A limited memory algorithm for bound constrained optimization
SIAM Journal on Scientific Computing
Petri nets, commutative context-free grammars, and basic parallel processes
Fundamenta Informaticae
Machine Learning
Review: Stochastic approaches for modelling in vivo reactions
Computational Biology and Chemistry
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In this paper we propose a mathematical model of the proteolysis process. Protein digestion is modelled with the use of chemical master equation (CME), i.e. the system of stochastic differential equations corresponding to the network of enzymatic reactions. We present an efficient approach to model parameters' estimation (i.e. enzyme activities) from time series of mass spectrometry data. These results extend previous results in three directions: by relaxing the stationarity of the proteolysis process assumption, by allowing cuts at arbitrary sites in the peptide sequence and by incorporating knowledge from biological databases.