Université Paris Cité and Université des Antilles and Université de la Réunion, BIGR, UMR_S1134, DSIMB Team, Inserm, Paris, France.
Methods Mol Biol. 2024;2836:235-252. doi: 10.1007/978-1-0716-4007-4_13.
AlphaFold2 (AF2) has emerged in recent years as a groundbreaking innovation that has revolutionized several scientific fields, in particular structural biology, drug design, and the elucidation of disease mechanisms. Many scientists now use AF2 on a daily basis, including non-specialist users. This chapter is aimed at the latter. Tips and tricks for getting the most out of AF2 to produce a high-quality biological model are discussed here. We suggest to non-specialist users how to maintain a critical perspective when working with AF2 models and provide guidelines on how to properly evaluate them. After showing how to perform our own structure prediction using ColabFold, we list several ways to improve AF2 models by adding information that is missing from the original AF2 model. By using software such as AlphaFill to add cofactors and ligands to the models, or MODELLER to add disulfide bridges between cysteines, we guide users to build a high-quality biological model suitable for applications such as drug design, protein interaction, or molecular dynamics studies.
近年来,AlphaFold2(AF2)作为一项突破性的创新技术出现,彻底改变了多个科学领域,特别是结构生物学、药物设计和疾病机制的阐明。现在,许多科学家包括非专业用户都在日常使用 AF2。本章针对的是后者。这里讨论了一些技巧和窍门,可帮助非专业用户充分利用 AF2 来生成高质量的生物学模型。我们建议非专业用户在使用 AF2 模型时保持批判性思维,并提供关于如何正确评估它们的指导方针。在展示如何使用 ColabFold 进行我们自己的结构预测之后,我们列出了通过添加原始 AF2 模型中缺失的信息来改进 AF2 模型的几种方法。通过使用 AlphaFill 等软件向模型中添加辅助因子和配体,或者使用 MODELLER 添加半胱氨酸之间的二硫键,我们指导用户构建适用于药物设计、蛋白质相互作用或分子动力学研究等应用的高质量生物学模型。
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