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The following topics were dealt with: bioinformatics and its applications in protein and gene sciences; biomechanics; biometrics; system biology; pattern recognition; machine learning techniques; biomedical engineering; theory and applications of NMR, CT and ECG technology; medical signal and imaging processing; clinical engineering, surgery simulation and healthcare information systems; and other...
In this paper, a recently proposed dimensionality reduction method called twin kernel embedding (TKE) is applied in 2-dimensional visualization of protein structure relationships. By matching the similarity measures of the input and the embedding spaces expressed by their respective kernels, TKE ensures that both local and global proximity information are preserved simultaneously. Experiments conducted...
Homology modeling, as a successful protein structure prediction method, has two major deficiencies, i.e., the lack of the templates (known structures), and the accuracy of alignment between the query (unknown structure) and its templates. To solve these problems, we have constructed a conservative domain clustering template database, and proposed a profile-based alignment algorithm based on the profile...
Fokl is a special enzyme in the family of restriction endonucleases. The Fokl restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands at fixed positions downstream of the site. Because of the high efficiency of catalyzing and the fast rate of the reaction, it is widely used in many operations in molecular biology including DNA computer. Researchers have made great effort...
A model of electrical characteristics of protein-DNA complex and computer simulation are presented in this paper. A protein-DNA complex called the nucleosome is used to test this new model. The salt dependences of the nucleosome wrapping in the high salt regime, the intermediate salt regime and low salt regime are numerically simulated and discussed. This method should also be useful for the biological...
Knowledge of structural classes is useful in understanding folding patterns in proteins. Numerous structural class prediction methods were proposed in the past. Although virtually all state-of-the-art classifiers were already tried, many of these methods use very simple protein sequence representation that often includes amino acid (AA) composition. To this end, we propose a novel sequence representation,...
The secondary structure prediction of protein plays an important role to obtain its tertiary structure and function. In the past thirty years, a huge amount of algorithms have been employed to this task. The better predicators are based on machine learning techniques, especially based on neural networks. But the architecture of neural network is hard to define, and the training process is time-consuming...
Superimpose one protein tertiary structure to another can help to find similarity between them and further identify functional and evolutionary relationships. We first extract invariant features under rigid body transformation for each protein backbone which is represented by alpha-carbons of all the residues. Then, the invariant features are embedded with Iterative Closest Point algorithm for superposition...
Identifying protein interface is crucial for the prediction of protein-protein interactions and for protein functional classification. In this work, the protein structure is modeled as an undirected graph with the conservation amino- acid residues the vertices and all atom contacts between them the edges. We find that the conservation residue networks are characterized by intermediate values of clustering...
Predicting protein function is one of the most challenging problems of the post-genomic era. The development of experimental methods for genome scale analysis of molecular interaction networks has provided new approaches to inferring protein function. There are various approaches available for deducing the function of proteins of unknown function using protein information. In this paper, the reliable...
Predicted relative solvent accessibility (RSA) provides useful information for prediction of binding sites and reconstruction of the 3D-structure based on a protein sequence, which are at the very core of proteomics. Several RSA prediction methods including those that generate real values and those that predict discrete states (buried vs. exposed) have been published. We propose a novel method for...
Many studies have examined the biological activities of Alpha-fetoprotein (AFP); however, the modulatory role of AFP in neoplastic growth remains unclear. Three hairpin siRNA expressing plasmids (pSIREN-DNR-DsRed-Express Donor-Vector-AFP-siRNAl/2/3) were constructed and transfected into FU97(AFP-producing gastric adenocarcinoma cell line). At 48h after transfection, the silencing efficiency to AFP...
Piezoelectric biosensor combines the sensitivity of piezoelectric sensor and specificity of biological reaction. Compared with traditional biochemical assay, it has the features of simple structure, having no use of label and fast detection speed. In recent years, piezoelectric biosensor has been applied in the area of clinical analysis, biological technology and food sanitary detection. In this paper,...
One of the main problems of protein folding prediction is optimization computation. On basis of toy model, this paper proposes an improved particle swarm optimization algorithm for protein folding prediction. The algorithm introduces a new architecture that is characterized by balancing exploration and exploitation capability of particle swarm optimization algorithm. In the architecture, the population...
Glutaraldehyde was used as cross linker to make glufosinate-ovalbumin. The identification and identified artificial antigen by UV abstraction and 31P NMR scanning methods, and then used this antigen immunize mice. The result showed that UV spectrogram of artificial antigen was changed when compared with OVA. 3 IP NMR spectrum of artificial antigen, the distance of artificial antigen and Glufosinate-ammonium...
Based on the free radical theory, considerable effort has been made in biochemistry to develop SOD mimics as therapeutic agents to eliminate excessive free radicals. Among widely used mimics, the SOD mimics (also named as the model of SOD, MSOD) have been indicated promising results with the possible future applications as a new antitumor medicine in clinic. The present study showed that this SOD...
We analyzed the generalized Hurst exponents for the amino acid sequences of proteins and secretory signal peptides used the multifractal detrended fluctuation analysis (MF-DFA) method. The numeralization of the amino acid sequences was completed according to the three amino acid indice: EIIP, polarity and accessible surface area. The results show that the proteins sequences have multifractal properties...
Large scale identification of APltarget genes will be helpful for elucidating the whole biological function. But in natural enhancer regions, the sequences of API regulatory elements often deviate from the optimal recognition consensus sequence TGA(C/G) TCA. We therefore fabricated a double- stranded DNA (dsDNA) microarray with all possible single- nucleotide mutated (SNM) sequences of API consensus...
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