Evidence map›Paper›PMID 29056756›Full record

ArticleJournal of chemical and engineering data2017

Approaches for calculating solvation free energies and enthalpies demonstrated with an update of the FreeSolv database.

Guilherme Duarte Ramos Matos, Daisy Y Kyu, Hannes H Loeffler, John D Chodera, Michael R Shirts, David L Mobley

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical and engineering data, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers.

0numbers the graph read from it
0cells of the map it votes in
65citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

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.

2 · The registry

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.

3 · Its place in the literature

Who cites it

65 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Elucidating the Solvent-Dependent Solvation and Structural Stability of Irinotecan: A Molecular Simulation Study.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026
    Article
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  6. Article
  7. Review
  8. Article
  9. Review
  10. Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. How to Sample Dozens of Substitutions per Site with λ Dynamics.Journal of chemical theory and computation · 2024
    Article
  16. Article
  17. Article
  18. Tuning Potential Functions to Host-Guest Binding Data.Journal of chemical theory and computation · 2024
    Article
  19. Article
  20. Article

5 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

6 authors.

Guilherme Duarte Ramos MatosDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.
Daisy Y KyuDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.
Hannes H LoefflerDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.
John D ChoderaDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.
Michael R ShirtsDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.
David L MobleyDepartment of Chemistry, University of California, Irvine, Department of Pharmaceutical Sciences, University of California, Irvine, Scientific Computing Department, STFC, UK, Computational and Systems Biology Program, Sloan Kettering Institute, Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, and Departments of Pharmaceutical Sciences and Chemistry, University of California, Irvine.

Funding

X-RAY CRYSTALLOGRAPHYP30CA008748 · NCI · SLOAN-KETTERING INSTITUTE FOR CANCER RES · PI Hongbiao Carl Lekaye · 1985 to 2026
$347.4M
NCI NIH HHS P30 CA008748
6 · The paper itself

Abstract

Solvation free energies can now be calculated precisely from molecular simulations, providing a valuable test of the energy functions underlying these simulations. Here, we briefly review "alchemical" approaches for calculating the solvation free energies of small, neutral organic molecules from molecular simulations, and illustrate by applying them to calculate aqueous solvation free energies (hydration free energies). These approaches use a non-physical pathway to compute free energy differences from a simulation or set of simulations and appear to be a particularly robust and general-purpose approach for this task. We also present an update (version 0.5) to our FreeSolv database of experimental and calculated hydration free energies of neutral compounds and provide input files in formats for several simulation packages. This revision to FreeSolv provides calculated values generated with a single protocol and software version, rather than the heterogeneous protocols used in the prior version of the database. We also further update the database to provide calculated enthalpies and entropies of hydration and some experimental enthalpies and entropies, as well as electrostatic and nonpolar components of solvation free energies.

Identifiers

PMID29056756
PMCPMC5648357

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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.