Evidence map›Paper›PMID 41174311›Full record

ArticleMethods in molecular biology (Clifton, N.J.)2026

Allosteric Network Analysis Toolkit for Single-Domain Phosphoproteins.

Maham Hamid, Safee Ullah Chaudhary, Alessandro Pandini, Shahid M Khan

Abstract read
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In one paragraph

Article in Methods in molecular biology (Clifton, N.J.), 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.

  1. Article
  2. Review
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.

Maham HamidBiomedical Informatics and Engineering Research Laboratory (BIRL), Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan.
Safee Ullah ChaudharyBiomedical Informatics and Engineering Research Laboratory (BIRL), Department of Life Sciences, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan.
Alessandro PandiniDepartment of Computer Science, Brunel University of London, Uxbridge, UK.
Shahid M KhanSyed Babar Ali School of Science & Engineering, Lahore University of Management Sciences (LUMS), Lahore, Pakistan. smkhan@lbl.gov.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Single-domain protein superfamilies mediate essential signaling functions in both prokaryotes and eukaryotes. Signal transduction mediated by single-residue phosphorylation involves subtle secondary structure, side chain rotamer, and hydrogen-bond fluctuations for transitions between active and inactive conformational states, rather than large fold variations. Its study requires molecular dynamics simulations for adequate sampling of the conformational landscape. Discrimination between functional states and subfamilies is achieved by subsequent network analysis designed to couple variations at the local residue or fragment levels to functional collective motions. We describe an integrated protocol for quantitative measurement of local fluctuations and their coupling to functional motions with phosphorylation of the CheY bacterial chemotaxis signal protein as a case study.

Indexed as

PhosphoproteinsAllosteric RegulationEscherichia coli ProteinsMethyl-Accepting Chemotaxis ProteinsMolecular Dynamics SimulationPhosphorylationProtein ConformationSignal TransductioncheY protein, E coliEscherichia coli ProteinsMethyl-Accepting Chemotaxis ProteinsPhosphoproteinsCovalent modificationMolecular dynamicsMutual informationResponse regulatorsSignal phosphorelaysStructural alphabet

Identifiers

PMID41174311

What Socratic 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 Socratic graph.