Evidence map›Paper›PMID 41000976›Full record

ArticlebioRxiv : the preprint server for biology2025

Jasper Butcher, Rohith Krishna, Raktim Mitra, Rafael I Brent, Yanjing Li, Nathaniel Corley, Paul T Kim, Jonathan Funk, Simon Mathis, Saman Salike and 13 more

Abstract readPreprint
PubMed Full text at PMC Publisher
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. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing 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

2 citing papers in PubMed.

  1. Review
  2. Review
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

23 authors.

Jasper ButcherInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0004-4864-1330
Rohith KrishnaInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0003-6387-9622
Raktim MitraInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0003-1182-3742
Rafael I BrentInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-3233-7914
Yanjing LiInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0001-3116-525X
Nathaniel CorleyInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-6509-7144
Paul T KimInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-8950-7179
Jonathan FunkInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0006-9496-1890
Simon MathisInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-5246-6481
Saman SalikeInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0007-1060-0287
Aiko MuraishiInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0000-1212-2695
Helen EisenachInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-3201-4517
Tuscan Rock ThompsonInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0003-1876-106X
Jie ChenInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0009-0001-4650-7785
Yuliya PolitanskaInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-6766-988X
Enisha SehgalInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-6000-0999
Brian CoventryInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-6910-6255
Odin ZhangInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-6734-1534
Bo QiangInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0001-7428-4104
Kieran DidiInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0001-6839-3320
Max KazmanInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0003-4420-4016
Frank DiMaioInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0002-7524-8938
David BakerInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA.ORCID 0000-0001-7896-6217

Funding

Project 5: mRNA and mRNA-launched nanoparticle vaccinesU19AI181881 · NIAID · UNIVERSITY OF WASHINGTON · PI VEESLER, DAVID · 2024 to 2024
$41.1M
Protein structure determination from low-resolution experimental dataR01GM123089 · NIGMS · UNIVERSITY OF WASHINGTON · PI DIMAIO, FRANK P · 2017 to 2025
$2.6M
Designed Vehicles for Blood Brain Barrier TraversalR01AG063845 · NIA · UNIVERSITY OF WASHINGTON · PI BAKER, DAVID · 2019 to 2023
$2.5M
Gates Foundation INV-010680NIAID NIH HHS U19 AI181881NIA NIH HHS R01 AG063845NIGMS NIH HHS R01 GM123089
6 · The paper itself

Abstract

Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFdiffusion3 (RFD3), a diffusion model that generates protein structures in the context of ligands, nucleic acids and other non-protein constellations of atoms. Because all polymer atoms are modeled explicitly, conditioning the model on complex sets of atom-level constraints for enzyme design and other challenges is both simpler and more effective than previous approaches. RFD3 achieves improved performance compared to prior approaches on a range of

Identifiers

PMID41000976
PMCPMC12458353

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.