Showing posts from October, 2020

2D Plot and 3D Visualization of Protein-Ligand and Protein-Protein Interactions

Intermolecular interactions are weak bonds formed due to electron sharing between two or more atoms to hold a molecule together. In molecular modelling or computer-aided drug designing (CADD), intermolecular interaction studies are performed to analyze the stability/energy of docking molecules. This video tutorial demonstrates two-dimensional (2D) plot and three-dimensional (3D) molecular visualization of protein-ligand and protein-protein inter-molecular interactions using LigPlot+/LigPlus tool. LigPlot+ is a successor of original LigPlot program. The protein-ligand inter-molecular interactions are computed using LigPlot program and protein-protein or domain-domain inter-molecular interactions using DimPlot program. Moreover, the interactive 3D molecular visualization of the computed result can be viewed using RasMol or PyMOL. List of softwares used in this tutorial are LigPlot+, LigPlus, RasMol, PyMOL, and JDK.

Splitting PDB File into Chains and Ligands Without using Tools

Protein Data Bank (PDB) file format is a representation of a three-dimensional (3D) structure of the protein and ligand data extracted by interpreting the experimental result of high-energy electromagnetic radiation (X-ray) or Nuclear Magnetic Resonance (NMR) through the computational method. The standard PDB file format was created by RCSB during the 1970s for parsing through software.The atomic coordinate entries of protein are represented by ATOM & TER fields, and ligand by HETATM field (given in the table below).Record TypeColumnsDescriptionATOM1 - 4"ATOM"7 - 11Atom serial number13 - 16Atom name17Alternate location indicator18 - 20Residue name22Chain identifier23 - 26Residue sequence number27Code for insertions of residues31 - 38X orthogonal Å coordinate39 - 46Y orthogonal Å coordinate47 - 54Z orthogonal Å coordinate55 - 60Occupancy61 - 66Temperature factor73 - 76Segment identifier77 - 78Element symbol79 - 80ChargeHETATM1 - 6"HETATM"7 - 80same as ATOM recor…