About — OrganiZymeDB

About OrganiZymeDB

OrganiZymeDB is a manually curated database dedicated to enzyme stability and function in the presence of organic solvents. This page describes the rationale behind the resource, its content, and how to use it.

Rationale

The use of enzymes as catalysts is steadily growing, driven by their often remarkable selectivity, catalytic efficiency and their environmental sustainability. Yet enzymes have evolved to function under conditions that are frequently drastically different from those required for real-world applications. In particular, the use of organic solvents is often indispensable in biocatalysis: they solubilize substrates with limited water solubility, including organic synthesis intermediates and (bio-)polymers, act as stoichiometric reactants in processes such as biodiesel production, suppress unwanted hydrolytic side reactions, and can even unlock entirely new chemistries, such as peptide synthesis by proteases or transesterification by lipases.

Despite this practical importance, no central and organized repository of such data existed prior to OrganiZymeDB. This gap particularly hinders computational scientists: without accessible, structured data, it is impossible to train machine-learning algorithms, fine-tune self-supervised AI models, or calibrate physics-based approaches aiming to predict enzyme stability and function in the presence of organic solvents.

OrganiZymeDB was built to address this need, with three main goals:

A resource for biocatalysis

To provide chemists and biotechnologists with a central, extensively annotated and manually curated repository of experimental data on enzyme stability and function in the presence of organic solvents. Such a resource makes it straightforward to assess whether and how an enzyme of interest or its homologs have been characterised in such conditions.

A reference dataset for computational methods

To supply a structured dataset for the development, training and evaluation of computational methods aimed at understanding and predicting enzyme stability and function in the presence of organic solvents.

Expanding the focus of enzyme engineering

To advance research on enzyme stability and function in the presence of organic solvents, driving the use of organic-solvent tolerance as a key parameter in enzyme engineering.

OrganiZymeDB Content

Data in OrganiZymeDB originates exclusively from peer-reviewed scientific publications and preprints, and covers experiments conducted on enzymes that are neither immobilized nor chemically modified. A substantial fraction of the data was manually extracted from figures (barplots, scatterplots, heatmaps) using WebPlotDigitizer, making it available in machine-readable numerical form for the first time.

The database is organized around enzyme entries, each corresponding to the experimental data reported across one or more publications for a given enzyme. Every entry includes enzyme annotations, experimental measurements with associated experimental conditions, barplot visualizations and an AlphaFold3-modeled structure of the studied enzyme. When applicable, each experimental value is paired with a control (the same property measured in pure aqueous conditions) and, for mutants, when available, with the wild-type value under identical conditions (thus in the presence of organic solvent). Experimental assays are classified according to a controlled vocabulary described below.

Each experimental assay is classified according to a two-level controlled vocabulary. The first level describes what the assay broadly measures; the second provides the specific assay type. In addition to this classification, a free-text assay description accompanies each experimental measurement.

Activity

Activity – Classical	Assays measuring enzyme activity, typically the quantity of product formed per amount of enzyme per unit time.
Activity – Michaelis-Menten	Assays measuring Michaelis-Menten kinetic constants such as V_max, k_cat, K_m, or k_cat/K_m.

Specificity

Specificity – Enantioselectivity	Assays measuring the preferential formation of one enantiomeric product over another.
Specificity – Reaction Selectivity	Assays measuring the preferential catalysis of a given chemical reaction over others (e.g., hydrolysis vs. transglycosylation yield for glucose hydrolases).

Stability

Stability – Incubation	Assays evaluating the enzyme organic solvent tolerance, including assays where residual activity is measured in an aqueous phase (in practice often a dilution of the organic solvent-containing incubation solution) and compared to an aqueous control, or measured in the presence of organic solvent and compared to a pre-incubation control also with organic solvent. Unfortunately, scientific publications are often unclear about the exact control and assay solution compositions; thus a degree of uncertainty exists about what exactly is being measured, and whether such assays would better fit in the Activity + Stability – Incubation category (see below). Manual annotations indicate the degree of certainty in the curation, with 'clear annotation' indicating high confidence.
Stability – T_m	Assays measuring the enzyme melting temperature.
Stability – Half-life	Assays measuring the time required for half-loss of activity in the presence of organic solvent.
Stability – C₅₀	Assays measuring the volume fraction of organic solvent required for 50% enzyme denaturation or loss of activity.
Stability – ΔH_Tm	Assays measuring the change in enthalpy upon protein unfolding.
Stability – Complete Inhibition	Assays measuring the amount of organic solvent required for complete loss of enzymatic activity.
Stability – Inactivation Rate	Assays measuring the rate of enzymatic activity loss over time.

