eSupervisor Detail

PyMol is the software used to visualise and analyse the protein structure, not just the protein itself. This helps you examine the interaction between the protein and its associated ligand. Protein structures are submitted to the RCSB Data Bank (https://www.rcsb.org/), and the submitted structures are viewed in PyMol. You can also download the structure of the Protein directly from the RCSB Data Bank and open the structure of the Protein in PyMol for further analysis. Link To PyMOL Basics. Link to download the softwareiCn3D (Interactive Cn3D, https://lnkd.in/gNPhx6xe) is a web-based tool developed by the National Center for Biotechnology Information for visualizing and analyzing 3D structures of biomolecules like proteins and DNA.It runs directly in a browser (no installation needed) and integrates sequence, structure, and annotation data in one interface. Researchers and students use it to explore molecular interactions, view protein domains, highlight mutations, and share interactive 3D scenes via links.In short: iCn3D is an easy-to-use online platform for interactive 3D visualization of biological molecules. You can understand about the effect of particular mutation in the protein active site whether mutation impair the binding of the protein ligand interaction so that you can easily manipulate and study the effect of the mutation in the enzyme activity and other binding assays

You can superimpose the homologous protein structures using PyMOL to better understand how structural conservation relates to substrate binding.Using PyMOL’s align and super commands, I superimposed protein structures based on their backbone atoms, minimizing RMSD and highlighting conserved folds and active-site geometry:Once the structures were aligned, the sequence alingment file of the superimposed structure is used to look at the conservation of the substrate binding site using differnt tools like Clutal Omega, Muscle, KA align and other tools.To visualize conserved regions—especially around the substrate-binding ESPript is used which integrates sequence alignment with secondary structure annotation. This makes it much easier to pinpoint conserved amino acids that are likely critical for substrate recognition and catalytic activity.This combined structural and sequence-based approach provides valuable insights into how proteins maintain function despite sequence variation.

Protein Structural superposition and RMSD calculation using RCSB pairwise alignment tools (https://www.rcsb.org/alignment). Steps involved in RCSB pairwise Alignment: A) Fetching the structure of all the homologous structures using the RCSB, and with the pairwise alignment option in RCSB, protein structures are superimposed. RMSD is easily calculated using a single reference structure.