Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy Article Swipe
Sudarshan Behera
,
David F. Hahn
,
Carter J. Wilson
,
Simone Marsili
,
Gary Tresadern
,
Vytautas Gapsys
,
Bert L. de Groot
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jcim.5c00947
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1021/acs.jcim.5c00947
Relative binding free energy (RBFE) calculations have emerged as a powerful tool in drug discovery, capable of achieving experimental-level accuracy. However, the accuracy is compromised by a multitude of factors, including the initial structure modeling. The current study contributes to the quantification of the impact of initial structure modeling on the accuracy across a diverse set of activity cliff pairs. Along with providing a quantitative relation between the resolution of the crystal structure and free energy accuracy, we also demonstrate the incorporation of a secondary solvation tool (SOLVATE) to increase the free energy accuracy, especially when crystal waters are missing. The study also evaluates the reliability of AI-predicted structures in RBFE calculations, showing their effectiveness in predicting RBFE directionality and assigning nominal resolutions to the predicted structures based on free energy accuracy. These findings provide a set of recommendations for the development of more robust RBFE protocols, informing the use of structural data, solvation techniques, and AI-predicted protein models in drug discovery.
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- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1021/acs.jcim.5c00947
- OA Status
- hybrid
- Cited By
- 2
- References
- 99
- Related Works
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- OpenAlex ID
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All OpenAlex metadata
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https://openalex.org/W4411780513Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1021/acs.jcim.5c00947Digital Object Identifier
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Quantification of the Impact of Structure Quality on Predicted Binding Free Energy AccuracyWork title
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articleOpenAlex work type
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enPrimary language
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2025Year of publication
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2025-06-30Full publication date if available
- Authors
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Sudarshan Behera, David F. Hahn, Carter J. Wilson, Simone Marsili, Gary Tresadern, Vytautas Gapsys, Bert L. de GrootList of authors in order
- Landing page
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https://doi.org/10.1021/acs.jcim.5c00947Publisher landing page
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YesWhether a free full text is available
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hybridOpen access status per OpenAlex
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https://doi.org/10.1021/acs.jcim.5c00947Direct OA link when available
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Quality (philosophy), Energy (signal processing), Computer science, Chemistry, Econometrics, Statistics, Mathematics, Physics, Quantum mechanicsTop concepts (fields/topics) attached by OpenAlex
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2Total citation count in OpenAlex
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2025: 2Per-year citation counts (last 5 years)
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10Other works algorithmically related by OpenAlex
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