Protein sequence

@article{hersh1967atlas,
    author = "Hersh, Robert T. and Eck, Richard V. and Dayhoff, Margaret O.",
    title = "Atlas of Protein Sequence and Structure, 1966.",
    year = "1967",
    journal = "Systematic Zoology",
    url = "https://doi.org/10.2307/2412074",
    doi = "10.2307/2412074",
    number = "3",
    pages = "262",
    volume = "16"
}

@misc{dayhoff1969atlas1,
    author = "Dayhoff, M. O",
    title = "Atlas of Protein Sequence and Structure",
    year = "1969",
    howpublished = "Silver Spring, Md., National Biomedical Research Foundation, v. 4",
    note = "talkorigins\_source = {true}; raw\_reference = {Dayhoff, M. O., 1969, Atlas of Protein Sequence and Structure: Silver Spring, Md., National Biomedical Research Foundation, v. 4.}"
}

@article{burger1970atlas,
    author = "Burger, Alfred.",
    title = "Atlas of Protein Sequence and Structure 1969",
    year = "1970",
    journal = "Journal of Medicinal Chemistry",
    url = "https://doi.org/10.1021/jm00296a903",
    doi = "10.1021/jm00296a903",
    number = "2",
    pages = "337-337",
    volume = "13"
}

@article{hersh1970atlas,
    author = "Hersh, Robert and Dayhoff, Margaret O.",
    title = "Atlas of Protein Sequence and Structure, 1969 Volume 4.",
    year = "1970",
    journal = "Systematic Zoology",
    url = "https://doi.org/10.2307/2412455",
    doi = "10.2307/2412455",
    number = "2",
    pages = "192",
    volume = "19"
}

@misc{dayhoff1972atlas2,
    author = "Dayhoff, M. O",
    title = "Atlas of Protein Sequence and Structure",
    year = "1972",
    howpublished = "Sliver Spring, Md., National Biomedical Research Foundation, v. 5",
    note = "talkorigins\_source = {true}; raw\_reference = {Dayhoff, M. O., 1972, Atlas of Protein Sequence and Structure: Sliver Spring, Md., National Biomedical Research Foundation, v. 5.}"
}

@article{fitch1973atlas,
    author = "Fitch, Walter M. and Dayhoff, Margaret O.",
    title = "Atlas of Protein Sequence and Structure, 1972.",
    year = "1973",
    journal = "Systematic Zoology",
    url = "https://doi.org/10.2307/2412105",
    doi = "10.2307/2412105",
    number = "2",
    pages = "196",
    volume = "22"
}

Protein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-guided atlas of the human and Drosophila kinome, built by applying a new interface-aware scoring framework (iLIS) to AlphaFold-Multimer predictions. The resulting atlas recapitulates hallmark sequence preferences, confirms previously reported and functionally related protein-protein interactions, and uncovers unrecognized docking interactions. Notably, our analysis predicts a potentially widespread docking motif on homeodomain transcription factors that mediates interactions with basophilic kinases. Furthermore, we map putative allosteric interaction hotspots across the kinome and provide proof-of-concept evidence that targeting these surfaces can inhibit kinase activity. Finally, we demonstrate the physiological utility of the atlas by identifying a novel regulatory mechanism between Sgg/GSK3 and Hnf4 that controls lipid metabolism in vivo. This resource provides a blueprint for dissecting signaling networks and for the rational design of docking-site-specific kinase modulators.

