Dr Jayarama Reddy Foundation| Homology Modeling| SWISS-MODEL| Query Sequence| Protein Data Bank скачать в хорошем качестве

Dr Jayarama Reddy Foundation| Homology Modeling| SWISS-MODEL| Query Sequence| Protein Data Bank

Subscribe to    / @drjayaramareddyfoundation:   You are welcome to join Dr. Jayarama Reddy Online University in a way that suits you. Visit: www.drjayaramareddy.com Homology Modeling Using SWISS-MODEL: Protocol and Uses: Introduction: Homology modeling (comparative modeling) is a computational method used to predict the three-dimensional (3D) structure of a protein based on its amino acid sequence and the known structure of a homologous protein (template). SWISS-MODEL is an automated, web-based protein structure homology modeling server developed by the Swiss Institute of Bioinformatics. ________________________________________ Protocol for Homology Modeling Using SWISS-MODEL 1. Accessing SWISS-MODEL • Open the SWISS-MODEL server: https://swissmodel.expasy.org • Choose “Start Modelling” → Automated Mode or Template Search Mode. ________________________________________ 2. Input Query Sequence • Paste the protein sequence in FASTA format or upload a sequence file. • Ensure the sequence is complete and contains only standard amino acids. ________________________________________ 3. Template Identification • SWISS-MODEL automatically searches the Protein Data Bank (PDB) for suitable templates using BLAST and HHblits. • Templates are selected based on: o Sequence identity o Alignment coverage o Experimental resolution of structure ________________________________________ 4. Target–Template Alignment • The query sequence is aligned with the selected template. • Accurate alignment ensures reliable structural prediction, especially in conserved regions. ________________________________________ 5. Model Building • The 3D model is generated by: o Copying conserved backbone coordinates from the template o Remodeling insertions and deletions o Optimizing side-chain conformations ________________________________________ 6. Model Quality Assessment SWISS-MODEL provides several validation scores: • GMQE (Global Model Quality Estimation) • QMEAN score (overall and per-residue quality) • Ramachandran plot • Local quality estimates Higher GMQE and QMEAN values indicate better model reliability. ________________________________________ 7. Visualization and Download • The predicted structure can be viewed in the interactive 3D viewer. • Models can be downloaded in PDB format for further analysis. ________________________________________ Uses of Homology Modeling Using SWISS-MODEL 1. Protein Structure Prediction o Predicts 3D structures when experimental methods are unavailable. 2. Functional Annotation of Proteins o Helps infer protein function based on structural similarity. 3. Drug Design and Molecular Docking o Provides structural models for ligand binding and drug screening. 4. Understanding Structure–Function Relationships o Identifies active sites, binding pockets, and functional residues. 5. Mutation and Disease Studies o Analyzes structural effects of mutations and polymorphisms. 6. Comparative Structural Analysis o Compares protein structures across species. 7. Protein Engineering o Assists in rational design and modification of proteins. 8. Teaching and Research Applications o Widely used in bioinformatics and structural biology education. ________________________________________ Conclusion Homology modeling using SWISS-MODEL is a robust and user-friendly approach for predicting protein 3D structures. Its automated workflow, reliable template selection, and comprehensive quality assessment make it an essential tool in bioinformatics, structural biology, and biotechnology research.