Evidence map›Paper›PMID 25760612›Full record

ArticleActa crystallographica. Section D, Biological crystallography2015

FEM: feature-enhanced map.

Pavel V Afonine, Nigel W Moriarty, Marat Mustyakimov, Oleg V Sobolev, Thomas C Terwilliger, Dusan Turk, Alexandre Urzhumtsev, Paul D Adams

Abstract read
In one paragraph

Article in Acta crystallographica. Section D, Biological crystallography, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 106 papers.

0numbers the graph read from it
0cells of the map it votes in
106citing 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

106 citing papers in PubMed.

  1. Article
  2. Article
  3. Crystal structure ofProceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  4. Article
  5. Reconstructing biological molecules with help from video gamers.Acta crystallographica. Section D, Structural biology · 2025
    Article
  6. Article
  7. Article
  8. Targeted degradation of Pin1 by protein-destabilizing compounds.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  9. ProgramJournal of applied crystallography · 2024
    Article
  10. Article
  11. Article
  12. Tetracycline-modifying enzyme SmTetX from Stenotrophomonas maltophilia.Acta crystallographica. Section F, Structural biology communications · 2023
    Article
  13. Article
  14. Article
  15. Article
  16. Engineering C-C Bond Cleavage Activity into a P450 Monooxygenase Enzyme.Journal of the American Chemical Society · 2023
    Article
  17. Article
  18. Article
  19. Article
  20. Article

46 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

8 authors.

Pavel V AfoninePhysical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.
Nigel W MoriartyPhysical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.
Marat MustyakimovBiology and Soft Matter Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831, USA.
Oleg V SobolevPhysical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.
Thomas C TerwilligerLos Alamos National Laboratory, Mail Stop M888, Los Alamos, NM 87545, USA.
Dusan TurkBiochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
Alexandre UrzhumtsevCentre for Integrative Biology, IGBMC, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.
Paul D AdamsPhysical Biosciences Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, MS64R0121, Berkeley, CA 94720, USA.

Funding

PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
NIGMS NIH HHS 1P01 GM063210NIGMS NIH HHS P01 GM063210
6 · The paper itself

Abstract

A method is presented that modifies a 2mFobs - DFmodel σA-weighted map such that the resulting map can strengthen a weak signal, if present, and can reduce model bias and noise. The method consists of first randomizing the starting map and filling in missing reflections using multiple methods. This is followed by restricting the map to regions with convincing density and the application of sharpening. The final map is then created by combining a series of histogram-equalized intermediate maps. In the test cases shown, the maps produced in this way are found to have increased interpretability and decreased model bias compared with the starting 2mFobs - DFmodel σA-weighted map.

Indexed as

Models, Molecularcctbxdensity modificationfeature-enhanced mapFEMFourier mapmap improvementmap kurtosismap sharpeningmodel biasOMITPHENIX

Identifiers

PMID25760612
PMCPMC4356370

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.