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; Dong Liu; Jian Liu; Quancheng Liu; Liam J McGuffin; Pawan Neupane; Chunxiang Peng; David R Shortle; Meng Sun; Haodong Wang; Qiqige Wuyun; Guijun Zhang; Xuanfeng Zhao; Wei Zheng; Randy J Read

doi:10.1002/prot.70035

Highlights of Model Quality Assessment in CASP16

Proteins. 2026 Jan;94(1):314-329. doi: 10.1002/prot.70035. Epub 2025 Aug 14.

Authors

Alisia Fadini¹, Recep Adiyaman², Shaima N Alhaddad², Behnosh Behzadi², Jianlin Cheng³, Xinyue Cui⁴, Nicholas S Edmunds², Lydia Freddolino^{5

6}, Ahmet G Genc², Fang Liang⁴, Dong Liu⁴, Jian Liu³, Quancheng Liu⁶, Liam J McGuffin², Pawan Neupane³, Chunxiang Peng⁵, David R Shortle⁷, Meng Sun⁴, Haodong Wang⁴, Qiqige Wuyun⁸, Guijun Zhang⁴, Xuanfeng Zhao⁴, Wei Zheng^{6

9}, Randy J Read¹

Affiliations

¹ Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
² School of Biological Sciences, University of Reading, Reading, UK.
³ Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA.
⁴ College of Information Engineering, Zhejiang University of Technology, Hangzhou, China.
⁵ Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA.
⁶ Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan, USA.
⁷ Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.
⁸ Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, USA.
⁹ NITFID, School of Statistics and Data Science, AAIS, LPMC and KLMDASR, Nankai University, Tianjin, China.

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.

Keywords: computational molecular biology; molecular models; protein conformation; protein domains.

MeSH terms

Computational Biology*
Models, Molecular*
Nucleic Acid Conformation
Protein Conformation
Protein Folding
Sequence Alignment

Abstract

MeSH terms

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