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Effects of Mapping Methods on Accuracy of Protein Coding Regions Prediction
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作者 马玉韬 张成 +2 位作者 杨泽林 李琦 杨婷 《Agricultural Science & Technology》 CAS 2011年第12期1802-1806,1860,共6页
[Objective] To discuss the effects of major mapping methods for DNA sequence on the accuracy of protein coding regions prediction,and to find out the effective mapping methods.[Method] By taking Approximate Correlatio... [Objective] To discuss the effects of major mapping methods for DNA sequence on the accuracy of protein coding regions prediction,and to find out the effective mapping methods.[Method] By taking Approximate Correlation(AC) as the full measure of the prediction accuracy at nucleotide level,the windowed narrow pass-band filter(WNPBF) based prediction algorithm was applied to study the effects of different mapping methods on prediction accuracy.[Result] In DNA data sets ALLSEQ and HMR195,the Voss and Z-Curve methods are proved to be more effective mapping methods than paired numeric(PN),Electron-ion Interaction Potential(EIIP) and complex number methods.[Conclusion] This study lays the foundation to verify the effectiveness of new mapping methods by using the predicted AC value,and it is meaningful to reveal DNA structure by using bioinformatics methods. 展开更多
关键词 Prediction accuracy protein coding regions Mapping method Windowed Narrow pass-band filter
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Construction of Prokaryotic Expression Vectors of EBP1 Gene from Nervilia Fordii (Hance) Schltr. 被引量:1
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作者 黄琼林 何瑞 +1 位作者 詹若挺 陈蔚文 《Agricultural Science & Technology》 CAS 2012年第6期1211-1214,共4页
[Objective] To construct prokaryotic expression vectors encoding gene Erb3binding protein (EBP1), which plays important roles in regulating plant organ size from Nervilia fordii (Hance) Schltr. [Methods] PCR produ... [Objective] To construct prokaryotic expression vectors encoding gene Erb3binding protein (EBP1), which plays important roles in regulating plant organ size from Nervilia fordii (Hance) Schltr. [Methods] PCR products of NfEBP1 with particular restriction sites and expression vectors, pET-28 and pET-16b were digested. Ligation, transformation and selection were performed to construct the recombinant plasmids pET-28-NfEBP1 and pET-16-NfEBP1. The recombinant plasmids were transformed into E. coli BL21 using heat -shock transformation. [Results] Recombinant plasmids pET-28-NfEBP1-1188 and pET-16-NfEBP1-1188 were constructed and transformed into expressional host cells, E. coli BL21, and validated by colony PCR, sequencing and double digestion. [Conclusion] Prokaryotic expression vectors of EBP1 gene from N. fordii were successfully constructed, which laid the foundation for characterization of the gene function. 展开更多
关键词 Nervilia fordii (Hance) Schltr. Coding gene of Erb3-binding protein (EBP1) Prokaryotic expression vector
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MULTISTAGE FILTERS FOR IDENTIFICATION OF EUKARYOTIC PROTEIN CODING REGIONS 被引量:1
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作者 MALAYA KUMAR HOTA VINAY KUMAR SRIVASTAVA 《International Journal of Biomathematics》 2012年第2期43-60,共18页
A class of multistage filters, namely, real narrowband bandpass filter (RNBPF) has been previously used for identification of protein coding regions. This filter passes the frequency component at 2π/3 along with it... A class of multistage filters, namely, real narrowband bandpass filter (RNBPF) has been previously used for identification of protein coding regions. This filter passes the frequency component at 2π/3 along with its conjugate. This conjugate frequency compo- nent may degrade the identification accuracy. To improve the identification accuracy, two types of multistage filters are proposed in this paper. A complex narrowband bandpass filter (CNBPF) is proposed for suppressing the conjugate frequency component which, in turn, reduces the background noise present in the deoxyribonucleic acid (DNA) spec- trum and improves identification accuracy. By cascading RNBPF with moving average filter (RNBPFMA), another type of multistage filter is proposed. As moving average filter smooth out the rapid variations in the DNA spectrum, RNBPFMA improves the identification accuracy. The computational complexity of RNBPFMA is less than that of CNBPF. The RNBPF and proposed multistage filters are compared with previously reported short-time discrete Fourier transform (ST-DFT) method in terms of compu- tational complexity. It is found that multistage filters reduce the computational load to a greater extent compared to ST-DFT method. The identification accuracy of the proposed CNBPF and RNBPFMA methods is compared with existing anti-notch filter and RNBPF methods. The results show that proposed methods outperform existing methods in terms of identification accuracy for benchmark data sets. 展开更多
关键词 BIOINFORMATICS multistage filter protein coding region period-3 property narrowband bandpass filter genomic signal processing.
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Probe Staurosporine Drug Binding Site on Protein Kinase by PFSC
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作者 ZHENG Kun YANG Hong +3 位作者 ZHAO Xiaofei JIANG Yang SUN Chuantao YANG Jia'an 《Chemical Research in Chinese Universities》 SCIE CAS CSCD 2014年第4期644-649,共6页
We used a new approach,protein folding shape code(PFSC),to predict the potential staurosporine binding sites in protein kinases.Firstly,all available three dimensioned(3D) structures of protein kinases in protein ... We used a new approach,protein folding shape code(PFSC),to predict the potential staurosporine binding sites in protein kinases.Firstly,all available three dimensioned(3D) structures of protein kinases in protein databank(PDB) were converted into one-dimensional PFSC description,based on which a PFSC-kinome library was constructed.Secondly,a set of protein kinase-staurosporine complexes were analyzed to define the common structural features of the binding sites.Thirdly,the structural features of the staurosporine binding sites were used to virtually screen the PFSC-kinome library to predict multiple protein receptors that have potential binding capacity for staurosporine.Collectively,the development of the similar method for predicting drug binding site demonstrates that virtual screening protein database can provide valuable information on drug discovery and understanding of pharmacological pathways. 展开更多
关键词 STAUROSPORINE Adenosine triphosphate(ATP)-binding site protein fold shape code(PFSC) protein folding structural alignment(PFSA) protein databank(PDB)
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