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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology
Identifying A Target Protein And Ligands For Autoimmune Disorders, Sarah Caruthers
Identifying A Target Protein And Ligands For Autoimmune Disorders, Sarah Caruthers
Computational and Data Sciences (MS) Theses
Systemic Lupus Erythematosus (SLE) is an autoimmune disorder characterized by unprovoked inflammatory responses that lead to tissue degradation. Patients suffering from SLE display an overexpression of master regulatory protein HIF-1 HIF-1is a transcription factor for pro-inflammatory cytokine interleukin-17A (IL-17A), which is highly involved in inflammatory reactions within the body. To search for a treatment for SLE, computer aided drug discovery techniques were utilized. The transcription factor complex for IL-17A was reconstructed through multiple protein docking techniques. The heteroprotein complex was profiled using 3D macromolecular visualization software and binding cavities within HIF-1 were calculated. Molecular docking simulations were run on the …
Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem
Automated Parsing Of Flexible Molecular Systems Using Principal Component Analysis And K-Means Clustering Techniques, Matthew J. Nwerem
Computational and Data Sciences (MS) Theses
Computational investigation of molecular structures and reactions of biological and pharmaceutical interests remains a grand scientific challenge due to the size and conformational flexibility of these systems. The work requires parsing and analyzing thousands of conformations in each molecular state for meaningful chemical information and subjecting the ensemble to costly quantum chemical calculations. The current status quo typically involves a manual process where the investigator must look at each conformation, separating each into structural families. This process is time-intensive and tedious, making this process infeasible in some cases, and limiting the ability of theoreticians to study these systems. However, the …
Computational Molecular Docking Models And Design Of Diarylpentanoids For The Androgen Receptor, Jarett Guillow
Computational Molecular Docking Models And Design Of Diarylpentanoids For The Androgen Receptor, Jarett Guillow
Computational and Data Sciences (MS) Theses
The androgen receptor (AR) is a member of the nuclear receptor protein family that, upon binding to its natural ligand dihydrotestosterone (DHT) in the cytoplasm, translocates to the nucleus and exerts nuclear transcription factor activity to drive gene expression related to normal prostate development. AR signaling becomes overactive during the development and progression of prostate cancer through different mechanisms, including over-expression and mutation of the AR. Therefore, the AR is a prominent molecular target in the clinical management of prostate cancer. However, all therapeutic modalities targeting the AR, including androgen ablation therapy and AR block suffer from transient efficacy and …