ArticleThe journal of physical chemistry. B2020
Computing Absolute Free Energy with Deep Generative Models.
Article in The journal of physical chemistry. B, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Accurate Lattice Free Energies of Packing Polymorphs from Probabilistic Generative Models.Journal of chemical theory and computation · 2025Article
- Assessing the Accuracy and Efficiency of Free Energy Differences Obtained fromJournal of chemical theory and computation · 2024Article
- Learned mappings for targeted free energy perturbation between peptide conformations.The Journal of chemical physics · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.Biophysical journal · 2023Article
- Efficient Hi-C inversion facilitates chromatin folding mechanism discovery and structure prediction.bioRxiv : the preprint server for biology · 2023Article
- Application of Computational Biology and Artificial Intelligence in Drug Design.International journal of molecular sciences · 2022Review
- Contrastive Learning of Coarse-Grained Force Fields.Journal of chemical theory and computation · 2022Article
- Unifying coarse-grained force fields for folded and disordered proteins.Current opinion in structural biology · 2022Review
- DeepBAR: A Fast and Exact Method for Binding Free Energy Computation.The journal of physical chemistry letters · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Fast and accurate evaluation of free energy has broad applications from drug design to material engineering. Computing the absolute free energy is of particular interest since it allows the assessment of the relative stability between states without intermediates. Here, we introduce a general framework for calculating the absolute free energy of a state. A key step of the calculation is the definition of a reference state with tractable deep generative models using locally sampled configurations. The absolute free energy of this reference state is zero by design. The free energy for the state of interest can then be determined as the difference from the reference. We applied this approach to both discrete and continuous systems and demonstrated its effectiveness. It was found that the Bennett acceptance ratio method provides more accurate and efficient free energy estimations than approximate expressions based on work. We anticipate the method presented here to be a valuable strategy for computing free energy differences.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.