ArticleBriefings in bioinformatics2023
FireProt 2.0: web-based platform for the fully automated design of thermostable proteins.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
19 citing papers in PubMed.
- Antibiotic- and inducer-free biosynthesis of indican from crude glycerol using engineered probiotic Escherichia coli Nissle 1917.Bioresources and bioprocessing · 2026Article
- Multicyclic D-Stereospecific Hydrolase Dimer With High Sustained Activity.Angewandte Chemie (International ed. in English) · 2026Article
- Elucidating carbohydrate preference and engineering glucose transport in Caldimonas thermodepolymerans for enhanced polyhydroxyalkanoate production.Applied microbiology and biotechnology · 2026Article
- Combined computational, rational, and empirical design of boiling-resistant keratinase.Applied and environmental microbiology · 2026Article
- Protein folding stability estimation with explicit consideration of unfolded states.Nature communications · 2026Article
- Optimizing Stability in Dynamic Small-Molecule Binding Proteins.Journal of the American Chemical Society · 2026Article
- AI-driven discovery in protein science for immunology and infectious disease research.Frontiers in bioinformatics · 2026Review
- Computationally Guided Design of a Soluble, Abundant and Functional AnfH Variant for the Expression of Fe-Only Nitrogenase in Plant Mitochondria.Plant biotechnology journal · 2025Article
- Microfluidic-Assisted Evolution of a Robust NADChemSusChem · 2025Article
- Allosteric Autoregulation of Ferroptosis Suppressor Protein 1 Activity by its N-myristoylated Tail.Journal of molecular biology · 2025Article
- Improvement of Catalytic Activity and Thermostability of Alginate Lyase VxAly7B-CM via Rational Computational Design Strategies.Marine drugs · 2025Article
- Article
- Thermostability Improvement of the Chitinase fromBiomolecules · 2025Article
- Enhancing recombinant growth factor and serum protein production for cultivated meat manufacturing.Microbial cell factories · 2025Review
- Improved Enzymatic Properties of Chitosanase CsnMY002 fromInternational journal of molecular sciences · 2025Article
- Codeine 3-O-demethylase catalyzed biotransformation of morphinan alkaloids in Escherichia coli: site directed mutagenesis of terminal residues improves enzyme expression, stability and biotransformation yield.Journal of biological engineering · 2025Article
- Enhancement of tryptophan 2-monooxygenase thermostability by semi-rational enzyme engineering: a strategic design to minimize experimental investigation.RSC chemical biology · 2024Article
- Revolutionizing Molecular Design for Innovative Therapeutic Applications through Artificial Intelligence.Molecules (Basel, Switzerland) · 2024Review
- Atomistic simulations reveal impacts of missense mutations on the structure and function of SynGAP1.Briefings in bioinformatics · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Thermostable proteins find their use in numerous biomedical and biotechnological applications. However, the computational design of stable proteins often results in single-point mutations with a limited effect on protein stability. However, the construction of stable multiple-point mutants can prove difficult due to the possibility of antagonistic effects between individual mutations. FireProt protocol enables the automated computational design of highly stable multiple-point mutants. FireProt 2.0 builds on top of the previously published FireProt web, retaining the original functionality and expanding it with several new stabilization strategies. FireProt 2.0 integrates the AlphaFold database and the homology modeling for structure prediction, enabling calculations starting from a sequence. Multiple-point designs are constructed using the Bron-Kerbosch algorithm minimizing the antagonistic effect between the individual mutations. Users can newly limit the FireProt calculation to a set of user-defined mutations, run a saturation mutagenesis of the whole protein or select rigidifying mutations based on B-factors. Evolution-based back-to-consensus strategy is complemented by ancestral sequence reconstruction. FireProt 2.0 is significantly faster and a reworked graphical user interface broadens the tool's availability even to users with older hardware. FireProt 2.0 is freely available at http://loschmidt.chemi.muni.cz/fireprotweb.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.