Alpha&ESMhFolds: A Web Server for Comparing AlphaFold2 and ESMFold Models of the Human Reference Proteome

IF 4.7 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Biology Pub Date : 2024-09-01 DOI:10.1016/j.jmb.2024.168593

引用次数: 0

Abstract

We develop a novel database Alpha&ESMhFolds which allows the direct comparison of AlphaFold2 and ESMFold predicted models for 42,942 proteins of the Reference Human Proteome, and when available, their comparison with 2,900 directly associated PDB structures with at least a structure to sequence coverage of 70%. Statistics indicate that good quality models tend to overlap with a TM-score >0.6 as long as some PDB structural information is available. As expected, a direct model superimposition to the PDB structure highlights that AlphaFold2 models are slightly superior to ESMFold ones. However, some 55% of the database is endowed with models overlapping with TM-score <0.6. This highlights the different outputs of the two methods. The database is freely available for usage at https://alpha-esmhfolds.biocomp.unibo.it/.

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Alpha&ESMhFolds：用于比较人类参考蛋白质组的 AlphaFold2 和 ESMFold 模型的网络服务器。

我们开发了一个新颖的 Alpha&ESMhFolds 数据库，可以直接比较 AlphaFold2 和 ESMFold 预测的 42,942 个参考人类蛋白质组的蛋白质模型，并在有数据的情况下，将其与 2,900 个直接相关的 PDB 结构（结构与序列的覆盖率至少为 70%）进行比较。统计结果表明，只要有一些 PDB 结构信息，高质量的模型往往会与 TM 分数大于 0.6 的模型重叠。不出所料，直接将模型叠加到 PDB 结构上会发现 AlphaFold2 模型略优于 ESMFold 模型。然而，数据库中约有 55% 的模型与 TM-score

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来源期刊

Journal of Molecular Biology 生物-生化与分子生物学

CiteScore

11.30

自引率

1.80%

发文量

412

审稿时长

28 days

期刊介绍： Journal of Molecular Biology (JMB) provides high quality, comprehensive and broad coverage in all areas of molecular biology. The journal publishes original scientific research papers that provide mechanistic and functional insights and report a significant advance to the field. The journal encourages the submission of multidisciplinary studies that use complementary experimental and computational approaches to address challenging biological questions. Research areas include but are not limited to: Biomolecular interactions, signaling networks, systems biology; Cell cycle, cell growth, cell differentiation; Cell death, autophagy; Cell signaling and regulation; Chemical biology; Computational biology, in combination with experimental studies; DNA replication, repair, and recombination; Development, regenerative biology, mechanistic and functional studies of stem cells; Epigenetics, chromatin structure and function; Gene expression; Membrane processes, cell surface proteins and cell-cell interactions; Methodological advances, both experimental and theoretical, including databases; Microbiology, virology, and interactions with the host or environment; Microbiota mechanistic and functional studies; Nuclear organization; Post-translational modifications, proteomics; Processing and function of biologically important macromolecules and complexes; Molecular basis of disease; RNA processing, structure and functions of non-coding RNAs, transcription; Sorting, spatiotemporal organization, trafficking; Structural biology; Synthetic biology; Translation, protein folding, chaperones, protein degradation and quality control.

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