AlphaFold3 at CASP16

Arne Elofsson

doi:10.1002/prot.70044

2025-08-25

Arne Elofsson *

DOI：10.1002/prot.70044

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摘要

En 中文

CASP16实验为评估AlphaFold3提供了首次机会。与AlphaFold2相比，AlphaFold3能够预测非蛋白质分子的结构。根据开发者提供的基准测试结果，预计其在蛋白质预测方面将略优于AlphaFold2。本研究中，我们通过自动服务器提交（AF3-server）和Elofsson小组的手动预测（Elofsson）评估了AlphaFold3的性能。所有预测均通过AlphaFold3网页服务器生成，并对大目标和配体进行了手动干预。与基于AlphaFold2的方法相比，我们发现AlphaFold3在蛋白质复合物预测上表现略优。然而，当对AlphaFold2应用大规模采样时，这种差异消失。此外，根据CASP官方排名，AF3-server在较易目标上的表现优于AlphaFold2，但在较难目标上则不然。进一步分析显示，当考虑最高排名预测时，AF3-server的性能与最佳方法相当；但在评估五个提交模型中的最佳模型时，其表现略逊。值得注意的是，存在某些目标，AF3-server作为排名最高的方法，其预测结果反而劣于排名较低的方法，这表明未来可改进的方向之一是开发更有效的策略以识别生成模型中的最佳结果。在使用AF3-server预测较大蛋白质复合物的计量比时，准确性有限，尤其是在异源复合物目标中。在分析包含核酸的预测时发现，总体准确性相对较低，但AF3-server的性能与排名最高的方法差距不大。总之，AF3-server提供了一个用户友好的工具，其预测结果在CASP的所有类别中均可与当前最佳方法相媲美。

Keyword:

AlphaFold

CASP

protein structure predictions

RNA structure prediction

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期刊

Proteins Structure Function and Bioinformatics

IF:

2.8

论文数:

6.6K

被引数:

1.4W

机构

Stockholm University

学者数:

1.8W

论文数: 1.7W

被引数: 32

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