ArticleComputational and structural biotechnology journal2022
HIT web server: A hybrid method to improve electrostatic calculations for biomolecules.
Article in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.Biophysical journal · 2024Article
- A Comparative Analysis of SARS-CoV-2 Variants of Concern (VOC) Spike Proteins Interacting with hACE2 Enzyme.International journal of molecular sciences · 2024Article
- A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape.Briefings in bioinformatics · 2024Article
- HIT-2: Implementing machine learning algorithms to treat bound ions in biomolecules.Computational and structural biotechnology journal · 2023Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
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Authors and funding
6 authors.
Funding
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.
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