Software Tools
Hybrid Ions Treatment
Calculate the bound ions for biomolecules from MD simulation trajectories.
HIT-2 Download HIT DownloadWe humbly ask to cite this reference if your results from this web server are used in publications.
Sun, Shengjie, et al. "HIT-2: Implementing machine learning algorithms to treat bound ions in biomolecules." Computational and Structural Biotechnology Journal 21 (2023): 1383-1389.
Sun, Shengjie, et al. "Hybrid method for representing ions in implicit solvation calculations." Computational and Structural Biotechnology Journal 19 (2021): 801-811.
Biomolecule Structure Manipulation
A tool to perform some geometric operations for biomolecules, which can be used to study molecule-molecule interactions. The operations includes shifting a ligand at distances from receptor, rotate a ligand around the receptor, spin a ligand, expand capsomers of a virus, etc.
DownloadWe humbly ask to cite this reference if your results from this web server are used in publications.
Xian, Y., Xie, Y., Silva, S. M., Karki, C. B., Qiu, W., & Li, L. (2021). StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions. Frontiers in molecular biosciences, 7, 476.
Other useful tools
DelPhi
A package which is widely used to calculate the electrostatic potential, electrostatic surfaces, electrostatic binding energies for biomolecules.
http://compbio.clemson.edu/delphi
DelPhiForce
A tool to calculate the electrostatic binding forces for biomolecules. It can be used to study molecule-molecule recognitions.
http://compbio.clemson.edu/delphi-force/