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Peer-reviewedCC BY 4.0Journal of Chemical Information and Modeling

GroScore: Automated Scoring of Protein–Protein Interactions Using Bidirectional Steered Molecular Dynamics

  • Jan Walther Perthold1
  • Dražen Petrov2
  • Chris Oostenbrink2,3
  1. 1Independent Researcher, Vienna 1130, Austria
  2. 2Institute for Molecular Modeling and Simulation, Department of Natural Sciences and Sustainable Resources, BOKU University, Muthgasse 18, Vienna 1190, Austria
  3. 3Christian Doppler Laboratory for Molecular Informatics in the Biosciences, BOKU University, Muthgasse 18, Vienna 1190, Austria
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Abstract

GroScore is an open-source Python toolkit that automates the scoring of protein–protein structures using bidirectional steered molecular dynamics (SMD) simulations with explicit solvent. Building on a previously published unidirectional pulling approach, the current version introduces bidirectional pulling (unbinding and rebinding), interface cutout for reduced computational cost, support for three force fields (AMBER19SB, CHARMM36m, GROMOS 54A8), and automated handling of small molecules and noncanonical amino acids (using OpenFF), structural ions, and crystal waters. GroScore integrates with GROMACS and SLURM for high-performance computing and is validated on protein–protein affinity benchmarks, showing significant correlation between computed scores and experimental binding affinities across all tested force fields. The software is freely available at https://github.com/jwperthold/GroScore under the MIT License.

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Cite

BibTeXRIS
BibTeX
@article{perthold2026groscore,
  title = {{GroScore: Automated Scoring of Protein–Protein Interactions Using Bidirectional Steered Molecular Dynamics}},
  author = {Jan Walther Perthold and Dražen Petrov and Chris Oostenbrink},
  journal = {Journal of Chemical Information and Modeling},
  year = {2026},
  month = oct,
  doi = {10.1021/acs.jcim.6c01771},
  url = {https://doi.org/10.1021/acs.jcim.6c01771},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - GroScore: Automated Scoring of Protein–Protein Interactions Using Bidirectional Steered Molecular Dynamics
AU  - Jan Walther Perthold
AU  - Dražen Petrov
AU  - Chris Oostenbrink
PY  - 2026
DA  - 2026/10/02
JO  - Journal of Chemical Information and Modeling
DO  - 10.1021/acs.jcim.6c01771
UR  - https://doi.org/10.1021/acs.jcim.6c01771
AB  - GroScore is an open-source Python toolkit that automates the scoring of protein–protein structures using bidirectional steered molecular dynamics (SMD) simulations with explicit solvent. Building on a previously published unidirectional pulling approach, the current version introduces bidirectional pulling (unbinding and rebinding), interface cutout for reduced computational cost, support for three force fields (AMBER19SB, CHARMM36m, GROMOS 54A8), and automated handling of small molecules and noncanonical amino acids (using OpenFF), structural ions, and crystal waters. GroScore integrates with GROMACS and SLURM for high-performance computing and is validated on protein–protein affinity benchmarks, showing significant correlation between computed scores and experimental binding affinities across all tested force fields. The software is freely available at https://github.com/jwperthold/GroScore under the MIT License.
SN  - 1549-9596
SN  - 1549-960X
ER  -