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24
datasets available to search
ShareScore release 0.7.1
Dataset results
24 results for “glycosaminoglycans”
Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations to Accurately Model Glycosaminoglycan Electrostatic Interactions
<p>To cite and for more details: Riopedre-Fernandez et al. <em>J. Chem. Inf. Model.</em> <strong>2024</strong>, 64 (18), 7122–7134. DOI: <a href="https://doi.org/10.1021/acs.jcim.4c00981">https://doi.org/10.1021/acs.jcim.4c00981</a></p> <p>The dataset includes molecular dynamics simulations of sulfated saccharides and their sulfated analogs in the presence of calcium cations in aqueous solution. Several force field parameter sets were compared (CHARMM36, GLYCAM06, AMOEBA, Drude) and new have been developed (prosECCo75 and GLYCAM-ECC75).</p> <p>The uploaded files contain the following simulation input files or/and simulation trajectories:</p> <p>1) Sulfated_Molecules_Umbrella_Sampling_AIMD: Umbrella sampling ab initio molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.</p> <p>2) Sulfated_Molecules_Umbrella_Sampling_FFMD: Umbrella sampling force field molecular dynamics simulations of calcium-methylsufate and calcium N-methylsulfamate ion pairs in water.</p> <p>3) Sulfated_Molecules_AWH_FFMD: Accelerated weight histogram force field molecular dynamics simulations of calcium interacting with both methylsufate and N-methylsulfamate in water.</p> <p>4) Disaccharides_FFMD: Unbiased force field molecular dynamics simulations of calcium-sulfated disaccharide aqueous solutions.</p> <p>UPD. Version 2.0 has updated one of the disaccharide-containing simulations (GLYCAM06, N-sulfation) due to incorrect calcium LJ parameters in the original upload.</p>
Molecular dynamics simulation files for: a molecular machine efficiently drives glycosaminoglycan assembly and secretion for osteoarthritis therapy
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MRI Analysis of Glycosaminoglycan Modifications Inside the Intervertebral Disk After Distraction and Posterior Fusion
ClinicalTrials.gov study NCT02815696. IPD Sharing: NO. Countries: 1. Publications: 5.
Glycosaminoglycan Scores as Monitoring Biomarkers in Advanced Renal Cell Carcinoma
ClinicalTrials.gov study NCT02732665. IPD Sharing: YES. Countries: 1. Publications: 1.
Intravesical Glycosaminoglycan Instillation and Urinary Tract Infection in Acute Spinal Cord Injury
ClinicalTrials.gov study NCT03945110. IPD Sharing: YES. Countries: 1. Publications: 4.
Effects of Osteotomies Around the Knee on Cartilage Glycosaminoglycan Content Using dGEMRIC Non-invasive Imaging
ClinicalTrials.gov study NCT01269944. IPD Sharing: Not stated. Countries: 1. Publications: 3.
Benign Prostatic Hyperplasia and Glycosaminoglycan
ClinicalTrials.gov study NCT03955484. IPD Sharing: UNDECIDED. Countries: 1. Publications: 6.
Glycosaminoglycan Scores as Monitoring Biomarkers in Confined Renal Cell Carcinoma
ClinicalTrials.gov study NCT02732652. IPD Sharing: YES. Countries: 1. Publications: 1.
Respiratory Cathepsins, Proteases Inhibitors and Glycosaminoglycans (GAG) in Mucopolysaccharidosis
ClinicalTrials.gov study NCT04112602. IPD Sharing: Not stated. Countries: 1. Publications: 9.
Selectin-targeting glycosaminoglycan-peptide conjugate limits neutrophil-mediated cardiac reperfusion injury
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Data from: Influences of sodium and glycosaminoglycans on skin edema and the potential for ulceration: a finite element approach
Venous ulcers are chronic transcutaneous wounds common in the lower legs. They are resistant to healing and have a 78% chance of recurrence within two years. It is commonly accepted that venous ulcers are caused by the insufficiency of the calf muscle pump, leading to blood pooling in the lower legs, resulting in inflammation, skin edema, tissue necrosis and eventually skin ulceration. However, the detailed physiological events by which inflammation contributes to wound formation are poorly understood. We therefore sought to develop a model that simulated the inflammation, using it to determine the internal stresses and pressure on the skin that contribute to venous ulcer formation. A three-layer Finite Element skin model (epidermis, dermis and hypodermis) was developed to explore the roles in wound formation of two inflammation identifiers: Glycosaminoglycans (GAGs) and sodium. A series of parametric studies showed that increased GAGs and sodium content lead to edema and increased tissue stresses of 1.5 MPa, which was within the reported range of skin tissue Ultimate Tensile Stress (0.1-40 MPa). These results suggested that both the edema and increased fluid pressure could reach a threshold for tissue damage and eventual ulcer formation. The models presented here provide insights to the pathological events associated with venous insufficiency including inflammation, edema, and skin ulceration.
Plasma Glycosaminoglycans as Diagnostic and Prognostic Biomarkers in Surgically Treated Renal Cell Carcinoma
ClinicalTrials.gov study NCT03471897. IPD Sharing: NO. Countries: 0. Publications: 1.
Data from: Influences of sodium and glycosaminoglycans on skin edema and the potential for ulceration: a finite element approach
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Glycosaminoglycan-driven lipoprotein uptake protects tumours from ferroptosis
GEO Series GSE296260. Homo sapiens. 36 samples. Type: Expression profiling by high throughput sequencing.
AURORAX-0093A: Glycosaminoglycan Profiling for Prognostication of Muscle-invasive Bladder Cancer - a Pilot Study
ClinicalTrials.gov study NCT05028660. IPD Sharing: UNDECIDED. Countries: 3. Publications: 0.
Glycosaminoglycan Scores as Early Detection Biomarkers in Bladder Urothelial Carcinoma
ClinicalTrials.gov study NCT05799456. IPD Sharing: NO. Countries: 1. Publications: 0.
A Study Investigating the Relationship Between the Development of Laronidase Antibody and Urinary GAG (Glycosaminoglycan) Levels in Aldurazyme® Treated Patients
ClinicalTrials.gov study NCT00144768. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Glycosaminoglycans During Septic Shock - a Temporal Study
ClinicalTrials.gov study NCT00814112. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Patient iPSC-derived neural stem cells display progressive enlargement of lysosomes and disruptions of glycosaminoglycan pathway and autophagy in concordance with clinical severity of Mucopolysacchari
GEO Series GSE111906. Homo sapiens. 12 samples. Type: Expression profiling by high throughput sequencing.
To study glycosaminoglycan (GAG) glycogene expression in cutaneous lupus erythematosus (CLE) skin lesions and normal skin
GEO Series GSE29938. Homo sapiens. 27 samples. Type: Expression profiling by array.
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