HIV-1 Infected Subjects Commencing Either Boosted Atazanavir With Truvada or Boosted Darunavir With Maraviroc and Kivexa
ClinicalTrials.gov study NCT01367236. IPD Sharing: NO. Countries: 1. Publications: 1.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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International Brain Laboratory public data
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OpenNeuro
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