PROTEIN STRUCTURE VISUALIZATION AND COMPARISION S. Madhumitha 123011356021

Protein structural visualization tools

1. PROTEIN STRUCTURE VISUALIZATION AND COMPARISION SUBMITTED TO : Ms.P.MALA Assistant professor Department of biotechnology PMIST SUBMITTED BY; MADHUMITHA .S ll-M.Sc Biotechnology Computational biology

2. Protein structure visualization Protein structure visualization tools are software applications that allow users to view, manipulate, and analyze the three-dimensional (3D) structures of proteins and other biomolecules. These tools are essential for understanding the; molecular architecture , function, and interactions of proteins, designing new drugs and vaccines. There are many protein structure visualization tools available, each with different features, capabilities, and limitation.

3. Various types of tools are used in protein structure visualization: It includes; PyMOL RasMol CHIMERA PyMOL PyMOL is a popular and powerful molecular graphics software. Editing , and analyzing 3D structures of proteins and other biomolecules. PyMOL is written in Python and C, and can be extended and customized with Python scripts and plugins .

4. Features of PyMOL : Molecular visualization Structure manipulation (rotating, zooming, translating) Selection and labeling of atoms, residues, and chains Molecular surface and volume calculations Support for various file formats (PDB, CIF, MOL2, SDF, etc .) Visualization Options Cartoon representation Sticks representation Spheres representation

5. Steps involved in PyMOL : Step 1: Installation Download PyMOL . Install (e.g., Python, OpenGL). Step 2: Launching PyMOL 3D visualization window Step 3: Loading Molecules Open a molecular structure file (e.g., PDB, CIF, MOL2): File > Open Drag -and-drop file into PyMOL window Select molecule format (e.g., PDB, CIF): File > Open > Format

6. Step 4: Visualization Rotate, zoom, and translate molecule : Change representation: Cartoon Sticks Step 5: Selection and Labeling Select atoms, residues, or chains : Label selected atoms, residues, or chains Step 6: Measurements and Calculations Measure distances, angles, and torsions : Calculate molecular surface area and volume:

7. Step 7: Structure Analysis Analyze secondary structure: Tools > Secondary Structure Detect hydrogen bonds and salt bridges: Tools > Hydrogen Bonds/Salt Bridges  Step 8: Scripting and Automation Write scripts using PyMOL command language ( PyMOL CLI): Command line Step 9: Saving and Exporting Save molecular structure: File > Save Export images and movies: File > Export

8. RasMol RasMol is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules . The program has been developed at the University of Edinburgh's Biocomputing Research Unit and the Biomolecular Structure Department at Glaxo Research and Development, Greenford, UK. Features of RasMOL Molecular visualization Structure manipulation (rotating, zooming, translating) Selection and labeling of atoms, residues, and chains Support for various file formats (PDB, CIF, MOL2, SDF, etc.)

9. File Formats PDB (Protein Data Bank) CIF (Crystallographic Information File ) SDF (Structure Data File ) Steps involved in RasMol : Step 1: Installation Follow installation instructions for your operating system (Windows, macOS , or Linux ). Step 2: Launching RasMol Open RasMol on your computer . 3D visualization window

10. Step 3: Loading Molecules Open a molecular structure file (e.g., PDB, CIF, MOL2 ) Drag-and-drop file into RasMol window Step 4: Visualization Rotate, zoom, and translate molecule Change representation( ball,stick,cartoon ) Step 5: Selection and Labeling Select atoms, residues, or chains : Label selected atoms, residues, or chains: Step 6: Measurements and Calculations Measure distances, angles, and torsions : Calculate molecular surface area and volume:

11. Step 7: Structure Analysis Analyze secondary structure: Tools > Secondary Structure Detect hydrogen bonds and salt bridges: Tools > Hydrogen Bonds/Salt Bridges Step8: Scripting and Automation Write scripts using RasMol command language: Command line Use external scripts and plugins: Script Editor Step 9: Saving and Exporting Save molecular structure Export images and movies

12. UCSF CHIMERA : Definition: UCSF Chimera is a free, open-source molecular visualization and analysis software tool for displaying, manipulating, and analyzing molecular structures . Particularly visualize proteins, nucleic acids, and other biomolecules . Features: Molecular visualization Measurements and calculations Structure analysis Scripting and automation

13. Developed by: Resource for Biocomputing, Visualization, and Informatics (RBVI), University of California, San Francisco (UCSF ) steps to use UCSF Chimera: Step 1: Installation Download UCSF Chimera Step 2: Launching Chimera     - 3D visualization window     - Command line interface (CLI) Step 3: Loading Molecules 1. Open a molecular structure file     - Drag-and-drop file into Chimera window 2. Select the molecule format (e.g., PDB, CIF )    

14. Step 5: Selection and Labeling Select atoms, residues, or chains:     - Mouse selection     - Command line Label selected atoms, residues, or chains: Step 6: Measurements and Calculations Measure distances, angles, and torsions : 2 Calculate molecular surface area and volume : Step 7: Structure Analysis Analyze secondary structure:     Tools > Secondary Structure Detect hydrogen bonds and salt bridges:     - Tools > Hydrogen Bonds/Salt Bridges Step 8: Scripting and Automation     - Command line    

15. THANK YOU