Evidence map›Paper›PMID 24505217›Full record

ArticleJournal of chemical theory and computation2014

Roadmaps through free energy landscapes calculated using the multi-dimensional vFEP approach.

Tai-Sung Lee, Brian K Radak, Ming Huang, Kin-Yiu Wong, Darrin M York

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Journal of chemical theory and computation, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.

0numbers the graph read from it
0cells of the map it votes in
32citing 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

32 citing papers in PubMed.

  1. Article
  2. Unveiling Cas8 dynamics and regulation within a transposon-encoded Cascade-TniQ complex.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  3. Surface-Accelerated String Method for Locating Minimum Free Energy Paths.Journal of chemical theory and computation · 2024
    Article
  4. Review
  5. AmberTools.Journal of chemical information and modeling · 2023
    Article
  6. Article
  7. Article
  8. ACES: Optimized Alchemically Enhanced Sampling.Journal of chemical theory and computation · 2023
    Article
  9. Article
  10. Organic & biomolecular chemistry · 2022
    Article
  11. Article
  12. Article
  13. Article
  14. Article
  15. Article
  16. Article
  17. Using AMBER18 for Relative Free Energy Calculations.Journal of chemical information and modeling · 2019
    Article
  18. Article
  19. Article
  20. Article
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

5 authors.

Tai-Sung LeeCenter for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA, Scientific Computation Program, University of Minnesota, Minneapolis, MN 55455, USA, and Department of Physics, High Performance Cluster Computing Centre, and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Brian K RadakCenter for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA, Scientific Computation Program, University of Minnesota, Minneapolis, MN 55455, USA, and Department of Physics, High Performance Cluster Computing Centre, and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Ming HuangCenter for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA, Scientific Computation Program, University of Minnesota, Minneapolis, MN 55455, USA, and Department of Physics, High Performance Cluster Computing Centre, and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Kin-Yiu WongCenter for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA, Scientific Computation Program, University of Minnesota, Minneapolis, MN 55455, USA, and Department of Physics, High Performance Cluster Computing Centre, and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong.
Darrin M YorkCenter for Integrative Proteomics Research and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA, Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA, Scientific Computation Program, University of Minnesota, Minneapolis, MN 55455, USA, and Department of Physics, High Performance Cluster Computing Centre, and Institute of Computational and Theoretical Studies, Hong Kong Baptist University, Kowloon Tong, Hong Kong.

Funding

Multi-Scale Quantum Models for Ribozyme CatalysisR01GM062248 · NIGMS · UNIVERSITY OF MINNESOTA TWIN CITIES · PI Darrin M York · 2001 to 2026
$7.1M
NIGMS NIH HHS R01 GM062248
6 · The paper itself

Abstract

The variational free energy profile (vFEP) method is extended to two dimensions and tested with molecular simulation applications. The proposed 2D-vFEP approach effectively addresses the two major obstacles to constructing free energy profiles from simulation data using traditional methods: the need for overlap in the re-weighting procedure and the problem of data representation. This is especially evident as these problems are shown to be more severe in two dimensions. The vFEP method is demonstrated to be highly robust and able to provide stable, analytic free energy profiles with only a paucity of sampled data. The analytic profiles can be analyzed with conventional search methods to easily identify stationary points (

Identifiers

PMID24505217
PMCPMC3912246

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Registered trials

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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.