Evidence map›Paper›PMID 27599739›Full record

ArticleActa crystallographica. Section D, Structural biology2016

From deep TLS validation to ensembles of atomic models built from elemental motions. Addenda and corrigendum.

Alexandre Urzhumtsev, Pavel V Afonine, Andrew H Van Benschoten, James S Fraser, Paul D Adams

Abstract readPublished Erratum
PubMed Full text at PMC Publisher
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Alexandre UrzhumtsevCentre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, 1 rue Laurent Fries, BP 10142, 67404 Illkirch, France.
Pavel V AfonineMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.
Andrew H Van BenschotenDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California, USA.
Paul D AdamsMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, 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
STRUCTURAL BIOLOGY TRAINING PROGRAMT32GM008284 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI KORTEMME, TANJA · 1988 to 2022
$10.1M
NIGMS NIH HHS P01 GM063210NIGMS NIH HHS T32 GM008284
6 · The paper itself

Abstract

Researcher feedback has indicated that in Urzhumtsev et al. [(2015) Acta Cryst. D71, 1668-1683] clarification of key parts of the algorithm for interpretation of TLS matrices in terms of elemental atomic motions and corresponding ensembles of atomic models is required. Also, it has been brought to the attention of the authors that the incorrect PDB code was reported for one of test models. These issues are addressed in this article.

Indexed as

addenda and corrigendumatomic displacement matricesensemble of atomic modelsmodel validationTLS matricesTLS model

Identifiers

PMID27599739
PMCPMC5013599

What OpenQuestion holds

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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.