共查询到20条相似文献,搜索用时 31 毫秒
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We have developed a new method for the prediction of peptide sequences that bind to a protein, given a three-dimensional structure of the protein in complex with a peptide. By applying a recently developed sequence prediction algorithm and a novel ensemble averaging calculation, we generate a diverse collection of peptide sequences that are predicted to have significant affinity for the protein. Using output from the simulations, we create position-specific scoring matrices, or virtual interaction profiles (VIPs). Comparison of VIPs for a collection of binding motifs to sequences determined experimentally indicates that the prediction algorithm is accurate and applicable to a diverse range of structures. With these VIPs, one can scan protein sequence databases rapidly to seek binding partners of potential biological significance. Overall, this method can significantly enhance the information contained within a protein- peptide crystal structure, and enrich the data obtained by experimental selection methods such as phage display. 相似文献
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We developed a method of effective peptide screening that combines experiments and computational analysis. The method is based on the concept that screening efficiency can be enhanced from even limited data by use of a model derived from computational analysis that serves as a guide to screening and combining the model with subsequent repeated experiments. Here we focus on cell-adhesion peptides as a model application of this peptide-screening strategy. Cell-adhesion peptides were screened by use of a cell-based assay of a peptide array. Starting with the screening data obtained from a limited, random 5-mer library (643 sequences), a rule regarding structural characteristics of cell-adhesion peptides was extracted by fuzzy neural network (FNN) analysis. According to this rule, peptides with unfavored residues in certain positions that led to inefficient binding were eliminated from the random sequences. In the restricted, second random library (273 sequences), the yield of cell-adhesion peptides having an adhesion rate more than 1.5-fold to that of the basal array support was significantly high (31%) compared with the unrestricted random library (20%). In the restricted third library (50 sequences), the yield of cell-adhesion peptides increased to 84%. We conclude that a repeated cycle of experiments screening limited numbers of peptides can be assisted by the rule-extracting feature of FNN. 相似文献
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Sidoti F Bergallo M Terlizzi ME Piasentin Alessio E Astegiano S Gasparini G Cavallo R 《Molecular biotechnology》2012,50(3):221-228
Evidence demonstrating that human rhinovirus (HRV) disease is not exclusively limited to the upper airways and may cause lower
respiratory complications, together with the frequency of HRV infections and the increasing number of immunocompromised patients
underline the need for rapid and accurate diagnosis of HRV infections. In this study, we developed the first quantitative
real-time nucleic acid sequence-based amplification assay with an internal control using molecular beacon probes for selective
and sensitive detection of human rhinovirus serotypes. We described a simple method to accurately quantify RNA target by computing
the time to positivity (TTP) values for HRV RNA. Quantification capacity was assessed by plotting these TTP values against
the starting number of target molecules. By using this simple method, we have significantly increased the diagnostic accuracy,
precision, and trueness of real-time NASBA assay. Specificity of the method was verified in both in silico and experimental
studies. Moreover, for assessment of clinical reactivity of the assay, NASBA has been validated on bronchoalveolar lavage
(BAL) specimens. Our quantitative NASBA assay was found to be very specific, accurate, and precise with high repeatability
and reproducibility. 相似文献
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Heat shock factor 1 is a transcription factor of Fas gene 总被引:1,自引:0,他引:1
E. Shunmei Yuanbo Zhao Yunhong Huang Kun Lai Cha Chen Jianming Zeng Jiangying Zou 《Molecules and cells》2010,29(5):527-531