Evidence map›Paper›PMID 40130765›Full record

ArticleProtein science : a publication of the Protein Society2025

Tutorial on integrative spatiotemporal modeling by integrative modeling platform.

Andrew P Latham, Miha Rožič, Benjamin M Webb, Andrej Sali

Abstract read
In one paragraph

Article in Protein science : a publication of the Protein Society, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Tutorial on integrative spatiotemporal modeling by integrative modeling platform.Protein science : a publication of the Protein Society · 2025
    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

4 authors.

Andrew P LathamQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.ORCID 0000-0002-9338-7253
Miha RožičQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.
Benjamin M WebbQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.ORCID 0000-0003-3360-4540
Andrej SaliQuantitative Biosciences Institute, University of California, San Francisco, San Francisco, California, USA.ORCID 0000-0003-0435-6197

Funding

IMP: Software for Hybrid Determination of Macromolecular Assembly StructuresR01GM083960 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI SALI, ANDREJ · 2008 to 2024
$5.2M
Uncovering the molecular mechanism of interphase nuclear pore complex assembly with spatiotemporal integrative modelingF32GM150243 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LATHAM, ANDREW · 2024 to 2024
$74k
American Slovenian Education Foundation Junior FellowshipNIGMS NIH HHS F32 GM150243NIGMS NIH HHS R01 GM083960NIH HHS F32GM150243NIH HHS R01GM083960
6 · The paper itself

Abstract

Cells function through dynamic interactions between macromolecules. Detailed characterization of the dynamics of large biomolecular systems is often not feasible by individual biophysical methods. In such cases, it may be possible to compute useful models by integrating multiple sources of information. We have previously developed an integrative method to model dynamic processes by computing biomolecular heterogeneity at fixed time points, then generating static integrative structural modes for each of these heterogeneity models, and finally connecting these static models to produce a scored trajectory model that depicts the process. Here, we demonstrate how to compute, score, and assess these integrative spatiotemporal models using our open-source Integrative Modeling Platform (IMP) program (https://integrativemodeling.org/).

Indexed as

Models, MolecularSoftwarebiomolecular processesintegrative structure modelingmolecular dynamicsstructural biology

Identifiers

PMID40130765
PMCPMC11934212

What OpenQuestion holds

Textmetadata
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.