Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
451
datasets available to search
ShareScore release 0.9.0
Dataset results
451 results for “Angiogenesis”
Angiogenesis Induced in the Elderly by Hyperbaric Oxygen Therapy
ClinicalTrials.gov study NCT02790541. IPD Sharing: UNDECIDED. Countries: 1. Publications: 1.
Angiogenesis Using VEGF-A165/bFGF Plasmid Delivered Percutaneously in No-option CAD Patients; a Controlled Trial
ClinicalTrials.gov study NCT00620217. IPD Sharing: Not stated. Countries: 1. Publications: 2.
Study of Cardiac Lesions Angiogenesis by 68Ga-NODAGA-RGD Cardiac PET
ClinicalTrials.gov study NCT03809689. IPD Sharing: NO. Countries: 1. Publications: 0.
Endothelial Damage and Angiogenesis Biomarkers During COVID-19
ClinicalTrials.gov study NCT04609332. IPD Sharing: NO. Countries: 1. Publications: 1.
Comparative analysis of angiogenesis models: MATLAB data files
Open the record for dataset details and reuse information.
Enhanced stromal H2S production via CBS upregulation promotes estrogen-stimulated human endometrial angiogenesis
Open the record for dataset details and reuse information.
Therapeutic Potential of the Laminin-1-Derived Peptide C16 in Interactions with αvβ3 and α5β1 Integrins: In Silico Analysis and Implications for Angiogenesis, Cancer, and Tissue Regeneration
<p>Molecular Dynamics<br><br>Molecular Docking there has also been performed molecular dynamics simulation studies by GROMACS 2023 to study the relationship between structure and function and properties by the analysis of molecular conformation sampling (cluster analysis, dominant conformation identification), interaction analysis (hydrogen bonding network, Contact-Map, Binding free energy calculations (MM-PBSA), backbone fluctuation analysis (RMSD, RMSF), Conformational transition analysis (simple normal mode analysis, dominant conformation identification), and physicochemical property analysis (energy, volume, pressure, temperature, density monitoring) (Luzik et al., 2019; Zhang et al., 2003).</p> <p>For simulation purposes, a simulation system was set up for the protein-ligand complex with solvent using GPU-enabled GROMACS 2024.2 package (Abraham et al., 2024). The αvβ3 and α5β1 in water simulation were performed with GROMACS standard protocols also, αvβ3_S1@C16, αvβ3_S2@C16, α5β1@C16 complex, and αvβ3, αvβ3 proteins MD simulation was carried out in triplicate. All necessary topology files were generated using CHARMM-GUI (Lee et al., 2016; Park et al., 2023). <br>CHARMM-GUI was used to build the simulation system (Allouche, 2012). And provided scripts compatible with GROMACS (Lee et al., 2016), provideding TIP3P water model to solvate the system.</p> <p>The dimensions of the box were defined by ensuring at least a 10 Å distance between the protein and the box edges to avoid boundary effects. Proper neutralization of the system was achieved by adding counterions (Na+ and Cl−) based on the protein’s charge automatically calculated by CHARMM-GUI. CHARMM36 force field was chosen, which provides parameters for proteins and peptides. Before the production MD simulation, energy minimization was performed to remove any unfavorable contacts or steric clashes in the system. CHARMM-GUI The system was equilibrated in two stages. First, the system was equilibrated under an NVT ensemble (constant number of particles, volume, and temperature) with restraints applied to the heavy atoms of the protein to allow the water and ions to relax around the solute. This phase runs for 100 ps. Second, the restraints were removed, and the system was equilibrated under an NPT ensemble (constant number of particles, pressure, and temperature) for an additional 1 ns to stabilize the density of the system (Galmozzi et al., 2014; K. W. Wang et al., 2022).</p> <p>The minimization, equilibration, and production steps were performed using the GROMACS 2024.2 The steepest-descent energy minimization was used, and the maximum force was set to 100 kJ/(mol∙nm) on any atom. The solvated system was equilibrated with two steps. First, the system was equilibrated for 1 ns under a constant volume ensemble (NVT) without restraints applied. Second, the system was equilibrated for another 1 ns under a constant pressure ensemble (NPT) without any restraint. Production simulation was conducted for 100 ns under the NPT ensemble. All bonds containing hydrogen atoms were constrained using the default LINCS constraint algorithm. The coupling algorithm of Nose-Hoover was used to maintain temperature (310 K) and Parrinello-Rahman algorithm to maintain temperature pressure (1 atm, 101 325 Pa) with a constant of 1.0 ps. The electrostatic interactions were treated with the particle mesh-Ewald (PME) method. The integration time step was set to 2 fs and periodic boundary conditions were applied in all directions (Bansal et al., 2021; H. Yu et al., 2015). </p> <p>2.4.1. MMPBSA analyses <br>GROMACS modules gmx rms for root mean square deviation (RMSD), gmx rmsf for root mean square fluctuation (RMSF), gmx hbond for numbers of hydrogen-bond (Hbond), gmx gyrate for the radius of gyration (Rg), gmx sasa for solvent accessible surface area (SASA) were used to analyze each complex system. The xmgrace module was employed to generate plots and graphs to represent binding energies, interaction frequencies, and structural changes. The Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) binding free energies like van der Waals and electrostatic interactions, potential energy, polar, and non-polar solvation energies were calculated by gmx_MMPBSA a tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files (Valdés-Tresanco et al., 2021). It has employed the visualization tools VMD and PyMOL to examine the trajectory and interaction details.