ArticleScientific reports2016
Multiscale method for modeling binding phenomena involving large objects: application to kinesin motor domains motion along microtubules.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Electrostatics and disease: Large-scale assessment of human missense variants causing protein charge alterations and their implications for disease.Biophysical journal · 2026Article
- Deciphering the role of tubulin's C-terminal tail in kinesin binding using computational and clustering approaches.Scientific reports · 2026Article
- Electrostatics in Computational Biophysics and Its Implications for Disease Effects.International journal of molecular sciences · 2022Review
- Long-range electrostatic interactions significantly modulate the affinity of dynein for microtubules.Biophysical journal · 2022Article
- Computational Study on E-Hooks of Tubulins in the Binding Process with Kinesin.International journal of molecular sciences · 2022Article
- 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
- Hybrid method for representing ions in implicit solvation calculations.Computational and structural biotechnology journal · 2021Article
- A computational model of ESAT-6 complex in membrane.Journal of theoretical & computational chemistry · 2020Article
- StructureMan: A Structure Manipulation Tool to Study Large Scale Biomolecular Interactions.Frontiers in molecular biosciences · 2020Article
- Spike Proteins of SARS-CoV and SARS-CoV-2 Utilize Different Mechanisms to Bind With Human ACE2.Frontiers in molecular biosciences · 2020Article
- DelPhi Suite: New Developments and Review of Functionalities.Journal of computational chemistry · 2019Article
- Modeling Electrostatic Force in Protein-Protein Recognition.Frontiers in molecular biosciences · 2019Article
- Prediction of pKa Values for Neutral and Basic Drugs based on Hybrid Artificial Intelligence Methods.Scientific reports · 2018Article
- Divide-and-conquer strategy for large-scale Eulerian solvent excluded surface.Communications in information and systems · 2018Article
- Forces and Disease: Electrostatic force differences caused by mutations in kinesin motor domains can distinguish between disease-causing and non-disease-causing mutations.Scientific reports · 2017Article
- Accurate, robust, and reliable calculations of Poisson-Boltzmann binding energies.Journal of computational chemistry · 2017Article
- A New DelPhi Feature for Modeling Electrostatic Potential around Proteins: Role of Bound Ions and Implications for Zeta-Potential.Langmuir : the ACS journal of surfaces and colloids · 2017Article
- Cytoplasmic dynein binding, run length, and velocity are guided by long-range electrostatic interactions.Scientific reports · 2016Article
- Revealing the mechanism of SARS-CoV-2 spike protein binding with ACE2.Computing in science & engineeringArticle
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Many biological phenomena involve the binding of proteins to a large object. Because the electrostatic forces that guide binding act over large distances, truncating the size of the system to facilitate computational modeling frequently yields inaccurate results. Our multiscale approach implements a computational focusing method that permits computation of large systems without truncating the electrostatic potential and achieves the high resolution required for modeling macromolecular interactions, all while keeping the computational time reasonable. We tested our approach on the motility of various kinesin motor domains. We found that electrostatics help guide kinesins as they walk: N-kinesins towards the plus-end, and C-kinesins towards the minus-end of microtubules. Our methodology enables computation in similar, large systems including protein binding to DNA, viruses, and membranes.
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