Evidence map›Paper›PMID 41279793›Full record

ArticlebioRxiv : the preprint server for biology2025

Bayesian multi-state multi-condition modeling of a protein structure based on X-ray crystallography data.

Matthew Hancock, James Holton, James S Fraser, Paul D Adams, Andrej Sali

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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.

Matthew HancockDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0001-9127-4485
James HoltonDepartment of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
James S FraserDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0002-5080-2859
Paul D AdamsDepartment of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Andrej SaliDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.ORCID 0000-0003-0435-6197

Funding

Targeting Viroporins and Coronavirus M ProteinU19AI171110 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$103.4M
IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Equipment for Discovering and Manipulating Macromolecular Conformational EnsemblesR35GM145238 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James Solomon Fraser · 2022 to 2026
$3.1M
Eliminating Critical Systematic Errors In Structural Biology With Next-Generation SimulationR01GM124149 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI HOLTON, JAMES M · 2017 to 2024
$2.5M
Bridging the Gap Between Prediction and Reality in Structural BiologyR35GM158447 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI James M Holton · 2025 to 2026
$952k
NIAID NIH HHS U19 AI171110NIGMS NIH HHS R01 GM083960NIGMS NIH HHS R01 GM124149NIGMS NIH HHS R35 GM145238NIGMS NIH HHS R35 GM158447
6 · The paper itself

Abstract

An atomic structure model of a protein can be computed from a diffraction pattern of its crystal. While most crystallographic studies produce a single set of atomic coordinates, the billions of protein molecules in a crystal sample many conformational modes during data collection. As a result, a 'multi-state' model that depicts these conformations could reproduce the X-ray data better than a single conformation, and thus likely be more accurate. Computing such a multi-state model is challenging due to a lower data-to-parameter ratio than that for single-state modeling. To address this challenge, additional information could be considered, such as X-ray datasets collected for the same system under distinct experimental conditions (

Identifiers

PMID41279793
PMCPMC12632541

What OpenQuestion holds

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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.