ReviewBiophysical reviews2017
Development of constant-pH simulation methods in implicit solvent and applications in biomolecular systems.
Review in Biophysical reviews, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed.
- The Effects of pH on Orientations of Adsorbed Lysozyme on Negatively Charged Surfaces.The journal of physical chemistry. B · 2026Article
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- "Air-Lock" gating mechanism of CsoS1D for metabolite translocation through the α-carboxysome shell.Plant physiology · 2026Article
- Challenges in simulating whole virus particles and how to fix them with the SIRAH force field.Biophysical reviews · 2025Review
- 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
- phbuilder: A Tool for Efficiently Setting up Constant pH Molecular Dynamics Simulations in GROMACS.Journal of chemical information and modeling · 2024Article
- Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants.Colloids and surfaces. B, Biointerfaces · 2023Article
- Rheology and Gelation of Hyaluronic Acid/Chitosan Coacervates.Biomolecules · 2022Article
- Protein pJournal of chemical theory and computation · 2022Article
- Prediction of protein pChemical science · 2022Article
- Titr-DMD-A Rapid, Coarse-Grained Quasi-All-Atom Constant pH Molecular Dynamics Framework.Journal of chemical theory and computation · 2021Article
- Up State of the SARS-COV-2 Spike Homotrimer Favors an Increased Virulence for New Variants.Frontiers in medical technology · 2021Article
- Molecular simulations unravel the molecular principles that mediate selective permeability of carboxysome shell protein.Scientific reports · 2020Article
- Theoretical Modeling of Chemical Equilibrium in Weak Polyelectrolyte Layers on Curved Nanosystems.Polymers · 2020Review
- On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2.Virus research · 2020Article
- Understanding and Controlling Food Protein Structure and Function in Foods: Perspectives from Experiments and Computer Simulations.Annual review of food science and technology · 2020Review
- Article
- Coarse-grained dynamic RNA titration simulations.Interface focus · 2019Article
- Insights into the ZIKV NS1 Virology from Different Strains through a Fine Analysis of Physicochemical Properties.ACS omega · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
pH is a critical parameter for biological and technological systems directly related with electrical charges. It can give rise to peculiar electrostatic phenomena, which also makes them more challenging. Due to the quantum nature of the process, involving the forming and breaking of chemical bonds, quantum methods should ideally by employed. Nevertheless, due to the very large number of ionizable sites, different macromolecular conformations, salt conditions, and all other charged species, the CPU time cost simply becomes prohibitive for computer simulations, making this a quite complex problem. Simplified methods based on Monte Carlo sampling have been devised and will be reviewed here, highlighting the updated state-of-the-art of this field, advantages, and limitations of different theoretical protocols for biomolecular systems (proteins and nucleic acids). Following a historical perspective, the discussion will be associated with the applications to protein interactions with other proteins, polyelectrolytes, and nanoparticles.
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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.