eQuilibrator--the biochemical thermodynamics calculator.

Area of Science:

• Biochemistry
• Thermodynamics
• Computational Biology

Background:

• Biochemical systems are governed by thermodynamic laws, but accessing and calculating relevant data is challenging.
• Manual thermodynamic calculations for biochemical compounds are complex and time-consuming.
• Accurate thermodynamic data is crucial for understanding cellular processes and metabolic pathways.

Purpose of the Study:

• To develop an integrated system for accessing and calculating thermodynamic properties of biochemicals.
• To simplify the process of answering thermodynamic questions related to biochemical reactions.
• To provide an open-source platform with downloadable thermodynamic data.

Main Methods:

• Developed eQuilibrator, a comprehensive database of thermodynamic properties for biochemical compounds and reactions.
• Implemented a user-friendly web interface for calculating Gibbs energies under various conditions (pH, ionic strength, metabolite concentrations).
• Ensured the eQuilibrator code is open-source and thermodynamic data is freely downloadable.

Main Results:

• eQuilibrator provides accurate thermodynamic data and facilitates easy calculation of Gibbs energies.
• The system successfully addresses the complexity of manual thermodynamic data retrieval and calculation.
• Demonstrated the utility of eQuilibrator for diverse thermodynamic queries, such as ATP hydrolysis at specific pH.

Conclusions:

• eQuilibrator offers a powerful and accessible solution for biochemical thermodynamics research.
• The open-source nature and free data availability promote wider adoption and scientific advancement.
• This tool significantly lowers the barrier to entry for complex thermodynamic analyses in biochemistry.