Protein Complex Structure Prediction With AlphaFold-Enhanced HDOCK in CAPRI Rounds 47-55.

IF 3.2 4区生物学 Q2 BIOCHEMISTRY & MOLECULAR BIOLOGY

Proteins-Structure Function and Bioinformatics Pub Date : 2025-04-01 DOI:10.1002/prot.26823

Hao Li, Peicong Lin, Yurui Li, Sheng-You Huang

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Abstract

Protein-protein interactions play a critical role in numerous biological processes, and understanding these interactions is essential for deciphering cellular mechanisms and designing therapeutic interventions. Predicting protein-protein complex structures by computational methods is an important approach to studying protein-protein interactions. The CAPRI (Critical Assessment of PRediction of Interactions) experiment has served as a benchmark for evaluating computational methods for predicting protein complex structures. We participated in CAPRI Rounds 47-55 and continuously refined our complex structure prediction strategies throughout this period. Initially, our approach was based on a hybrid docking strategy that combined template-based and ab initio docking methods. However, starting from Round 53, we integrated AlphaFold into our prediction pipeline. Inspired by the experiences of other participants in Round 54, we further refined our use of AlphaFold by enhancing the sampling strategy, which significantly improved our prediction accuracy in Round 55.

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利用alphafold增强的HDOCK预测CAPRI蛋白复合体结构47-55。

蛋白质-蛋白质相互作用在许多生物过程中起着关键作用，理解这些相互作用对于破译细胞机制和设计治疗干预措施至关重要。用计算方法预测蛋白质-蛋白质复合物结构是研究蛋白质-蛋白质相互作用的重要途径。CAPRI（相互作用预测的关键评估）实验已经成为评估预测蛋白质复合体结构的计算方法的基准。我们参加了CAPRI第47-55轮，并在此期间不断完善我们的复杂结构预测策略。最初，我们的方法是基于混合对接策略，结合了基于模板和从头算的对接方法。然而，从第53轮开始，我们将AlphaFold集成到我们的预测管道中。受第54轮其他参与者经验的启发，我们进一步改进了AlphaFold的使用，增强了采样策略，这大大提高了我们在第55轮的预测精度。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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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.