Performance of Hybrid Strategies Combining MDockPP and AlphaFold2 in CAPRI Rounds 47-55.

IF 3.2 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-02-04 DOI:10.1002/prot.26805

Rui Duan, Xianjin Xu, Liming Qiu, Shuang Zhang, Xiaoqin Zou

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Abstract

CAPRI challenges offer a range of blind tests for biomolecule interaction prediction. This study evaluates the performance of our prediction protocols for the human group Zou and the server group MDockPP in CAPRI rounds 47-55, highlighting the impact of AlphaFold2 (AF2) and the effectiveness of massive sampling approaches. Prior to AlphaFold2's release, our methods relied on homology modeling and docking-based protocols, achieving limited accuracy due to constraints in structural templates and inherent docking limitations. After AlphaFold2's public release, which demonstrated breakthrough accuracy in protein structure prediction, we integrated its multimer models and massive sampling techniques into our protocols. This integration significantly improved prediction accuracy, with human predictions increasing from 1 correct interface of 19 pre-AlphaFold2 to 4 of 8 post-AlphaFold2. The massive sampling approach further enhanced performance, particularly for targets T231 and T233, yielding medium-quality models that default parameters could not achieve.

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来源期刊

Proteins-Structure Function and Bioinformatics 生物-生化与分子生物学

CiteScore

5.90

自引率

3.40%

发文量

172

审稿时长

3 months

期刊介绍： PROTEINS : Structure, Function, and Bioinformatics publishes original reports of significant experimental and analytic research in all areas of protein research: structure, function, computation, genetics, and design. The journal encourages reports that present new experimental or computational approaches for interpreting and understanding data from biophysical chemistry, structural studies of proteins and macromolecular assemblies, alterations of protein structure and function engineered through techniques of molecular biology and genetics, functional analyses under physiologic conditions, as well as the interactions of proteins with receptors, nucleic acids, or other specific ligands or substrates. Research in protein and peptide biochemistry directed toward synthesizing or characterizing molecules that simulate aspects of the activity of proteins, or that act as inhibitors of protein function, is also within the scope of PROTEINS. In addition to full-length reports, short communications (usually not more than 4 printed pages) and prediction reports are welcome. Reviews are typically by invitation; authors are encouraged to submit proposed topics for consideration.