IGERS: Inferring Gibbs Energy Changes of Biochemical Reactions from Reaction Similarities
| Autor: | Sascha Bulik, Herrmann-Georg Holzhütter, Sabrina Hoffmann, Andreas Hoppe, Kristian Rother, Johann Gasteiger |
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| Rok vydání: | 2010 |
| Předmět: |
Databases
Factual Chemistry Biophysics Energy metabolism Value (computer science) Chemical similarity Bioinformatics Full coverage Biological Systems and Multicellular Dynamics Gibbs free energy Set (abstract data type) symbols.namesake Models Chemical Similarity (network science) Software Design symbols Biochemical reactions Computer Simulation Energy Metabolism Biological system Software |
| Zdroj: | Biophysical Journal. 98:2478-2486 |
| ISSN: | 0006-3495 |
| Popis: | Mathematical analysis and modeling of biochemical reaction networks requires knowledge of the permitted directionality of reactions and membrane transport processes. This information can be gathered from the standard Gibbs energy changes (DeltaG(0)) of reactions and the concentration ranges of their reactants. Currently, experimental DeltaG(0) values are not available for the vast majority of cellular biochemical processes. We propose what we believe to be a novel computational method to infer the unknown DeltaG(0) value of a reaction from the known DeltaG(0) value of the chemically most similar reaction. The chemical similarity of two arbitrary reactions is measured by the relative number (T) of co-occurring changes in the chemical attributes of their reactants. Testing our method across a validated reference set of 173 biochemical reactions with experimentally determined DeltaG(0) values, we found that a minimum reaction similarity of T = 0.6 is required to infer DeltaG(0) values with an error of10 kJ/mol. Applying this criterion, our method allows us to assign DeltaG(0) values to 458 additional reactions of the BioPath database. We believe our approach permits us to minimize the number of DeltaG(0) measurements required for a full coverage of a given reaction network with reliable DeltaG(0) values. |
| Databáze: | OpenAIRE |
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