Evidence map›Paper›PMID 39605739›Full record

ArticlebioRxiv : the preprint server for biology2025

KaMLs for Predicting Protein p

Mingzhe Shen, Daniel Kortzak, Simon Ambrozak, Shubham Bhatnagar, Ian Buchanan, Ruibin Liu, Jana Shen

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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

5 · Who and what money

Authors and funding

7 authors.

Mingzhe ShenDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A.ORCID 0000-0001-7461-3764
Daniel KortzakDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A.ORCID 0000-0001-9098-3466
Simon AmbrozakDepartment of Computer Science, University of Maryland College Park, College Park, MD 20742, U.S.A.
Shubham BhatnagarDepartment of Computer Science, University of Maryland College Park, College Park, MD 20742, U.S.A.ORCID 0009-0007-1355-807X
Ian BuchananStuyvesant High School, New York, NY 10282, U.S.A.
Ruibin LiuDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A.ORCID 0000-0001-8395-9353
Jana ShenDepartment of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201, U.S.A.ORCID 0000-0002-3234-0769

Funding

Molecular mechanisms of proton-coupled dynamic processes in biologyR35GM148261 · NIGMS · UNIVERSITY OF MARYLAND BALTIMORE · PI Jana Shen · 2023 to 2026
$1.5M
A Multi-pronged Computational Approach to Advance Kinase Drug DiscoveryR01CA256557 · NCI · UNIVERSITY OF MARYLAND BALTIMORE · PI SHEN, JANA · 2021 to 2024
$1.4M
NCI NIH HHS R01 CA256557NIGMS NIH HHS R35 GM148261
6 · The paper itself

Abstract

Despite its importance in understanding biology and computer-aided drug discovery, the accurate prediction of protein ionization states remains a formidable challenge. Physics-based approaches struggle to capture the small, competing contributions in the complex protein environment, while machine learning (ML) is hampered by scarcity of experimental data. Here we report the development of p

Identifiers

PMID39605739
PMCPMC11601431

What Socratic 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 Socratic graph.