Information Processing Letters
Symbolic Model Checking of Biochemical Networks
CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
Probabilistic symbolic model checking with PRISM: a hybrid approach
International Journal on Software Tools for Technology Transfer (STTT) - Special section on tools and algorithms for the construction and analysis of systems
Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis
Computational Biology and Chemistry
Probabilistic model checking of complex biological pathways
CMSB'06 Proceedings of the 2006 international conference on Computational Methods in Systems Biology
Analysis of signalling pathways using continuous time markov chains
Transactions on Computational Systems Biology VI
Rule-based modelling of cellular signalling
CONCUR'07 Proceedings of the 18th international conference on Concurrency Theory
Theoretical Computer Science
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We present a formal analysis of amino acid replacement during mRNA translation. Building on an abstract stochastic model of arrival of tRNAs and their processing at the ribosome, we compute probabilities of the insertion of amino acids into the nascent polypeptide chain. To this end, we integrate the probabilistic model checker Prism in the Matlab environment. We construct the substitution matrix containing the probabilities of an amino acid replacing another. The resulting matrix depends on various parameters, including availability and concentration of tRNA species, as well as their assignment to individual codons. We draw a parallel with the standard mutation matrices like Dayhoff and PET91, and analyze the mutual replacement of biologically similar amino acids.