PROTEOMICS HOMOLOGY MODELING AND NGS ANALYSIS OF ACUTE MYELOID LEUKEMIA

Abstract

The research employed an integrated approach utilizing various bioinformatics tools and databases to comprehensively analyze the molecular and structural aspects of the studied protein. PubChem was utilized for extracting information about the drugs used in the study, showcasing its significance in providing access to biological activities of small molecules. The protein structure, identified by the PDB ID 6U9N, was retrieved from the Protein Data Bank (PDB), emphasizing the importance of this repository in offering three-dimensional structural data crucial for diverse scientific applications. Rasmol and PyMOL were employed for visualizing and analyzing the protein structure, demonstrating their roles in facilitating molecular visualization and structural analysis. Sequence similarity and phylogenetic analysis were performed using BLAST and COBALT, respectively, showcasing their utility in exploring biological sequences and conducting multiple sequence alignments. KEGG software was employed for pathway analysis, highlighting its importance in understanding complex biological pathways. For protein-drug docking, CB Dock2 was used, emphasizing its user-friendly approach to blind docking. Further analysis of protein properties utilized ExPASyProtParam and PDBePISA, demonstrating their roles in computing physicochemical properties and analyzing macromolecular interfaces. Phyre2 was employed for secondary structure prediction and sequence similarity, showcasing its utility in predicting protein structures. STRING was used to predict protein-protein interactions and functional associations. ERRAT and SAVES were employed for assessing the quality of protein structures, emphasizing their significance in structural validation. The comprehensive use of these tools and databases provides a thorough understanding of the protein's structural, functional, and interaction characteristics, contributing valuable insights to the field of molecular and structural biology.