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A study of different annealing schedules in SArna-predict A permutation based SA algorithm for rna folding

International Journal of Intelligent Computing and Cybernetics 2015年第2期8卷 152-171页

作者： Herbert H.Tsang Kay C.Wiese Applied Research Lab Trinity Western UniversityLangleyCanada School of Computing Science Simon Fraser UniversitySurreyCanada

Purpose–The purpose of this paper is to present a study of the effect of different types of annealing schedules for a ribonucleic acid(rna)secondary structure prediction algorithm based on simulated annealing(SA).Design/methodology/approach–An rna folding algorithm was implemented that assembles the final structure from potential substructures(helixes).Structures are encoded as a permutation of helixes.An SA searches this space of permutations.Parameters and annealing schedules were studied and fine-tuned to optimize algorithm performance.Findings–In comparing with mfold,the SA algorithm shows comparable results(in terms of F-measure)even with a less sophisticated thermodynamic model.In terms of average specificity,the SA algorithm has provided surpassing results.Research limitations/implications–Most of the underlying thermodynamic models are too simplistic and incomplete to accurately model the free energy for larger structures.This is the largest limitation of free energy-based rna folding algorithms in general.Practical implications–The algorithm offers a different approach that can be used in practice to fold rna sequences quickly.Originality/value–The algorithm is one of only two SA-based rna folding algorithms.The authors use a very different encoding,based on permutation of candidate helixes.The in depth study of annealing schedules and other parameters makes the algorithm a strong contender.Another benefit is that new thermodynamic models can be incorporated with relative ease(which is not the case for algorithms based on dynamic programming).

关键词： Annealing schedule Simulated annealing rna secondary structure prediction Ribonucleic acid rna folding Permutation

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Molecular Phylogenetics and Functional Evolution of Major rna Recognition Domains of Recently Cloned and Characterized Autoimmune rna-Binding Particle

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Genomics, Proteomics & Bioinformatics 2003年第4期1卷 310-320页

作者： ErhanSüleymanoglu Medical Faculty Vienna Biocenter Institute of Biochemistry University of Vienna Vienna Austria.

Heterogeneous nuclear ribonucleoproteins (hnRNPs) are spliceosomal macromole-cular assemblages and thus actively participate in pre-mrna metabolism. They are composed of evolutionary conserved and tandemly repeated motifs, where both rna-binding and protein-protein recognition occur to achieve cellular activities. By yet unknown mechanisms, these ribonucleoprotein (RNP) particles are targeted by autoantibodies and hence play significant role in a variety of human systemic autoimmune diseases. This feature makes them important prognostic markers in terms of molecular epidemiology and pathogenesis of autoimmunity. Since RNP domain is one of the most conserved and widespread scaffolds, evolutionary analyses of these rna-binding domains can provide further clues on disease-specific epitope formation. The study presented herein represents a sequence comparison of rna-recognition regions of recently cloned and characterized human hnRNP A3 with those of other relevant hnRNP A/B-type proteins. Their implications in human autoimmunity are particularly emphasized.

关键词： hnRNP proteins rna folding rna-protein interactions molecular evolution

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Quantum conformational transition in biological macromolecule

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Frontiers of Electrical and Electronic Engineering in China 2017年第2期5卷 143-158页

作者： Liaofu Luo Jun Lv School of Physical Science and Technology Inner Mongolia University Hohhot 010021 China Center for Physics Experiment College of Science Inner Mongolia University of Technology Hohhot 010051 China

Background： Recently we proposed a quantum theory on the conformational change of biomolecule, deduced several equations on protein folding rate from the first principles and discussed the experimental tests of the theory. The article is a review of these works. Methods： Based on the general equation of the conformation-transitional rate several theoretical results are deduced and compared with experimental data through bioinformatics methods. Results： The temperature dependence and the denaturant concentration dependence of the protein folding rate are deduced and compared with experimental data. The quantitative relation between protein folding rate and torsional mode number （or chain length） is deduced and the obtained formula can be applied to rna folding as well. The quantum transition theory of two-state protein is successfully generalized to multi-state protein folding. Then, how to make direct experimental tests on the quantum property of the conformational transition of biomolecule is discussed, which includes the study of protein photo-folding and the observation of the fluctuation of the fluorescence intensity emitted from the protein folding/unfolding event. Finally, the potential applications of the present quantum folding theory to molecular biological problems are sketched in two examples： the glucose transport across membrane and the induced pluripotency in stem cell. Conclusions： The above results show that the quantum mechanics provides a unifying and logically simple theoretical starting point in studying the conformational change of biological macromoleeules. The far-reachlng results in practical application of the theory are expected.

关键词： conformational change quantum transition protein folding rna folding temperature dependence

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