HIT web server: A hybrid method to improve electrostatic calculations for biomolecules

Shengjie Sun; Juan A Lopez; Yixin Xie; Wenhan Guo; Dongfang Liu; Lin Li

doi:10.1016/j.csbj.2022.03.022

HIT web server: A hybrid method to improve electrostatic calculations for biomolecules

Comput Struct Biotechnol J. 2022 Mar 24:20:1580-1583. doi: 10.1016/j.csbj.2022.03.022. eCollection 2022.

Authors

Shengjie Sun¹, Juan A Lopez², Yixin Xie¹, Wenhan Guo¹, Dongfang Liu³, Lin Li^{1

4}

Affiliations

¹ Computational Science Program, The University of Texas at El Paso, 500 W University Ave, TX 79968, USA.
² Department of Computer Science, The University of Texas at El Paso, 500 W University Ave, TX 79968, USA.
³ Department of Computer Engineering, Rochester Institute of Technology, Rochester, NY 14623, USA.
⁴ Department of Physics, the University of Texas at El Paso, 500 W University Ave, TX 79968, USA.

Abstract

The electrostatic features of highly charged biomolecules are crucial and challenging tasks in computational biophysics. The electrostatic calculations by traditional implicit solvent methods are efficient but have difficulties on highly charged biomolecules. We have developed a Hybridizing Ion Treatment (HIT) tool, which successfully hybridizes the explicit ions and implicit solvation model to accurately calculate the electrostatic potential for highly charged biomolecules. Here we implemented the HIT tool into a web server. In this study, a training set was prepared to optimize the number of frames for the HIT web server. The results on tubulins, DNAs, and RNAs, reveal the mechanisms for the motor proteins, DNA of HIV, and tRNA. This HIT web server can be widely used to study highly charged biomolecules, including DNAs, RNAs, molecular motors, and other highly charged biomolecules.

Keywords: DNA; Electrostatic calculation; Explicit solvent model; HIT; RNA; Tubulin.

Abstract

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