Evidence map›Paper›PMID 39091799›Full record

ArticlebioRxiv : the preprint server for biology2024

Suhaas Bhat, Kalyan Palepu, Lauren Hong, Joey Mao, Tianzheng Ye, Rema Iyer, Lin Zhao, Tianlai Chen, Sophia Vincoff, Rio Watson and 10 more

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

20 authors.

Suhaas BhatDepartment of Biomedical Engineering, Duke University.
Kalyan PalepuDepartment of Biomedical Engineering, Duke University.
Lauren HongDepartment of Biomedical Engineering, Duke University.
Joey MaoDepartment of Cell Biology, Duke University.
Tianzheng YeRobert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
Rema IyerCancer Genome and Epigenetics Program, Sanford Burnham Prebys Institute, San Diego, CA, USA.
Lin ZhaoDepartment of Biomedical Engineering, Duke University.
Tianlai ChenDepartment of Biomedical Engineering, Duke University.
Sophia VincoffDepartment of Biomedical Engineering, Duke University.
Rio WatsonDepartment of Biomedical Engineering, Duke University.
Tian WangDepartment of Biomedical Engineering, Duke University.
Divya SrijayDepartment of Biomedical Engineering, Duke University.
Venkata Srikar KavirayuniDepartment of Biomedical Engineering, Duke University.
Kseniia KholinaDepartment of Biomedical Engineering, Duke University.
Shrey GoelDepartment of Biomedical Engineering, Duke University.
Pranay VureDepartment of Biomedical Engineering, Duke University.
Aniruddha J DesphandeCancer Genome and Epigenetics Program, Sanford Burnham Prebys Institute, San Diego, CA, USA.
Scott H SoderlingDepartment of Cell Biology, Duke University.
Matthew P DeLisaRobert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, USA.
Pranam ChatterjeeDepartment of Biomedical Engineering, Duke University.ORCID 0000-0003-3957-8478

Funding

Tumor Microenvironment and Cancer ImmunologyP30CA030199 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI ELENA B PASQUALE · 1985 to 2026
$107.2M
Molecular Analysis of Developmental Brain Disorders Associated with Synaptic PathologyR01MH111684 · NIMH · DUKE UNIVERSITY · PI SCOTT H SODERLING · 2017 to 2026
$6.6M
Proteomic and Functional Analysis of Presynaptic Physiology and PlasticityR01MH126954 · NIMH · DUKE UNIVERSITY · PI SODERLING, SCOTT H · 2021 to 2025
$2.9M
Molecular Pathogenesis of AF10-Rearranged LeukemiasR01CA262746 · NCI · SANFORD BURNHAM PREBYS MEDICAL DISCOVERY INSTITUTE · PI Aniruddha J. Deshpande · 2022 to 2026
$2.2M
Programmable peptide-guided protein degradationR21CA278468 · NCI · DUKE UNIVERSITY · PI CHATTERJEE, PRANAM · 2023 to 2023
$388k
NCI NIH HHS P30 CA030199NCI NIH HHS R01 CA262746NCI NIH HHS R21 CA278468NIMH NIH HHS R01 MH111684NIMH NIH HHS R01 MH126954
6 · The paper itself

Abstract

Designing binders to target undruggable proteins presents a formidable challenge in drug discovery, requiring innovative approaches to overcome the lack of putative binding sites. Recently, generative models have been trained to design binding proteins via three-dimensional structures of target proteins, but as a result, struggle to design binders to disordered or conformationally unstable targets. In this work, we provide a generalizable algorithmic framework to design short, target-binding linear peptides, requiring only the amino acid sequence of the target protein. To do this, we propose a process to generate naturalistic peptide candidates through Gaussian perturbation of the peptidic latent space of the ESM-2 protein language model, and subsequently screen these novel linear sequences for target-selective interaction activity via a CLIP-based contrastive learning architecture. By integrating these generative and discriminative steps, we create a

Identifiers

PMID39091799
PMCPMC11291000

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.