Contact Cluster Modeling of Allosteric Communication in PDZ Domains.

Emanuel Dorbath, Fabian Rudolf, Adnan Gulzar, Gerhard Stock

Abstract readReview

In one paragraph

Review in The journal of physical chemistry. B, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it

0cells of the map it votes in

2citing 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

2 citing papers in PubMed.

Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States.The journal of physical chemistry letters · 2026
Article
Revealing GRK5 Activation Features by Interpretable Machine Learning and Molecular Dynamics Simulation.International journal of molecular sciences · 2026
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.

Emanuel DorbathBiomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany.ORCID 0009-0003-0148-0907

Fabian RudolfBiomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany.

Adnan GulzarBiomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany.

Gerhard StockBiomolecular Dynamics, Institute of Physics, University of Freiburg, 79104 Freiburg, Germany.ORCID 0000-0002-3302-3044

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Allostery, the intriguing phenomenon of long-range communication between distant sites in proteins, plays a central role in biomolecular regulation and signal transduction. While it is commonly attributed to conformational rearrangements, the underlying dynamical mechanisms remain poorly understood. The contact cluster model of allostery [

Indexed as

Molecular Dynamics SimulationPDZ DomainsAllosteric RegulationHumansLigandsProtein Tyrosine Phosphatase, Non-Receptor Type 13LigandsProtein Tyrosine Phosphatase, Non-Receptor Type 13

Identifiers

PMID41514486

DOI10.1021/acs.jpcb.5c07737

PMCPMC12862798

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.