Evidence map›Paper›PMID 40810260›Full record

ArticleProteins2026

Highlights of Model Quality Assessment in CASP16.

Alisia Fadini, Recep Adiyaman, Shaima N Alhaddad, Behnosh Behzadi, Jianlin Cheng, Xinyue Cui, Nicholas S Edmunds, Lydia Freddolino, Ahmet G Genc, Fang Liang and 14 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Proteins, 2026. 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. Article
  2. 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

24 authors.

Alisia FadiniCambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.ORCID https://orcid.org/0000-0001-5246-9124
Recep AdiyamanSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0000-0001-8124-5381
Shaima N AlhaddadSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0009-0001-1937-0373
Behnosh BehzadiSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0009-0008-8980-0894
Jianlin ChengDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.ORCID https://orcid.org/0000-0003-0305-2853
Xinyue CuiCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0005-6015-2449
Nicholas S EdmundsSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0000-0002-7238-6008
Lydia FreddolinoDepartment of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.ORCID https://orcid.org/0000-0002-5821-4226
Ahmet G GencSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0009-0001-7195-9353
Fang LiangCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0006-4834-5755
Dong LiuCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0003-8512-9005
Jian LiuDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.ORCID https://orcid.org/0000-0002-7570-8690
Quancheng LiuDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.ORCID https://orcid.org/0009-0004-8207-2629
Liam J McGuffinSchool of Biological Sciences, University of Reading, Reading, UK.ORCID https://orcid.org/0000-0003-4501-4767
Pawan NeupaneDepartment of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.ORCID https://orcid.org/0009-0008-5283-4951
Chunxiang PengDepartment of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.ORCID https://orcid.org/0009-0006-9735-0278
David R ShortleDepartment of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.ORCID https://orcid.org/0009-0009-4903-5865
Meng SunCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0002-7123-7788
Haodong WangCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0000-1896-9408
Qiqige WuyunDepartment of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA.ORCID https://orcid.org/0000-0002-7228-903X
Guijun ZhangCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0000-0002-7815-5884
Xuanfeng ZhaoCollege of Information Engineering, Zhejiang University of Technology, Hangzhou, China.ORCID https://orcid.org/0009-0005-0455-9500
Wei ZhengDepartment of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.ORCID https://orcid.org/0000-0002-2984-9003
Randy J ReadCambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.ORCID https://orcid.org/0000-0001-8273-0047

Funding

Prospective analysis to determine model accuracy performance and boundaries in the post-AlphaFold2 environmentR01GM100482 · NIGMS · UNIVERSITY OF CALIFORNIA AT DAVIS · PI FIDELIS, KRZYSZTOF A · 2012 to 2025
$11.1M
Structure-based functional annotation of microbial genomesR01AI134678 · NIAID · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Lydia Petra Freddolino, SCOTT J. HULTGREN · 2018 to 2026
$6.5M
Integrated Prediction of Protein Struture at 1D, 2D and 3D LevelsR01GM093123 · NIGMS · UNIVERSITY OF MISSOURI-COLUMBIA · PI CHENG, JIANLIN · 2010 to 2023
$3.8M
Biotechnology and Biological Sciences Research Council BB/T018496/1Biotechnology and Biological Sciences Research Council BB/Y009398/1David R Shortle Protein Research FundFundamental Research Funds for the Central Universities 054-63253109Kuwaiti GovernmentNational Institute of Allergy and Infectious Diseases AI134678National Institutes of Health (USA)National Key Research and Development Program of China 2022ZD0115103National Natural Science Foundation of China 12426303National Natural Science Foundation of China 62173304National Science Foundation DBI2308699National Science Foundation MTM2025426NIAID NIH HHS R01 AI134678NIGMS NIH HHS R01 GM093123NIGMS NIH HHS R01 GM100482"Pioneer" and "Leading Goose" R&D Program of Zhejiang 2025C01190Pioneer and Leading Goose R&D Program of ZhejiangRepublic of Turkey Ministry of National EducationTianjin Science and Technology Program 24ZXZSSS00320US National Institute of General Medical Sciences (NIGMS/NIH) R01GM100482US National Institute of Health R01GM093123U.S. National Science Foundation 2137603U.S. National Science Foundation 2138259U.S. National Science Foundation 2138286U.S. National Science Foundation 2138296U.S. National Science Foundation 2138307Wellcome TrustWellcome Trust 209407/Z/17/ZZhejiang Province High-level Talent Special Support Program 2023R5248
6 · The paper itself

Abstract

Model quality assessment (MQA) remains a critical component of structural bioinformatics for both structure predictors and experimentalists seeking to use predictions for downstream applications. In CASP16, the Evaluation of Model Accuracy (EMA) category featured both global and local quality estimation for multimeric assemblies (QMODE1 and QMODE2), as well as a novel QMODE3 challenge-requiring predictors to identify the best five models from thousands generated by MassiveFold. This paper presents detailed results from several leading CASP16 EMA methods, highlighting the strengths and limitations of the approaches.

Indexed as

Computational BiologyModels, MolecularNucleic Acid ConformationProtein ConformationProtein FoldingSequence Alignmentcomputational molecular biologymolecular modelsprotein conformationprotein domains

Identifiers

PMID40810260
PMCPMC12750036

What OpenQuestion holds

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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.