Ensemble Sensitivity to Chemical Modifications in Free and Bound Macrocyclic Peptides.

Yisel Martínez-Noa, Wen-Ting Chen, Cheng-Yu Li, Steven D Bruner, Alberto Perez

Abstract read

In one paragraph

Article 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. 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.

Yisel Martínez-NoaDepartment of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States.

Wen-Ting ChenDepartment of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States.ORCID 0009-0006-5712-2967

Cheng-Yu LiDepartment of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States.

Steven D BrunerDepartment of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States.ORCID 0000-0002-0522-480X

Alberto PerezDepartment of Chemistry, University of Florida, P.O. Box 117200, Gainesville, Florida 32611-7200, United States.ORCID 0000-0002-5054-5338

Funding

Targeting the ET domain of BET proteins: specificity and selectivityR01GM149646 · NIGMS · UNIVERSITY OF FLORIDA · PI Alberto Perez · 2023 to 2026

$1.2M

NIGMS NIH HHS R01 GM149646

6 · The paper itself

Abstract

Macrocyclic peptides present a challenging regime for molecular modeling in which minimal chemical modifications can strongly reweight conformational ensembles while leaving binding function largely intact. The combination of topological constraint, residual flexibility, and noncanonical linkages complicates both conformational sampling and force-field parametrization, particularly when differences in binding arise from ensemble redistribution rather than distinct bound geometries.

Indexed as

Macrocyclic CompoundsPeptidesPeptides, CyclicModels, MolecularMolecular Dynamics SimulationProtein ConformationMacrocyclic CompoundsPeptidesPeptides, Cyclic

Identifiers

PMID41975608

DOI10.1021/acs.jpcb.6c00660

PMCPMC13198942

What OpenQuestion holds

Textmetadata

LicenceTDM

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.