VMD-SS: A graphical user interface plug-in to calculate the protein secondary structure in VMD program

Area of Science:

• Biochemistry and Molecular Biology
• Computational Biology
• Structural Biology

Background:

• Protein secondary structure (SS) analysis is crucial for understanding protein function and dynamics.
• Tracking SS evolution during molecular dynamics (MD) simulations provides insights into protein structural changes.
• Existing methods may not fully capture the dynamic nature of SS during simulations.

Purpose of the Study:

• To introduce VMD-SS, a novel software plugin for identifying secondary structure elements.
• To analyze the trajectories of secondary structures during molecular dynamics simulations.
• To provide quantitative measures of secondary structure evolution in proteins.

Main Methods:

• Developed VMD-SS using TCL script and the STRIDE algorithm.
• Utilized known protein structures from the Protein Data Bank (PDB).
• Simulated protein dynamics to generate trajectories for analysis.

Main Results:

• VMD-SS calculates percentage of secondary structure.
• It determines secondary structure occurrence per residue.
• The tool quantifies percentage secondary structure and residue distribution over simulation time.

Conclusions:

• VMD-SS facilitates the detailed analysis of protein secondary structure dynamics.
• The software aids in understanding protein folding pathways and conformational changes.
• It serves as a valuable tool for researchers studying protein structure-function relationships.