ArticleJournal of computational chemistry2017
DelPhiForce, a tool for electrostatic force calculations: Applications to macromolecular binding.
Article in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Local microenvironments of capsomer variants in the PBCV-1.Journal of structural biology · 2025Article
- Membrane Composition Modulates Vp54 Binding: A Combined Experimental and Computational Study.Pathogens (Basel, Switzerland) · 2025Article
- Elucidating the interactions between Kinesin-5/BimC and the microtubule: insights from TIRF microscopy and molecular dynamics simulations.Briefings in bioinformatics · 2025Article
- Review
- Bound ion effects: Using machine learning method to study the kinesin Ncd's binding with microtubule.Biophysical journal · 2024Article
- A novel approach to study multi-domain motions in JAK1's activation mechanism based on energy landscape.Briefings in bioinformatics · 2024Article
- Redox driven BNature communications · 2023Article
- Phosphorylation of Tyrosine 841 Plays a Significant Role in JAK3 Activation.Life (Basel, Switzerland) · 2023Article
- A Comprehensive Study on the Electrostatic Properties of Tubulin-Tubulin Complexes in Microtubules.Cells · 2023Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin.International journal of molecular sciences · 2022Article
- Molecular mechanisms of cardiac actomyosin transforming from rigor state to post-rigor state.The Journal of chemical physics · 2022Article
- Using a comprehensive approach to investigate the interaction between Kinesin-5/Eg5 and the microtubule.Computational and structural biotechnology journal · 2022Article
- HIT web server: A hybrid method to improve electrostatic calculations for biomolecules.Computational and structural biotechnology journal · 2022Article
- Computational Study on the Function of Palmitoylation on the Envelope Protein in SARS-CoV-2.Journal of chemical theory and computation · 2021Article
- In silico studies on stilbenolignan analogues as SARS-CoV-2 Mpro inhibitors.Chemical physics letters · 2021Article
- Electrostatic features for nucleocapsid proteins of SARS-CoV and SARS-CoV-2.Mathematical biosciences and engineering : MBE · 2021Article
- Computational Study on DNA Repair: The Roles of Electrostatic Interactions Between Uracil-DNA Glycosylase (UDG) and DNA.Frontiers in molecular biosciences · 2021Article
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3 authors.
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Abstract
Long-range electrostatic forces play an important role in molecular biology, particularly in macromolecular interactions. However, calculating the electrostatic forces for irregularly shaped molecules immersed in water is a difficult task. Here, we report a new tool, DelPhiForce, which is a tool in the DelPhi package that calculates and visualizes the electrostatic forces in biomolecular systems. In parallel, the DelPhi algorithm for modeling electrostatic potential at user-defined positions has been enhanced to include triquadratic and tricubic interpolation methods. The tricubic interpolation method has been tested against analytical solutions and it has been demonstrated that the corresponding errors are negligibly small at resolution 4 grids/Å. The DelPhiForce is further applied in the study of forces acting between partners of three protein-protein complexes. It has been demonstrated that electrostatic forces play a dual role by steering binding partners (so that the partners recognize their native interfaces) and exerting an electrostatic torque (if the mutual orientations of the partners are not native-like). The output of DelPhiForce is in a format that VMD can read and visualize, and provides additional options for analysis of protein-protein binding. DelPhiForce is available for download from the DelPhi webpage at http://compbio.clemson.edu/downloadDir/delphiforce.tar.gz © 2017 Wiley Periodicals, Inc.
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