ArticleProteins2015
pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.
Article in Proteins, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 63 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
63 citing papers in PubMed, 126 citations in OpenAlex.
- In silico conformational dynamics of the α-actinin-2 actin-binding domain upon phosphorylation.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
- Osimertinib's Proton-Catalyzed, Pseudoconcerted EGFR Inhibition Guides Next-Generation Inhibitor Design.Journal of chemical information and modeling · 2026Article
- Structural analysis of the impact of germline mutations of p16 in melanoma prone families.Molecular diversity · 2025Article
- Article
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- A role for pH dynamics regulating transcription factor DNA-binding selectivity.Nucleic acids research · 2025Article
- Improved Structure-Based Histidine pJournal of chemical information and modeling · 2025Article
- On delivering polar solvation free energy of proteins from energy minimized structures using a regularized super-Gaussian Poisson-Boltzmann model.Journal of computational chemistry · 2025Article
- Adsorption of Diclofenac and PFBS on a Hair Keratin Dimer.The journal of physical chemistry. B · 2024Article
- Accurately Predicting Protein pJournal of chemical theory and computation · 2023Article
- Molecular Dynamics Force Field Parameters for the EGFP Chromophore and Some of Its Analogues.The journal of physical chemistry. B · 2023Article
- Article
- Protein pJournal of chemical theory and computation · 2022Article
- Prediction of protein pChemical science · 2022Article
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Pathogens (Basel, Switzerland) · 2022Article
- Evolutionary information helps understand distinctive features of the angiotensin II receptors AT1 and AT2 in amniota.PLoS computational biology · 2022Article
- Using a comprehensive approach to investigate the interaction between Kinesin-5/Eg5 and the microtubule.Computational and structural biotechnology journal · 2022Article
- Protein pACS omega · 2021Article
- The pH Effects on SARS-CoV and SARS-CoV-2 Spike Proteins in the Process of Binding to hACE2.Research square · 2021Article
3 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
We developed a Poisson-Boltzmann based approach to calculate the pKa values of protein ionizable residues (Glu, Asp, His, Lys and Arg), nucleotides of RNA and single stranded DNA. Two novel features were utilized: the dielectric properties of the macromolecules and water phase were modeled via the smooth Gaussian-based dielectric function in DelPhi and the corresponding electrostatic energies were calculated without defining the molecular surface. We tested the algorithm by calculating pKa values for more than 300 residues from 32 proteins from the PPD dataset and achieved an overall RMSD of 0.77. Particularly, the RMSD of 0.55 was achieved for surface residues, while the RMSD of 1.1 for buried residues. The approach was also found capable of capturing the large pKa shifts of various single point mutations in staphylococcal nuclease (SNase) from pKa-cooperative dataset, resulting in an overall RMSD of 1.6 for this set of pKa's. Investigations showed that predictions for most of buried mutant residues of SNase could be improved by using higher dielectric constant values. Furthermore, an option to generate different hydrogen positions also improves pKa predictions for buried carboxyl residues. Finally, the pKa calculations on two RNAs demonstrated the capability of this approach for other types of biomolecules.
Indexed as
Identifiers
What OpenQuestion holds
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.