A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each s...A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial stage.Furthermore,a more realistic formula is used to compute the energy ofmulti-branch loop in the following iteration.Then a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different stems.Finally by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values forparameters.The measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.展开更多
The importance of understanding the protein folding pathway and intermediates is well recognized on the basis of extensive studies of protein folding in vitro and in vivo. Creatine kinase (CK) is a typical model fo...The importance of understanding the protein folding pathway and intermediates is well recognized on the basis of extensive studies of protein folding in vitro and in vivo. Creatine kinase (CK) is a typical model for studying unfolding and refolding of proteins due to several interesting properties. Recent studies on the folding of CK show that its partially folded monomeric intermediate is present kinetically and is stable at equilibrium. The present paper contains 33 references as a mini review to characterize the properties of CK from studies on the CK folding pathway. Characterization of these intermediates is an essential step toward understanding the mechanism of protein folding. Some well determined schemes are suggested as protein folding models.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.60971089)the Specialized Research Foundation for the Doctoral Program of Higher Education of China(Grant No.20070183057)
文摘A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial stage.Furthermore,a more realistic formula is used to compute the energy ofmulti-branch loop in the following iteration.Then a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different stems.Finally by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values forparameters.The measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.
基金Supported by the National Key Basic Research Specific Foundation of China (No. G19990 75 60 7)
文摘The importance of understanding the protein folding pathway and intermediates is well recognized on the basis of extensive studies of protein folding in vitro and in vivo. Creatine kinase (CK) is a typical model for studying unfolding and refolding of proteins due to several interesting properties. Recent studies on the folding of CK show that its partially folded monomeric intermediate is present kinetically and is stable at equilibrium. The present paper contains 33 references as a mini review to characterize the properties of CK from studies on the CK folding pathway. Characterization of these intermediates is an essential step toward understanding the mechanism of protein folding. Some well determined schemes are suggested as protein folding models.
