ArticleComputational science & discovery2012
Finite Element Estimation of Protein-Ligand Association Rates with Post-Encounter Effects: Applications to Calcium binding in Troponin C and SERCA.
Article in Computational science & discovery, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
14 citing papers in PubMed.
- Myofilament-associated proteins with intrinsic disorder (MAPIDs) and their resolution by computational modeling.Quarterly reviews of biophysics · 2023Review
- Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.Biophysical journal · 2022Article
- Structural Changes beyond the EF-Hand Contribute to Apparent Calcium Binding Affinities: Insights from Parvalbumins.The journal of physical chemistry. B · 2021Article
- Co-localization and confinement of ecto-nucleotidases modulate extracellular adenosine nucleotide distributions.PLoS computational biology · 2020Article
- Structural and dynamic basis of substrate permissiveness in hydroxycinnamoyltransferase (HCT).PLoS computational biology · 2018Article
- Quantifying the Influence of the Crowded Cytoplasm on Small Molecule Diffusion.The journal of physical chemistry. B · 2016Article
- Enzyme localization, crowding, and buffers collectively modulate diffusion-influenced signal transduction: Insights from continuum diffusion modeling.The Journal of chemical physics · 2015Article
- Computing volume potentials for noninvasive imaging of cardiac excitation.Annals of noninvasive electrocardiology : the official journal of the International Society for Holter and Noninvasive Electrocardiology, Inc · 2015Article
- Electrostatic channeling in P. falciparum DHFR-TS: Brownian dynamics and Smoluchowski modeling.Biophysical journal · 2014Article
- Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation.The Journal of chemical physics · 2014Article
- Computational modeling of subcellular transport and signaling.Current opinion in structural biology · 2014Review
- A model study of sequential enzyme reactions and electrostatic channeling.The Journal of chemical physics · 2014Article
- Molecular and subcellular-scale modeling of nucleotide diffusion in the cardiac myofilament lattice.Biophysical journal · 2013Article
- Influence of neighboring reactive particles on diffusion-limited reactions.The Journal of chemical physics · 2013Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
We introduce a computational pipeline and suite of software tools for the approximation of diffusion-limited binding based on a recently developed theoretical framework. Our approach handles molecular geometries generated from high-resolution structural data and can account for active sites buried within the protein or behind gating mechanisms. Using tools from the FEniCS library and the APBS solver, we implement a numerical code for our method and study two Ca(2+)-binding proteins: Troponin C and the Sarcoplasmic Reticulum Ca(2+) ATPase (SERCA). We find that a combination of diffusional encounter and internal 'buried channel' descriptions provide superior descriptions of association rates, improving estimates by orders of magnitude.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.