Evidence map›Paper›PMID 39946508›Full record

ArticleScience (New York, N.Y.)2025

Computational design of serine hydrolases.

Anna Lauko, Samuel J Pellock, Kiera H Sumida, Ivan Anishchenko, David Juergens, Woody Ahern, Jihun Jeung, Alexander F Shida, Andrew Hunt, Indrek Kalvet and 11 more

Abstract read
In one paragraph

Article in Science (New York, N.Y.), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 papers.

0numbers the graph read from it
0cells of the map it votes in
97citing 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

97 citing papers in PubMed.

  1. Article
  2. Review
  3. Article
  4. Article
  5. High-throughput physics-based enzyme engineering.bioRxiv : the preprint server for biology · 2026
    Article
  6. Review
  7. Article
  8. Article
  9. Article
  10. Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Article
  16. Review
  17. Applications and limitations of AI tools in enzyme design.Protein science : a publication of the Protein Society · 2026
    Review
  18. Article
  19. Article
  20. Article

37 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

21 authors.

Anna Lauko *Department of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-5903-3518
Samuel J Pellock *Department of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0002-7557-7985
Kiera H Sumida *Department of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-2773-9676
Ivan AnishchenkoDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-3645-2044
David JuergensDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-6425-8391
Woody AhernDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0009-0006-1247-8847
Jihun JeungDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0009-0004-8604-908X
Alexander F ShidaDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0003-4140-6085
Andrew HuntDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-9620-593X
Indrek KalvetDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0002-6610-2857
Christoffer NornDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0002-1450-4651
Ian R HumphreysDepartment of Biochemistry, University of Washington, Seattle, WA, USA.
Cooper JamiesonDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.
Rohith KrishnaDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0009-0003-6387-9622
Yakov KipnisDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0002-3057-4916
Alex KangDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-5487-0499
Evans BrackenbroughDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0009-0004-1476-0219
Asim K BeraDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-9473-2912
Banumathi SankaranDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0002-3266-8131
K N HoukDepartment of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA.ORCID 0000-0002-8387-5261
David BakerDepartment of Biochemistry, University of Washington, Seattle, WA, USA.ORCID 0000-0001-7896-6217

Funding

User Training and OutreachP30GM124169 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI PAUL David ADAMS, Gregory L Hura · 2017 to 2026
$28.6M
TRAINING IN MOLECULAR BIOPHYSICST32GM008268 · NIGMS · UNIVERSITY OF WASHINGTON · PI KOLLMAN, JUSTIN M, ZHENG, NING · 1988 to 2023
$8.6M
Howard Hughes Medical InstituteNIGMS NIH HHS P30 GM124169NIGMS NIH HHS T32 GM008268
6 · The paper itself

Abstract

The design of enzymes with complex active sites that mediate multistep reactions remains an outstanding challenge. With serine hydrolases as a model system, we combined the generative capabilities of RFdiffusion with an ensemble generation method for assessing active site preorganization at each step in the reaction to design enzymes starting from minimal active site descriptions. Experimental characterization revealed catalytic efficiencies (

Indexed as

Computer-Aided DesignProtein EngineeringSerine ProteasesBiocatalysisCatalytic DomainCrystallography, X-RayKineticsModels, MolecularProtein ConformationProtein FoldingSerine Proteases

Identifiers

PMID39946508
PMCPMC12288761

What OpenQuestion holds

Textmetadata
LicenceTDM
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.