Name
Abstract | ||
|---|---|---|
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. |
Year | DOI | Venue |
|---|---|---|
2008 | 10.1007/978-3-540-88562-7_25 | CMSB |
Keywords | Field | DocType |
amino acid replacement,stochastic analysis,probabilistic model checker prism,abstract stochastic model,mutual replacement,amino acid,biologically similar amino acid,substitution matrix,matlab environment,protein synthesis,amino acid substitution,standard mutation matrix,resulting matrix,stochastic model,probabilistic model | Discrete mathematics,Amino acid,Biochemistry,Computer science,Matrix (mathematics),Transfer RNA,Protein biosynthesis,Stochastic modelling,Ribosome,Computational biology,Substitution matrix,Translation (biology) | Conference |
Volume | ISSN | Citations |
5307 | 0302-9743 | 5 |
PageRank | References | Authors |
0.44 | 9 | 4 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Dragan Bosnacki | 1 | 276 | 26.95 |
| H. M. M. Ten Eikelder | 2 | 33 | 3.55 |
| m n steijaert | 3 | 6 | 1.16 |
| E. P. de Vink | 4 | 241 | 17.20 |