ArticleBiophysical journal2018
GRPY: An Accurate Bead Method for Calculation of Hydrodynamic Properties of Rigid Biomacromolecules.
Article in Biophysical journal, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- On the curvature and relaxation of microtubule plus-end tips.Biophysical journal · 2026Article
- Bead model hydrodynamics: an in-depth comparison between GRPY and ZENO.European biophysics journal : EBJ · 2025Article
- Hydrodynamic properties of macromolecules and nanoparticles in dilute solution: a brief essay on classical and modern concepts.European biophysics journal : EBJ · 2025Article
- On the importance of the diffusivity gradient term in Brownian dynamics simulations.Biophysical journal · 2024Article
- Hydrodynamic Radii of Intrinsically Disordered Proteins: Fast Prediction by Minimum Dissipation Approximation and Experimental Validation.The journal of physical chemistry letters · 2024Article
- Magnetically locked Janus particle clusters with orientation-dependent motion in AC electric fields.Nanoscale · 2023Article
- Beyond the US-SOMO-AF database: a new website for hydrodynamic, structural, and circular dichroism calculations on user-supplied structures.European biophysics journal : EBJ · 2023Article
- The hydrodynamic motion of Nanodiscs.Chemistry and physics of lipids · 2019Article
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Authors and funding
3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Two main problems that arise in the context of hydrodynamic bead modeling are an inaccurate treatment of bead overlaps and the necessity of using volume corrections when calculating intrinsic viscosity. We present a formalism based on the generalized Rotne-Prager-Yamakawa approximation that successfully addresses both of these issues. The generalized Rotne-Prager-Yamakawa method is shown to be highly effective for the calculation of transport properties of rigid biomolecules represented as assemblies of spherical beads of different sizes, both overlapping and nonoverlapping. We test the method on simple molecular shapes as well as real protein structures and compare its performance with other computational approaches.
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