ArticleBiophysical journal2004
Finite element solution of the steady-state Smoluchowski equation for rate constant calculations.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.PLoS computational biology · 2020Article
- Can enzyme proximity accelerate cascade reactions?Scientific reports · 2019Article
- Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).PLoS computational biology · 2018Article
- Understanding ligand-receptor non-covalent binding kinetics using molecular modeling.Frontiers in bioscience (Landmark edition) · 2017Review
- Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion.The journal of physical chemistry. B · 2016Article
- Multiscale Estimation of Binding Kinetics Using Brownian Dynamics, Molecular Dynamics and Milestoning.PLoS computational biology · 2015Article
- Numerical calculation of protein-ligand binding rates through solution of the Smoluchowski equation using smoothed particle hydrodynamics.BMC biophysics · 2015Article
- Multi-core CPU or GPU-accelerated Multiscale Modeling for Biomolecular Complexes.Molecular based mathematical biology · 2013Article
- Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.Computational science & discovery · 2012Article
- Hybrid finite element and Brownian dynamics method for diffusion-controlled reactions.The Journal of chemical physics · 2012Article
- Multi-Scale Continuum Modeling of Biological Processes: From Molecular Electro-Diffusion to Sub-Cellular Signaling Transduction.Computational science & discovery · 2012Article
- Differential geometry based solvation model II: Lagrangian formulation.Journal of mathematical biology · 2011Article
- Dynamical basis for drug resistance of HIV-1 protease.BMC structural biology · 2011Article
- MIBPB: a software package for electrostatic analysis.Journal of computational chemistry · 2011Article
- Mechanisms of protein-ligand association and its modulation by protein mutations.Biophysical journal · 2011Article
- Differential geometry based solvation model I: Eulerian formulation.Journal of computational physics · 2010Article
- Quantitative understanding of cell signaling: the importance of membrane organization.Current opinion in biotechnology · 2010Review
- Poisson-Nernst-Planck Equations for Simulating Biomolecular Diffusion-Reaction Processes I: Finite Element Solutions.Journal of computational physics · 2010Article
- Kinetics of diffusion-controlled enzymatic reactions with charged substrates.PMC biophysics · 2010Article
- Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer.Biophysical journal · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
This article describes the development and implementation of algorithms to study diffusion in biomolecular systems using continuum mechanics equations. Specifically, finite element methods have been developed to solve the steady-state Smoluchowski equation to calculate ligand binding rate constants for large biomolecules. The resulting software has been validated and applied to mouse acetylcholinesterase. Rates for inhibitor binding to mAChE were calculated at various ionic strengths with several different reaction criteria. The calculated rates were compared with experimental data and show very good agreement when the correct reaction criterion is used. Additionally, these finite element methods require significantly less computational resources than existing particle-based Brownian dynamics methods.
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Registered trials
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