@article{doi10110120251010681672,
    author = "Kim, Ah-Ram and Huang, Kerui and Johnson, Jared L and Yaron-Barir, Tomer M and Wang, Keven and Cantley, Lewis C and Hu, Yanhui and Perrimon, Norbert",
    title = "A Structure-Guided Kinase-Transcription Factor Interactome Atlas Reveals Docking Landscapes of the Kinome.",
    year = "2025",
    journal = "bioRxiv: the preprint server for biology",
    abstract = "Protein kinases orchestrate cellular processes through phosphorylation, yet the structural basis for their specific binding partner interactions remains largely unmapped. Here, we present a structure-guided atlas of the human and Drosophila kinome, built by applying a new interface-aware scoring framework (iLIS) to AlphaFold-Multimer predictions. The resulting atlas recapitulates hallmark sequence preferences, confirms previously reported and functionally related protein-protein interactions, and uncovers unrecognized docking interactions. Notably, our analysis predicts a potentially widespread docking motif on homeodomain transcription factors that mediates interactions with basophilic kinases. Furthermore, we map putative allosteric interaction hotspots across the kinome and provide proof-of-concept evidence that targeting these surfaces can inhibit kinase activity. Finally, we demonstrate the physiological utility of the atlas by identifying a novel regulatory mechanism between Sgg/GSK3 and Hnf4 that controls lipid metabolism in vivo. This resource provides a blueprint for dissecting signaling networks and for the rational design of docking-site-specific kinase modulators.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/PMC12632555/",
    doi = "10.1101/2025.10.10.681672",
    pmcid = "PMC12632555",
    pmid = "41279736"
}

Protein structure bridges the sequence-function relationship, enabling deep exploration of biological processes across diverse organisms. Insects, the most diverse animal lineage, accounting for over 50% of all described animal species, provide an exceptional system for exploring sequence-structure-function relationships. Here, we reconstructed a comprehensive and well-resolved phylogeny of 4854 insects, spanning all orders. Leveraging this framework, we created an atlas of 13.29 million predicted protein structures from 824 representative species, including 11.63 million newly predicted structures. Structural clustering revealed that proteins with divergent sequences but similar structures could be effectively grouped together. Structural similarity searches against proteins with well-characterized functions yielded annotations for 7.61 million insect proteins, including up to 14% of previously unannotated proteins. We further identified 750 million remote homologs between insect proteins, many of which trace back to ancient branches of the insect phylogeny. Remarkably, despite extensive sequence divergence, cGAS-like receptors (cGLRs) were structurally conserved across all 824 insects. Experimental assays demonstrated that these structurally identified cGLRs play a crucial role in antiviral defense in the yellow fever mosquito. Our findings highlight the significance of structural genomics for understanding protein function and evolution across the tree of life.

@article{doi101038s41422026012200,
    author = "Wu, Weiyin and Cui, Chunlai and Zhu, Yixiao and Chen, Jingxuan and Zhuang, Qiancheng and Wang, Yazhou and Liu, Zicheng and Gao, Han and Ou, Guo-Zheng and Liu, Chao and Tao, Mei and Chen, Yun and Pan, Ronghui and Zhang, Guojie and Cai, Hua and Yang, Jinghua and Chen, Xue-Xin and Zhou, Xiaofan and Wang, Sibao and Shen, Xing-Xing",
    title = "Structural genomics sheds light on protein functions and remote homologs across the insect tree of life.",
    year = "2026",
    journal = "Cell research",
    abstract = "Protein structure bridges the sequence-function relationship, enabling deep exploration of biological processes across diverse organisms. Insects, the most diverse animal lineage, accounting for over 50\% of all described animal species, provide an exceptional system for exploring sequence-structure-function relationships. Here, we reconstructed a comprehensive and well-resolved phylogeny of 4854 insects, spanning all orders. Leveraging this framework, we created an atlas of 13.29 million predicted protein structures from 824 representative species, including 11.63 million newly predicted structures. Structural clustering revealed that proteins with divergent sequences but similar structures could be effectively grouped together. Structural similarity searches against proteins with well-characterized functions yielded annotations for 7.61 million insect proteins, including up to 14\% of previously unannotated proteins. We further identified 750 million remote homologs between insect proteins, many of which trace back to ancient branches of the insect phylogeny. Remarkably, despite extensive sequence divergence, cGAS-like receptors (cGLRs) were structurally conserved across all 824 insects. Experimental assays demonstrated that these structurally identified cGLRs play a crucial role in antiviral defense in the yellow fever mosquito. Our findings highlight the significance of structural genomics for understanding protein function and evolution across the tree of life.",
    url = "https://pmc.ncbi.nlm.nih.gov/articles/8677620/",
    doi = "10.1038/s41422-026-01220-0",
    pmcid = "8677620",
    pmid = "41606168"
}