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Simulating the folding pathway of RNA Secondary Structure Using the Modified Ant Colony Algorithm

Journal of Bionic Engineering 2010年第4期7卷 382-389页

作者： Jun Yu~(1,2),Changhai Zhang~(1,2),Yuanning Liu~(1,2),Xin Li~(1,2) 1.College of Computer Science and Technology,Jilin University,Changchun 130012,P.R.China 2.Key Laboratory of Symbolic Computation and Knowledge Engineering (Ministry of Education,China) Jilin University,Changchun 130012,P.R.China College of Computer Science and Technology Jilin University Changchun P. R. China Key Laboratory of Symbolic Computation and Knowledge Engineering (Ministry of Education China) Jilin University Changchun P. R. China

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.

关键词： RNA secondary structure folding pathway ant colony algorithm

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Characterization of the Partially Folded Monomeric Intermediate of Creatine Kinase

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Tsinghua Science and Technology 2002年第4期7卷 347-351页

作者：朴龙斗周海梦 Department of Biological Sciences and Biotechnology Tsinghua University Beijing 100084 China

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.

关键词： creatine kinase intermediate partially folded state folding pathway

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