ArticleBriefings in bioinformatics2021
FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction.
Article in Briefings in bioinformatics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Structural and functional characterisation of a reconstructed ancestral strigolactone receptor.The Plant journal : for cell and molecular biology · 2026Article
- FireProtASR 2.0: evolution-guided Design of Protein Ancestors and Successors with phylogenetics and machine learning.Briefings in bioinformatics · 2026Article
- Advances and opportunities for computational interrogation of plant proteins.The Plant journal : for cell and molecular biology · 2026Review
- Designing Novel Aspartic Protease (NAP) Using Ancestral Sequence Reconstruction (ASR) for Cheesemaking.Molecular biotechnology · 2026Article
- Genetic comparisons of interleukin-17 reveal a framework for complex signaling evolution.bioRxiv : the preprint server for biology · 2026Article
- Computational rational design of unspecific peroxygenase for C-H oxidation.Science advances · 2026Article
- FireProtDB 2.0: large-scale manually curated database of the protein stability data.Nucleic acids research · 2026Article
- Dormancy Versus Germination: 3D Protein Modeling and Evolutionary Analyses Define the Roles of Genetic Variants in the Barley MKK3 Enzyme.International journal of molecular sciences · 2026Article
- A trimer ancestral spike-based mRNA vaccine confers cross-generational protection against SADS-CoV.Journal of nanobiotechnology · 2025Article
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- Directed evolution of hydrocarbon-producing enzymes.Biotechnology for biofuels and bioproducts · 2025Review
- Discovery to Engineering of Mycotoxin Deoxynivalenol Degrading Enzymes Based on the Specialized Glyoxalase I.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The structure and dynamics of water molecule networks underlie catalytic efficiency in a glycoside exo-hydrolase.Communications biology · 2025Article
- Anticipating protein evolution with successor sequence predictor.Journal of cheminformatics · 2025Article
- Recent advances on protein engineering for improved stability.Biodesign research · 2025Review
- Engineering Dehalogenase Enzymes Using Variational Autoencoder-Generated Latent Spaces and Microfluidics.JACS Au · 2025Article
- EzSEA: an interactive web interface for enzyme sequence evolution analysis.Bioinformatics advances · 2025Article
- Ancestral Sequence Reconstruction for Designing Biocatalysts and Investigating their Functional Mechanisms.JACS Au · 2024Review
- Do protein language models learn phylogeny?Briefings in bioinformatics · 2024Article
- Ancestral Reconstruction and the Evolution of Protein Energy Landscapes.Annual review of biophysics · 2024Review
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is a great interest in increasing proteins' stability to widen their usability in numerous biomedical and biotechnological applications. However, native proteins cannot usually withstand the harsh industrial environment, since they are evolved to function under mild conditions. Ancestral sequence reconstruction is a well-established method for deducing the evolutionary history of genes. Besides its applicability to discover the most probable evolutionary ancestors of the modern proteins, ancestral sequence reconstruction has proven to be a useful approach for the design of highly stable proteins. Recently, several computational tools were developed, which make the ancestral reconstruction algorithms accessible to the community, while leaving the most crucial steps of the preparation of the input data on users' side. FireProtASR aims to overcome this obstacle by constructing a fully automated workflow, allowing even the unexperienced users to obtain ancestral sequences based on a sequence query as the only input. FireProtASR is complemented with an interactive, easy-to-use web interface and is freely available at https://loschmidt.chemi.muni.cz/fireprotasr/.
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