ArticleJournal of computational biophysics and chemistry2023
PKAD-2: New entries and expansion of functionalities of the database of experimentally measured pKa's of proteins.
Article in Journal of computational biophysics and chemistry, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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13 citing papers in PubMed, 23 citations in OpenAlex.
- Genetic Incorporation of Diverse Noncanonical Amino Acids for Histidine Substitution.Journal of the American Chemical Society · 2026Article
- Protein Electrostatic Properties are Finetuned Through Evolution.bioRxiv : the preprint server for biology · 2026Article
- Graph-Based Deep Learning Models for Predicting pJournal of chemical information and modeling · 2026Article
- A diverse and chemically relevant solvation model benchmark set with flexible molecules and conformer ensembles.Chemical science · 2025Article
- PKAD-R: curated, redesigned and expanded database of experimental pKa values in proteins.Journal of computational biophysics and chemistry · 2025Article
- Predicting residue ionization of OmpF channel using Constant pH Molecular Dynamics as benchmark.PLoS computational biology · 2025Article
- Accurate Predictions of Molecular Properties of Proteins via Graph Neural Networks and Transfer Learning.Journal of chemical theory and computation · 2025Article
- Protein Electrostatic Properties are Fine-Tuned Through Evolution.Research square · 2025Article
- 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
- Enhanced and Efficient Predictions of Dynamic Ionization through Constant-pH Adiabatic Free Energy Dynamics.Journal of chemical theory and computation · 2024Article
- PypKa server: online pKa predictions and biomolecular structure preparation with precomputed data from PDB and AlphaFold DB.Nucleic acids research · 2024Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Almost all biological reactions are pH dependent and understanding the origin of pH dependence requires knowledge of the pKa's of ionizable groups. Here we report a new edition of PKAD, the PKAD-2, which is a database of experimentally measured pKa's of proteins, both wild type and mutant proteins. The new additions include 117 wild type and 54 mutant pKa values, resulting in total 1742 experimentally measured pKa's. The new edition of PKAD-2 includes 8 new wild type and 12 new mutant proteins, resulting in total of 220 proteins. This new edition incorporates a visual 3D image of the highlighted residue of interest within the corresponding protein or protein complex. Hydrogen bonds were identified, counted, and implemented as a search feature. Other new search features include the number of neighboring residues <4A from the heaviest atom of the side chain of a given amino acid. Here, we present PKAD-2 with the intention to continuously incorporate novel features and current data with the goal to be used as benchmark for computational methods.
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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 Socratic graph.