Benchmark data set for "PDBTools.jl: A Lightweight and High-Performance Julia Package for Molecular Structure File Handling and Analysis"

PDBTools.jl v3.24.2 Benchmark

Software Versions

Software
Version

PDBTools.jl
v3.24.2

GROMACS
2026.1

VMD
1.9.4a57

RustSASA
v0.9.2

Biopython
1.87

MDAnalysis
2.10

Hardware

Benchmarks were executed on a desktop computer with the following specifications:

CPU: 13th Gen Intel Core i7-13700KF

RAM: 32 GB

GPU: NVIDIA GeForce RTX 4060 Ti

Storage: Kingston NV2 NVMe SSD

Network: Realtek RTL8125 2.5GbE

All benchmarks were run single-threaded. VMD is the only package that uses the GPU in these computations.

Methodology

Reported times are the mean of three consecutive runs.

For PDBTools.jl, one warm-up run was performed before timing to exclude Julia just-in-time (JIT) compilation overhead.

Unless otherwise stated, timings exclude file reading, atom selection, and output writing.

GROMACS was the only exception, because these steps could not be separated from the command-line workflow.

For VMD, the file-opening overhead was estimated from the loading time of a single-atom PDB file and subtracted from the reported times.

Benchmark Systems

Structures were obtained from the Protein Data Bank and contained only protein atoms.

The first 11 systems were protein structures; the remaining nine were viral capsid structures.

No periodic boundary conditions were used.

Analysis Parameters

Analysis
Parameters

SASA
2000 surface points per atom; probe radius 1.4 Å

Contact maps
Contact cutoff 4.0 Å

Hydrogen bonds
Structures solvated in TIP3P water (Packmol); donor–acceptor distance cutoff 3.5 Å; angle cutoff 30°

For hydrogen-bond analysis, protein–water hydrogen bonds were analyzed.

References

Humphrey, W.; Dalke, A.; Schulten, K. VMD: Visual Molecular Dynamics. J Mol Graph 1996, 14 (1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5

Abraham, M. J. et al. GROMACS: High Performance Molecular Simulations through Multi-Level Parallelism from Laptops to Supercomputers. SoftwareX 2015, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001

Gowers, R. et al. MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations. In Proceedings of the Python in Science Conference; SciPy, 2016; pp 98–105. https://doi.org/10.25080/majora-629e541a-00e

Campbell, M. J. RustSASA: A Rust Crate for Accelerated Solvent Accessible Surface Area Calculations. J. Open Source Softw. 2026, 11 (117), 9537. https://doi.org/10.21105/joss.09537