Activity + Stability

Activity + Stability – Incubation	Assays in which the enzyme is incubated with organic solvent, followed by a residual activity assay in the same, undiluted, organic-solvent-containing solution, compared to an aqueous control. When assay conditions were ambiguous, entries were preferentially classified as Stability – Incubation, with uncertainty noted.
Activity + Stability – Conversion	Assays measuring substrate conversion after an incubation of the enzyme with both substrates and organic solvent for a defined period.
Activity + Stability – Product Formation	Assays measuring the amount of product formed after enzyme incubation with substrates and organic solvent for a defined period (in general in the form of percentage yield).

Enzyme Description

For each enzyme the following information is provided:

The amino acid sequence, including any modifications described by the authors (truncations, mutations relative to the canonical database sequence), with annotations on whether the sequence was explicitly provided by the authors or derived from a sequence database entry.
When available, the sequence database ID (e.g., UniProt or GenBank) and a direct link to the entry.
The EC number, with a link to the corresponding BRENDA page.
The protein source: whether it was commercially purchased, purified from an organism, or recombinantly expressed, and in the latter case the host organism.
Whether the source organism is extremophilic (and of which type), with a note when the authors themselves describe the enzyme as extremophilic irrespective of the canonical organism annotation.
An AlphaFold3-modelled structure based on the provided sequence.

Experimental Data

For each experimental measurement, the following fields are recorded where available:

Assay type (controlled vocabulary, see the assay classification scheme above) and a free-text description of the assay.
Organic solvent used, with the following information accessible by clicking on the solvent name: CAS and PubChem IDs, logP (water–octanol partition coefficient, with low values indicating hydrophilic compounds), a structural depiction, and the scores and guidelines of the CHEM21 solvent selection guide, which accounts for environmental, safety and human health criteria.
Solvent volume percentage in the assay solution.
Control value(s) (the same property measured in pure aqueous conditions in designated as "aqueous reference", and/or the wild-type value under identical organic-solvent-containing conditions for mutants designated as "WT reference").
Experimentally measured value.
Solution composition (buffer and additional compounds).
Solution pH.
Temperature.
Cofactor(s).
Substrate(s) and their concentrations. For substrates with a discrete molecular structure, clicking on the substrate name provides access to its CAS and PubChem IDs, SMILES string, and an RDKit-rendered depiction.
Reaction product(s), with the same chemical metadata accessible on click for products with a discrete molecular structure.
Shaking conditions where reported.
Free-text curator comments on data quality or noteworthy aspects of the assay.

Using OrganiZymeDB

Search

The search bar at the top of every page accepts queries across multiple categories: protein name, organism, EC number, article, author, substrate, product, and organic solvent. If no result is found in the selected category, the search automatically tries other categories, prioritising assay type matches.

Browse

Browse the full database by enzyme, by scientific publication, or by assay type.

BLAST

To identify whether measurements have been conducted on an enzyme of interest or its homologs, the BLAST page accepts one or more protein sequences and returns matching database entries ranked by E-value. The E-value threshold and maximum number of hits are user-configurable.

Citation & License

How to Cite

If you use OrganiZymeDB in your research, please cite:

        [Authors]. OrganiZymeDB: [Title]. [Journal], [Year].
        DOI: [DOI]
    

License

OrganiZymeDB data is distributed under the Creative Commons Attribution–NonCommercial 4.0 International (CC BY-NC 4.0) licence. For commercial use enquiries, please contact Romain.Debruyne@ulb.be and Fabrizio.Pucci@ulb.be.