ArticleJournal of cheminformatics2014
Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes.
Article in Journal of cheminformatics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
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- A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.bioRxiv : the preprint server for biology · 2026Article
- Deciphering the groove-binding mode of dolutegravir with salmon sperm DNA through spectroscopic and molecular modelling approaches.Scientific reports · 2026Article
- Natural Product-like Fragments Unlock Novel Chemotypes for a Kinase Target─Exploring Options beyond the Flatland.Journal of chemical information and modeling · 2026Article
- Structure-Guided Discovery of CHI3L1 Inhibitors from Ultralarge Chemical Spaces for Glioblastoma Therapy.ACS omega · 2026Article
- Design, synthesis, and anticancer activity of novel isocryptolepine 'aza' type acyl thiourea derivatives via combined experimental and computational approach.Bioscience reports · 2026Article
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- Article
- LigExtract: Large-scale Automated Identification of Ligands from Protein Structures in the Protein Data Bank.Genomics, proteomics & bioinformatics · 2025Article
- Aspartic acid residues in BBE-like enzymes fromProceedings of the National Academy of Sciences of the United States of America · 2025Article
- A Self-Consistent Approach to Rotamer and Protonation State Assignments (RAPA): Moving Beyond Single Protein Configurations.Journal of chemical information and modeling · 2025Article
- ProteinsPlus: a publicly available resource for protein structure mining.Nucleic acids research · 2025Article
- Discovery of Novel Inhibitors ofMolecules (Basel, Switzerland) · 2025Article
24 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The calculation of hydrogen positions is a common preprocessing step when working with crystal structures of protein-ligand complexes. An explicit description of hydrogen atoms is generally needed in order to analyze the binding mode of particular ligands or to calculate the associated binding energies. Due to the large number of degrees of freedom resulting from different chemical moieties and the high degree of mutual dependence this problem is anything but trivial. In addition to an efficient algorithm to take care of the complexity resulting from complicated hydrogen bonding networks, a robust chemical model is needed to describe effects such as tautomerism and ionization consistently. We present a novel method for the placement of hydrogen coordinates in protein-ligand complexes which takes tautomers and protonation states of both protein and ligand into account. Our method generates the most probable hydrogen positions on the basis of an optimal hydrogen bonding network using an empirical scoring function. The high quality of our results could be verified by comparison to the manually adjusted Astex diverse set and a remarkably low rate of undesirable hydrogen contacts compared to other tools.
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