Evidence map›Paper›PMID 41147133›Full record

ArticleChembiochem : a European journal of chemical biology2025

A Route to Design Novel Functional Peptides by Applying a Denoising Diffusional Model to mRNA Display Libraries.

Pearl Qi, Yash Pragnesh Gandhi, Kexin Zheng, Farzad Jalali-Yazdi, Justin N Ong, Terry T Takahashi, Rajiv K Kalia, Richard W Roberts

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Chembiochem : a European journal of chemical biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. 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

8 authors.

Pearl QiMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.ORCID https://orcid.org/0009-0007-0076-0500
Yash Pragnesh GandhiThomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA, 90089, USA.
Kexin ZhengThomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA, 90089, USA.
Farzad Jalali-YazdiMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.
Justin N OngMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.
Terry T TakahashiDepartment of Chemistry, University of Southern California, Los Angeles, CA, 90089, USA.ORCID http://orcid.org/0000-0002-6835-242X
Rajiv K KaliaMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.ORCID http://orcid.org/0000-0002-8835-5249
Richard W RobertsMork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA, 90089, USA.ORCID https://orcid.org/0000-0002-8587-5097

Funding

USC/NORRIS COMPREHENSIVE CANCER CENTER (CORE) SUPPORTP30CA014089 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Fumito Ito · 1985 to 2026
$181.4M
Genetically Encoded Probes of Huntingtin MisfoldingR01NS125769 · NINDS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI Jeannie Chen, Ralf Langen · 2022 to 2026
$3.2M
SUPR Peptides to Inhibit Undruggable Cancer Target (PQ18)R01CA170820 · NCI · UNIVERSITY OF SOUTHERN CALIFORNIA · PI ROBERTS, RICHARD W, TAKAHASHI, TERRY TORAO · 2012 to 2015
$1.8M
Developing novel affinity reagents for methyl-arginine proteomics using mRNA displayR21GM144910 · NIGMS · UNIVERSITY OF SOUTHERN CALIFORNIA · PI GRAHAM, NICHOLAS ALEXANDER, TAKAHASHI, TERRY TORAO · 2022 to 2023
$436k
Center for Advanced Research ComputingLos Angeles Rubber Group Inc.NCI NIH HHS P30 CA014089NCI NIH HHS R01 CA170820NIGMS NIH HHS R21 GM144910NIH grants R01CA170820NIH grants R01NS125769NIH grants R21GM144910NINDS NIH HHS R01 NS125769Norris Comprehensive Cancer Center CCSG grant P30CA014089
6 · The paper itself

Abstract

In vitro directed evolution techniques, such as mRNA display, enable peptide ligand discovery and optimization. However, physical libraries that rely on a genetic code can only search a small fraction of sequence space due to inherent biases in the genetic code and experimental limitations. To address this challenge, denoising diffusion implicit models (DDIMs) are applied to generate novel peptide ligands against B-cell lymphoma extra-large (Bcl-x

Indexed as

Peptide LibraryPeptidesRNA, Messengerbcl-X ProteinDiffusionHumansLigandsbcl-X ProteinLigandsPeptide LibraryPeptidesRNA, Messengerdeep learningdenoising diffusion implicit modelsdirected evolutionmRNA displaypeptide ligands

Identifiers

PMID41147133
PMCPMC12582155

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.