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Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series

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Francesc Sabanés Zariquiey, Adrià Pérez, Maciej Majewski, Emilio Gallicchio, Gianni De Fabritiis

Chemical Physics · Submitted 20 Mar 2023

abstract compiled · 2026-09-23 · no language-model review

The authors' main claim This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function.

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arXiv ID2303.11065 (version 1)
Pith IDR74RCG25, Pith's permanent record of this paper and its review
CitationAdri\`a P\'erez, Emilio Gallicchio, Francesc Saban\'es Zariquiey, Gianni de Fabritiis, Maciej Majewski. "Validation of the Alchemical Transfer Method for the Estimation of Relative Binding Affinities of Molecular Series." arXiv:2303.11065 (2023). https://pith.science/paper/R74RCG25
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The paper's own sentences, arranged. Each label is drawn from a closed vocabulary; the number beside it is the probability the classifier gave that label. Numbers in the tables are the authors', checked by code. No sentence in this record was written by a model.

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Compiled by classifier-1.13.0 via TypeSafe API, question bank abstract-p1-20260923, 2026-09-23: 1 request, 4,864 input tokens.

What the abstract itself states, as probabilities: claims first 0.12 · states limitation 0.87 · human participants 0.02 · controlled comparison 0.54 · randomized assignment 0.01 · states quantitative result 0.48 · compares with prior results 0.95 · mentions code or data availability 0.02.

The abstract, sentence by sentence

arXiv listing abstract v1. Results and the main claim are underlined; .

The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary depending on the methodology. In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function.

background contribution method result interpretation main claim

What the classifier reports for each sentence. The number is the probability it gave the label.
#sentencerolethe authors' own workstates the main conclusionstrength
s0 The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. background 1.00 0.03 0.02 asserted 1.00
s1 Alchemical free energy calculations have become a popular tool for this purpose. background 1.00 0.04 0.02 asserted 1.00
s2 However, the accuracy and reliability of these methods can vary depending on the methodology. background 0.56 0.05 0.02 asserted 0.72
s3 In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. contribution 0.90 0.67 0.07 asserted 0.93
s4 The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. result 1.00 0.95 0.32 asserted 1.00
s5 This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function. interpretation 0.89 0.87 0.78 asserted 1.00

What kind of paper the classifier reports this is: simulation study 0.55 · evidence from simulation or computation 0.99.

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Every quoted sentence on this record is the authors'. Every label is from Pith's closed vocabulary, with the probability shown beside it. Every number in the measurements table is the authors', checked by code. Record as JSON

The paper
Original abstract

The accurate prediction of protein-ligand binding affinities is crucial for drug discovery. Alchemical free energy calculations have become a popular tool for this purpose. However, the accuracy and reliability of these methods can vary depending on the methodology. In this study, we evaluate the performance of a relative binding free energy protocol based on the alchemical transfer method (ATM), a novel approach based on a coordinate transformation that swaps the positions of two ligands. The results show that ATM matches the performance of more complex free energy perturbation (FEP) methods in terms of Pearson correlation, but with marginally higher mean absolute errors. This study shows that the ATM method is competitive compared to more traditional methods in speed and accuracy and offers the advantage of being applicable with any potential energy function.

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