A kinetic model of RNA folding.
The RNA folding process is represented as a Markov process with states corresponding to RNA secondary structures and transition probabilities corresponding to transformations of a secondary structure caused by formation or disintegration of a helix. Transition probabilities (kinetic constants) are determined. A notion of a group of structures is introduced, and it allows to reduce the state space. Energetic and kinetic parameters of pseudoknots are estimated. Algorithms for computation of a kinetic ensemble for structures and groups of structures are presented, as well as their modifications that take into account pseudoknots. The described algorithms are implemented as a procedure for prediction of RNA secondary structure that is included in the package DNA-SUN.
Mironov
A A
AA
Institute of Genetics, Moscow, Russia.
Lebedev
V F
VF
D000465:Algorithms; D007700:Kinetics; D008390:Markov Chains; D008956:Models, Chemical; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D013816:Thermodynamics
D012313:RNA