ArticleJournal of chemical information and modeling2026
PDBTools.jl: A Lightweight and High-Performance Julia Package for Molecular Structure File Handling and Analysis.
Article in Journal of chemical information and modeling, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.
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Who cites it
1 citing paper in PubMed.
- From Hydrogen Bonding to Hydrophobic Control: The Shifting Solvation Mechanism of Ibuprofen in Deep Eutectic Solvents.The journal of physical chemistry. B · 2026Article
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2 authors.
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Abstract
We present PDBTools.jl, a lightweight and high-performance Julia package for reading, writing, selecting, and analyzing molecular structure data stored in PDB and mmCIF (PDBx) file formats. The package provides a compact and memory-efficient atom representation based on inline strings and single-precision floating-point coordinates, enabling the handling of very large structures on standard hardware. A flexible and customizable atom selection syntax inspired by VMD is augmented by native support for arbitrary Julia functions as selectors, offering exceptional expressiveness and performance for dynamic queries. Beyond file I/O and selection, PDBTools.jl includes high-performance implementations of key structural analysis algorithms: solvent-accessible surface area (SASA) calculation via the Shrake-Rupley method with Fibonacci lattice sampling, hydrogen bond detection, contact and distance maps, backbone dihedral angles for Ramachandran analysis, secondary structure assignment through integration with STRIDE and DSSP, and protein transfer free energy (
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