The Genome3D Consortium for Structural Annotations of Selected Model Organisms

Waman, Vaishali P.; Blundell, Tom L.; Buchan, Daniel W. A.; Gough, Julian; Jones, David T.; Kelley, Lawrence A.; Pandurangan, Arun Prasad; Sillitoe, Ian; Sternberg, Michael J.E.; Tôrres, Pedro; Orengo, Christine A.

doi:10.1007/978-1-0716-0708-4_3

Cited by 5 publications

(4 citation statements)

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“…Structure-based protein taxonomy developed by SCOP (Murzin et al, 1995 ) and CATH (Orengo et al, 1997 ) classification systems identify ≈1,500 and ≈1,400 folds, respectively. Despite being finite, and in spite of the remarkable advances in experimental 3D structure determination technologies, the protein universe is yet to be fully mapped (Levitt, 2009 ; Waman et al, 2020 ). Due to the relative ease of DNA sequencing, mapping genomes has far outpaced protein structure determination.…”

Section: Evolution Of the Protein Universe Recapitulates The Evolutio...mentioning

confidence: 99%

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Protein structures unravel the signatures and patterns of deep time evolution

Harish

2024

QRB Discovery

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The formulation and testing of hypotheses using ‘big biology data’ often lie at the interface of computational biology and structural biology. The Protein Data Bank (PDB), which was established about 50 years ago, catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. The comparative analysis of the structures of homologs, particularly of proteins, from different species has significantly improved the in-depth analyses of molecular and cell biological questions. In addition, computational tools that were developed to analyze the ‘protein universe’ are providing the means for efficient resolution of longstanding debates in cell and molecular evolution. In celebrating the golden jubilee of the PDB, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of fundamental interest—the reconstruction of the distant biological past—has gone almost unnoticed. Here, I discuss the recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting hypotheses in evolutionary biology. Specifically, I show that evolutionary characters defined by protein structure are superior compared to conventional sequence characters for reliable, data-driven resolution of competing hypotheses about the origins of the major clades of life and evolutionary relationship among those clades. Since the better quality data unequivocally support two primary domains of life, it is imperative that the primary classification of life be revised accordingly.

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Section: Evolution Of the Protein Universe Recapitulates The Evolutio...mentioning

confidence: 99%

“…At any rate, up to 70% of proteins of many species can be mapped to known structures (Kurland and Harish, 2015a ; Waman et al, 2020 ). This is already providing a substantial view of the distribution of proteomes in the cellular universe (Buchan et al, 2002 ; Chothia et al, 2003 ).…”

Section: Evolution Of the Protein Universe Recapitulates The Evolutio...mentioning

confidence: 99%

Protein structures unravel the signatures and patterns of deep time evolution

Harish

2024

QRB Discovery

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“…Template-based models have the distinct advantage of enabling the mapping of a model to homologues with known structures, thus mapping to experimentally derived structures which can be in distinct conformational states or in complex with other molecules. Some tools excel at general-purpose protein structure modelling; others specialise in placing relevant ligands in the context of a model or representing conformational flexibility with ensembles of potential conformations 14,16,[22][23][24] (Figure 2). For example, AlphaFold 2.0 cannot perform docking of small molecules, even if they are obligate ligands of the proteins, such as Zinc-finger proteins.…”

Section: Figure 1 -Growth Of the Uniprot And The Pdb Databasesmentioning

confidence: 99%

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Váradi

Nair

Sillitoe

et al. 2022

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While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated theoretical protein modelling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various data providers and perform comparative analysis to identify what models best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. 3D-Beacons allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and the Protein Data Bank.

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“…Despite being finite, and in spite of the remarkable advances in experimental 3D structure determination technologies, the protein universe is yet to be fully mapped (Levitt, 2009;Waman et al, 2020). Due to the relative ease of DNA sequencing, mapping genomes has far outpaced protein structure determination.…”

Section: Evolution Of the Protein Universe Recapitulates The Evolution Of Cellular Universementioning

confidence: 99%

Peering into the Abyss with Evolutionary Telescopes: How protein structure-telescopes can look further back in time (and why sequence-telescopes cannot)

Harish¹

2021

Preprint

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This year marks the Golden Jubilee celebrations of the Protein Data Bank (PDB), which catalogs three-dimensional (3D) shapes of organic macromolecules and showcases a structural view of biology. In celebrating this occasion, much has been written about the transformative impact of PDB on a broad range of fields of scientific inquiry and how structural biology transformed the study of the fundamental processes of life. Yet, the transforming influence of PDB on one field of inquiry of broad interest—the reconstruction of the distant evolutionary past—has gone almost unnoticed. Here, I review recent advances to highlight how insights and tools of structural biology are bearing on the data required for the empirical resolution of vigorously debated and apparently contradicting theories in evolutionary biology.

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The Genome3D Consortium for Structural Annotations of Selected Model Organisms

Cited by 5 publications

References 82 publications

Protein structures unravel the signatures and patterns of deep time evolution

Protein structures unravel the signatures and patterns of deep time evolution

3D-Beacons: Decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

Peering into the Abyss with Evolutionary Telescopes: How protein structure-telescopes can look further back in time (and why sequence-telescopes cannot)

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