Evidence map›Paper›PMID 40816097›Full record

ArticleJournal of chemical information and modeling2025

Solvation Energetic Costs of Cognate Binding Site Formation.

Yeonji Ji, Vjay Molino, Steven Ramsey, Tom Kurtzman

Abstract read
In one paragraph

Article in Journal of chemical information and modeling, 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. 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.

Yeonji JiPh.D. Program in Biochemistry, The Graduate Center, City University of New York, New York, New York 10016, United States.ORCID 0000-0001-9456-5085
Vjay MolinoPh.D. Program in Biochemistry, The Graduate Center, City University of New York, New York, New York 10016, United States.
Steven RamseyDepartment of Chemistry, Lehman College, City University of New York, Bronx, New York 10468, United States.ORCID 0000-0001-7441-3228
Tom KurtzmanPh.D. Program in Biochemistry, The Graduate Center, City University of New York, New York, New York 10016, United States.ORCID 0000-0003-0900-772X

Funding

Solvation directed drug design: from molecular physics to lead optimizationR35GM144089 · NIGMS · HERBERT H. LEHMAN COLLEGE · PI Thomas Philip Kurtzman · 2022 to 2026
$1.9M
NIGMS NIH HHS R35 GM144089
6 · The paper itself

Abstract

Structural fluctuations of proteins can reveal alternate binding site conformations or cryptic pockets that may be exploited to discover novel, tightly bound chemical compounds. While significant effort has been dedicated to the exploration of protein conformational space, the thermodynamic role of solvation and how it is coupled to a protein's structural fluctuations, particularly in binding site formation, has not been well characterized. In this study, we examine how binding site solvation energetics differ between unligated

Indexed as

ProteinsSolventsBinding SitesHydrogen BondingLigandsMolecular Dynamics SimulationProtein BindingProtein ConformationThermodynamicsWaterLigandsProteinsSolventsWater

Identifiers

PMID40816097
PMCPMC12421683

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.