Resumo (PT):
Abstract (EN):
Recent computational methodologies, such as individual-based modelling, pave the way to the search for explanatory insight
into the collective behaviour of molecules. Many reviews offer an up-to-date perspective about such methodologies, but little is
discussed about the practical information requirements involved. The biological information used as input should be easily
and routinely determined in the laboratory, publicly available and, preferably, organized in programmatically accessible databases. This review is the first to provide a systematic and comprehensive overview of available resources for the modelling of
metabolic events at the molecular scale. The glycolysis pathway of Escherichia coli, which is one of the most studied pathways
in Microbiology, serves as case study. This curation addressed structural information about E. coli (i.e. defining the simulation
environment), the reactions forming the glycolysis pathway including the enzymes and the metabolites (i.e. the molecules to
be represented), the kinetics of each reaction (i.e. behavioural logic of the molecules) and diffusion parameters for all enzymes
and metabolites (i.e. molecule movement in the environment). Furthermore, the interpretation of relevant biological features,
such as molecular diffusion and enzyme kinetics, and the connection of experimental determination and simulation validation
are detailed. Notably, the information from classical theories, such as enzymatic rates and diffusion coefficients, is translated
to simulation parameters, such as collision efficiency and particle velocity.
Idioma:
Inglês
Tipo (Avaliação Docente):
Científica
Nº de páginas:
14