eQuilibrator 3.0 -- a platform for the estimation of thermodynamic constants
eQuilibrator (equilibrator.weizmann.ac.il) is a calculator for biochemical equilibrium constants and Gibbs free energies, originally designed as a web-based interface. While the website now counts ${\sim}1000$ distinct monthly users, its design could not accommodate larger compound databases and it lacked an application programming interface (API) for integration in other tools developed by the systems biology community. Here, we report a new python-based package for eQuilibrator, that comes with many new features such as a 50-fold larger compound database, the ability to add novel compound structures, improvements in speed and memory use, and correction for Mg2+ ion concentrations. Moreover, it adds the ability to compute the covariance matrix of the uncertainty between estimates, for which we show the advantages and describe the application in metabolic modeling. We foresee that these improvements will make thermodynamic modeling more accessible and facilitate the integration of eQuilibrator into other software platforms.
Code (0)
등록된 구현이 없습니다.
Similar Papers 제목 키워드 기반
Hierarchical Bond Graph Modelling of Biochemical Networks
The bond graph approach to modelling biochemical networks is extended to allow hierarchical construction of complex models from simpler components. This is made possible by representing the simpler components as thermody…
Asymptotically Optimal Change Detection for Unnormalized Pre- and Post-Change Distributions
This paper addresses the problem of detecting changes when only unnormalized pre- and post-change distributions are accessible. This situation happens in many scenarios in physics such as in ferromagnetism, crystallograp…
Change DetectionThermodynamic Prediction Enabled by Automatic Dataset Building and Machine Learning
New discoveries in chemistry and materials science, with increasingly expanding volume of requisite knowledge and experimental workload, provide unique opportunities for machine learning (ML) to take critical roles in ac…
Thermodynamic bounds on ultrasensitivity in covalent switching
Switch-like motifs are among the basic building blocks of biochemical networks. A common motif that can serve as an ultrasensitive switch consists of two enzymes acting antagonistically on a substrate, one making and the…
Structural thermokinetic modelling
Translating metabolic networks into dynamic models is difficult if kinetic constants are unknown. Structural Kinetic Modelling (SKM) replaces reaction elasticities by independent random numbers. Here I propose a variant …