ArticleAlgorithms for molecular biology : AMB2022
Adding hydrogen atoms to molecular models via fragment superimposition.
Article in Algorithms for molecular biology : AMB, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Atomic Charge Calculator III: a modern platform for calculating partial atomic charges.Nucleic acids research · 2026Article
- PROPTIMUS LIVE: local constrained α-carbon optimization of proteins.Nucleic acids research · 2026Article
- Experiment-guided AlphaFold3 resolves measurement-consistent protein ensembles.Nature biotechnology · 2026Article
- Dynamic stability-driven machine learning improves binding pose identification on human serum albumin.Journal of computer-aided molecular design · 2026Article
- PDBCharges: Quantum-Mechanical Partial Atomic Charges for PDB Structures.Nucleic acids research · 2025Article
- AlphaFold-Multimer accurately captures interactions and dynamics of intrinsically disordered protein regions.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Biotite: new tools for a versatile Python bioinformatics library.BMC bioinformatics · 2023Article
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Authors and funding
3 authors.
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Abstract
backgroundMost experimentally determined structures of biomolecules lack annotated hydrogen positions due to their low electron density. However, thorough structure analysis and simulations require knowledge about the positions of hydrogen atoms. Existing methods for their prediction are either limited to a certain range of molecules or only work effectively on small compounds.
resultsWe present a novel algorithm that compiles fragments of molecules with known hydrogen atom positions into a library. Using this library the method is able to predict hydrogen positions for molecules with similar moieties. We show that the method is able to accurately assign hydrogen atoms to most organic compounds including biomacromolecules, if a sufficiently large library is used.
conclusionsWe bundled the algorithm into the open-source Python package and command line program Hydride. Since usually no additional parametrization is necessary for the problem at hand, the software works out-of-box for a wide range of molecular systems usually within a few seconds of computation time. Hence, we believe that Hydride could be a valuable tool for structural biologists and biophysicists alike.
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