ReviewMethods in enzymology2016
Continuum Electrostatics Approaches to Calculating pKas and Ems in Proteins.
Review in Methods in enzymology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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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
21 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
- Electrostatic Engineering of Phosphoketolase Enhances Activity on Small Nonphosphorylated Sugars and Improves Cell-Free ATP Regeneration from Inexpensive C2-Substrates.The journal of physical chemistry. B · 2026Article
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Development of a pKa predictor (pKaLearn) by leveraging teaching experience to improve machine learning.Communications chemistry · 2026Article
- Charge Neutralization During Peptide Transport in the Bacterial SecYEG Translocon.Biomolecules · 2025Article
- Testing a Heterogeneous Polarizable Continuum Model against Exact Poisson Boundary Conditions.Journal of chemical theory and computation · 2025Article
- Comparative Analysis of pACS omega · 2025Article
- Computation suggests that the cell adhesion sub-proteome is enriched for sites of pH-dependence and charge burial.PloS one · 2025Article
- Delineating redox cooperativity in water-soluble and membrane multiheme cytochromes through protein design.Protein science : a publication of the Protein Society · 2024Article
- The oxidation of the [4Fe-4S] cluster of DNA primase alters the binding energies with DNA and RNA primers.Biophysical journal · 2024Article
- Fluctuation Relations to Calculate Protein Redox Potentials from Molecular Dynamics Simulations.Journal of chemical theory and computation · 2024Article
- Tools for analyzing protonation states and for tracing proton transfer pathways with examples from the Rb. sphaeroides photosynthetic reaction centers.Photosynthesis research · 2023Article
- Cysteine Oxidation in Proteins: Structure, Biophysics, and Simulation.Biochemistry · 2022Review
- Characterizing Protein Protonation Microstates Using Monte Carlo Sampling.The journal of physical chemistry. B · 2022Article
- The Physical Basis for pH Sensitivity in Biomolecular Structure and Function, With Application to the Spike Protein of SARS-CoV-2.Frontiers in molecular biosciences · 2022Review
- A model for pH coupling of the SARS-CoV-2 spike protein open/closed equilibrium.Briefings in bioinformatics · 2021Article
- A Newton-like iterative method implemented in the DelPhi for solving the nonlinear Poisson-Boltzmann equation.Mathematical biosciences and engineering : MBE · 2020Article
- Standard state free energies, not pKJournal of computer-aided molecular design · 2020Article
- Molecular dynamics simulations in photosynthesis.Photosynthesis research · 2020Review
- Electrostatic Environment of Proteorhodopsin Affects the pKa of Its Buried Primary Proton Acceptor.Biophysical journal · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Proteins change their charge state through protonation and redox reactions as well as through binding charged ligands. The free energy of these reactions is dominated by solvation and electrostatic energies and modulated by protein conformational relaxation in response to the ionization state changes. Although computational methods for calculating these interactions can provide very powerful tools for predicting protein charge states, they include several critical approximations of which users should be aware. This chapter discusses the strengths, weaknesses, and approximations of popular computational methods for predicting charge states and understanding the underlying electrostatic interactions. The goal of this chapter is to inform users about applications and potential caveats of these methods as well as outline directions for future theoretical and computational research.
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Registered trials
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