ArticleProtein science : a publication of the Protein Society2018
The CaspBase: a curated database for evolutionary biochemical studies of caspase functional divergence and ancestral sequence inference.
Article in Protein science : a publication of the Protein Society, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 26 citations in OpenAlex.
- Evolution of the conformational ensemble and allosteric networks of apoptotic caspases in chordates.The Biochemical journal · 2025Article
- A histidine switch regulates pH-dependent filament formation by the caspase-9 CARD.bioRxiv : the preprint server for biology · 2025Article
- Caspases: structural and molecular mechanisms and functions in cell death, innate immunity, and disease.Cell discovery · 2025Review
- Enzyme Databases in the Era of Omics and Artificial Intelligence.International journal of molecular sciences · 2023Review
- Sequential Unfolding Mechanisms of Monomeric Caspases.Biochemistry · 2023Article
- Sequential unfolding mechanisms of monomeric caspases.bioRxiv : the preprint server for biology · 2023Article
- Comparing the folding landscapes of evolutionarily divergent procaspase-3.Bioscience reports · 2022Article
- Resurrection of an ancient inflammatory locus reveals switch to caspase-1 specificity on a caspase-4 scaffold.The Journal of biological chemistry · 2022Article
- The evolution of regulated cell death pathways in animals and their evasion by pathogens.Physiological reviews · 2022Review
- Evolution of the folding landscape of effector caspases.The Journal of biological chemistry · 2021Article
- Caspases from scleractinian coral show unique regulatory features.The Journal of biological chemistry · 2020Article
- Initiator and executioner caspases in salivary gland apoptosis of Rhipicephalus haemaphysaloides.Parasites & vectors · 2020Article
- Resurrection of ancestral effector caspases identifies novel networks for evolution of substrate specificity.The Biochemical journal · 2019Review
- RedoxiBase: A database for ROS homeostasis regulated proteins.Redox biology · 2019Article
- Tri-arginine exosite patch of caspase-6 recruits substrates for hydrolysis.The Journal of biological chemistry · 2019Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sequence databases are powerful tools for the contemporary scientists' toolkit. However, most functional annotations in public databases are determined computationally and are not verified by a human expert. While hypotheses generated from computational studies are now amenable to experimentation, the quality of the results relies on the quality of input data. We developed the CaspBase to expedite high-quality dataset compilation of annotated caspase sequences, to maximize phylogenetic signal, and to reduce the noise contributed from public databanks. We describe our methods of curation for the CaspBase and how researchers can acquire sequences from CaspBase.org. Our immediate goal for developing the CaspBase was to optimize the ancestral protein reconstruction (APR) of caspases, and we demonstrate the utility of the CaspBase in APR studies. We also developed the Common Position (CP) system for comparing human caspase family paralogs and suggest the CP system as an update to current reporting methods of caspase amino acid positions. We present a standardized multiple sequence alignment (MSA) for the CP system and show the advantage of using large databases such as the CaspBase in defining structural positions in proteins. Although the results described here pertain to caspase evolution and structure-function studies, the methods can be adapted to any gene family.
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