Evidence map›Paper›PMID 38168172›Full record

ArticlebioRxiv : the preprint server for biology2023

Optimizing representations for integrative structural modeling using Bayesian model selection.

Shreyas Arvindekar, Aditi S Pathak, Kartik Majila, Shruthi Viswanath

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. 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

5 · Who and what money

Authors and funding

4 authors.

Shreyas ArvindekarNational Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India 560065.ORCID 0000-0002-9945-8534
Aditi S PathakNational Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India 560065.
Kartik MajilaNational Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India 560065.
Shruthi ViswanathNational Center for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India 560065.ORCID 0000-0002-9061-8407

Funding

XRAY CRYSTALLOGRAPHIC STRUCTURE ANALYSIS: PROTEIN SORTINGP41RR001081 · NCRR · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI COHEN, BRUCE E · 1985 to 2011
$17.6M
ChimeraX -- Next Generation Visualization and Analysis Software for Multiscale ModelingR01GM129325 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI FERRIN, THOMAS E · 2018 to 2025
$5.2M
NCRR NIH HHS P41 RR001081NIGMS NIH HHS R01 GM129325
6 · The paper itself

Abstract

Motivation: Integrative structural modeling combines data from experiments, physical principles, statistics of previous structures, and prior models to obtain structures of macromolecular assemblies that are challenging to characterize experimentally. The choice of model representation is a key decision in integrative modeling, as it dictates the accuracy of scoring, efficiency of sampling, and resolution of analysis. But currently, the choice is usually made Results: Here, we report NestOR ( Availability: NestOR is implemented in the Integrative Modeling Platform (https://integrativemodeling.org) and is available at https://github.com/isblab/nestor.

Indexed as

Bayes factorsBayesian model selectioncoarse-grained representationintegrative modelingmacromolecular assembliesmodel evidencenested sampling

Identifiers

PMID38168172
PMCPMC10760022

What OpenQuestion holds

Textmetadata
LicenceCC BY
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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.