ArticleJournal of computational chemistry2009
MCCE2: improving protein pKa calculations with extensive side chain rotamer sampling.
Article in Journal of computational chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 111 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
111 citing papers in PubMed.
- Engineered Protein-Based Ionic Conductors for Sustainable Energy Storage Applications.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- High-yield charge separation along the alternative path in a photosynthetic reaction center: X-ray structure and electrostatic analysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Kinase inhibitors can change protonation or tautomeric state upon binding.bioRxiv : the preprint server for biology · 2026Article
- Benchmark Study for Calculations of pKa Values of Metal Ligands in Proteins.Journal of chemical theory and computation · 2026Article
- Mechanism of Hydrolytic Instability of ZIF‑8 in Aqueous and Buffered Media: Implications on Drug Delivery Applications.ACS omega · 2026Article
- Development of a pKa predictor (pKaLearn) by leveraging teaching experience to improve machine learning.Communications chemistry · 2026Article
- Binding pose depth modulates photoswitchable ligands' efficacy at the 5-HTCommunications chemistry · 2026Article
- The Protonic Brain: Nanoscale pH Dynamics, Proton Wires, and Acid-Base Information Coding in Neural Tissue.International journal of molecular sciences · 2026Review
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- KaMLs for Predicting Protein pJournal of chemical theory and computation · 2025Article
- Improved Structure-Based Histidine pJournal of chemical information and modeling · 2025Article
- KaMLs for Predicting Protein pbioRxiv : the preprint server for biology · 2025Article
- Article
- MFSD1 with its accessory subunit GLMP functions as a general dipeptide uniporter in lysosomes.Nature cell biology · 2024Article
- The oxidation of the [4Fe-4S] cluster of DNA primase alters the binding energies with DNA and RNA primers.Biophysical journal · 2024Article
- Titratable residues that drive RND efflux: Insights from molecular simulations.QRB discovery · 2024Review
- Accurately Predicting Protein pJournal of chemical theory and computation · 2023Article
- Comparative Performance of High-Throughput Methods for Protein pJournal of chemical information and modeling · 2023Article
- PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins.Journal of computational biophysics and chemistry · 2023Article
- A perspective on the sharing of docking data.Data in brief · 2023Article
51 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.
Funding
Abstract
Multiconformation continuum electrostatics (MCCE) explores different conformational degrees of freedom in Monte Carlo calculations of protein residue and ligand pK(a)s. Explicit changes in side chain conformations throughout a titration create a position dependent, heterogeneous dielectric response giving a more accurate picture of coupled ionization and position changes. The MCCE2 methods for choosing a group of input heavy atom and proton positions are described. The pK(a)s calculated with different isosteric conformers, heavy atom rotamers and proton positions, with different degrees of optimization are tested against a curated group of 305 experimental pK(a)s in 33 proteins. QUICK calculations, with rotation around Asn and Gln termini, sampling His tautomers and torsion minimum hydroxyls yield an RMSD of 1.34 with 84% of the errors being <1.5 pH units. FULL calculations adding heavy atom rotamers and side chain optimization yield an RMSD of 0.90 with 90% of the errors <1.5 pH unit. Good results are also found for pK(a)s in the membrane protein bacteriorhodopsin. The inclusion of extra side chain positions distorts the dielectric boundary and also biases the calculated pK(a)s by creating more neutral than ionized conformers. Methods for correcting these errors are introduced. Calculations are compared with multiple X-ray and NMR derived structures in 36 soluble proteins. Calculations with X-ray structures give significantly better pK(a)s. Results with the default protein dielectric constant of 4 are as good as those using a value of 8. The MCCE2 program can be downloaded from http://www.sci.ccny.cuny.edu/~mcce.
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.