Computational Biophysics and Bioinformatics
Professor Emil Alexov Group
Electrostatic interactions and forces play important role in molecular biology. DelPhiForce is a tool to calculate and visualize (via VMD) the electrostatic forces provided 3D structure of biological macromolecule(s). It can be used to calculate the electrostatic forces in protein-protein, protein-DNA/RNA complexes, and domains within the same biological macromolecule. The electrostatic forces are calculated at each atom, residue or molecule. The tcl file generated by DelPhiForce is visualized by VMD (see Figure 1).
Li, Lin, Arghya Chakravorty, and Emil Alexov. "DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding." Journal of Computational Chemistry 38.9 (2017): 584-593.
https://www.ncbi.nlm.nih.gov/pubmed/28130775
Figure 1: tubulin-dynein binding domain complex. Dynein binding domain (blue ribbon presentation) is moved 10A away from its X-ray position for better visualization. The electrostatic forces generated by tubulin are calculated with DelPhiForce and visualized with VMD (shown as arrows). The size of the arrows indicates the magnitude of the force.