</p> <p>References:</p> <p>Allouche, A. (2012). Software News and Updates Gabedit — A Graphical User Interface for Computational Chemistry Softwares. Journal of Computational Chemistry, 32, 174–182. https://doi.org/10.1002/jcc.</p> <p>Galmozzi, A., Dominguez, E., Cravatt, B. F., & Saez, E. (2014). CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application. Methods Enzymol., 538(1), 151–169.</p> <p>Bansal, R., Mohagaonkar, S., Sen, A., Khanam, U., & Rathi, B. (2021). In-silico study of peptide-protein interaction of antimicrobial peptides potentially targeting SARS and SARS-CoV-2 nucleocapsid protein. In Silico Pharmacology, 9(1), 1–14. https://doi.org/10.1007/s40203-021-00103-z.</p> <p>Park, S. J., Kern, N., Brown, T., Lee, J., & Im, W. (2023). CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation. Journal of Molecular Biology, 435(14), 167995. https://doi.org/10.1016/j.jmb.2023.167995.</p> <p>Lee, J., Cheng, X., Swails, J. M., Yeom, M. S., Eastman, P. K., Lemkul, J. A., Wei, S., Buckner, J., Jeong, J. C., Qi, Y., Jo, S., Pande, V. S., Case, D. A., Brooks, C. L., MacKerell, A. D., Klauda, J. B., & Im, W. (2016). CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field. Journal of Chemical Theory and Computation, 12(1), 405–413. https://doi.org/10.1021/acs.jctc.5b00935. </p> <p>Luzik, D. A., Rogacheva, O. N., Izmailov, S. A., Indeykina, M. I., Kononikhin, A. S., & Skrynnikov, N. R. (2019). Molecular Dynamics model of peptide-protein conjugation: case study of covalent complex between Sos1 peptide and N-terminal SH3 domain from Grb2. Scientific Reports, 9(1), 1–18. https://doi.org/10.1038/s41598-019-56078-7.</p> <p>Valdés-Tresanco, M. S., Valdés-Tresanco, M. E., Valiente, P. A., & Moreno, E. (2021). gmx\_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 17(10), 6281–6291. https://doi.org/10.1021/acs.jctc.1c00645.</p> <p>Wang, K. W., Lee, J., Zhang, H., Suh, D., & Im, W. (2022). CHARMM-GUI Implicit Solvent Modeler for Various Generalized Born Models in Different Simulation Programs. Journal of Physical Chemistry B, 126(38), 7354–7364. https://doi.org/10.1021/acs.jpcb.2c05294. </p> <p>Yu, H., Wang, M. jun, Xuan, N. xia, Shang, Z. cai, & Wu, J. (2015). Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides. Journal of Zhejiang University: Science B, 16(10), 883–896. https://doi.org/10.1631/jzus.B1500106. </p> <p>Zhang, Z., Shi, Y., & Liu, H. (2003). Molecular dynamics simulations of peptides and proteins with amplified collective motions. Biophysical Journal, 84(6), 3583–3593. https://doi.org/10.1016/S0006-3495(03)75090-5. </p>
Study of the Anti-Angiogenesis Agent Axitinib in Patients With Stage III Malignant Melanoma
ClinicalTrials.gov study NCT01321437. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Bone Marrow Angiogenesis in Acute Myeloid Leukemia - Evaluated by Dynamic Contrast Enhanced Magnetic Resonance (MR) Image
ClinicalTrials.gov study NCT00172562. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Angiogenesis With Positron Emission Tomography (PET) Tracer Uptake
ClinicalTrials.gov study NCT00671242. IPD Sharing: Not stated. Countries: 1. Publications: 1.
Effetivity of Dutasteride and Aloe Vera Extract Combination on Angiogenesis and Obstruction on Benign Prostatic Hyperplasia
ClinicalTrials.gov study NCT07065682. IPD Sharing: NO. Countries: 1. Publications: 0.
Anti-angiogenesis Agent AG-013736 in Patients With Advanced Non-Small Cell Lung Cancer
ClinicalTrials.gov study NCT00094094. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Study for Safety and Efficiency of Therapeutic Angiogenesis for Patients With Limb Ischemia by Transplantation of Human Cord Blood Mononuclear Cell
ClinicalTrials.gov study NCT00518934. IPD Sharing: Not stated. Countries: 1. Publications: 1.
A Proof-of-concept Study to Assess the Ability of [18F]AH-111585 PET Imaging to Detect Tumours and Angiogenesis
ClinicalTrials.gov study NCT00565721. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Neo-angiogenesis in Inguinal Henia Implant ProFlor
ClinicalTrials.gov study NCT04541316. IPD Sharing: YES. Countries: 0. Publications: 4.
The Inflammatory Response to Stress and Angiogenesis in Liver Resection
ClinicalTrials.gov study NCT03131778. IPD Sharing: NO. Countries: 0. Publications: 3.
Anti-Angiogenesis Agent AG-013736 In Patients With Metastatic Melanoma
ClinicalTrials.gov study NCT00094107. IPD Sharing: Not stated. Countries: 2. Publications: 0.
Functional Microscale Organotypic Assays to Predict Patient Response to Anti-Angiogenesis Therapies
ClinicalTrials.gov study NCT03387514. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Diabetic Kidney Disease Induces Transcriptome Alterations Associated with Angiogenesis Activity in Human Mesenchymal Stromal Cells [mRNA]
GEO Series GSE217709. Homo sapiens. 38 samples. Type: Expression profiling by high throughput sequencing.
Regulation of Angiogenesis by EZH2
GEO Series GSE20381. Homo sapiens. 12 samples. Type: Expression profiling by array.
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.