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Prediction of the 3D structure of protein-protein complexes is crucial for understanding the biological system of life and thus for designing drugs. However it is a challenging problem due to the flexibility of the backbone and side-chains of the receptor and ligand. In this paper, we present a new framework for fast and flexible protein-protein docking based on geometric and physicochemical complementarity...
Amomum villosum Lour. (officinal name Fructus Amomi) is one of the most well-known and authentic herbs in South China. Monoterpenes in its volatile oil are the main medicinal compounds. The condensation of pyruvate with D-glyceraldhyde-3-phosphate to form 1-deoxy-D-xylulose-5-phosphate (DXP) catalyzed by DXP synthase (DXS, EC: 2.2.1.7) and the conversion of DXP to 2-C-methyl-D-erythritol-4-phosphate...
A novel calibration model has been proposed for synchronous, rapid and non-destructive determination the content of adenosine and protein in the Cordyceps gunnii mycelia powder by near infrared spectroscopy. This model is a combination of wavelet packet transform (WPT) data disposal with multi-scale analysis and radial basis function neural network (WPT-RBFNN). Via using principal component analysis...
To investigate an efficient and cost effective method to catalyze transesterification reaction, the lipase immobilized on chitosan beads was introduced in the present paper with a hypothesis that the immobilized lipase could catalyze transesterification to get a high triglyceride conversion. Four immobilization methods namely cross-linking using glutaraldehyde (GLA), activation with 1-Ethyl-3 (3-dimethyl-aminopropyl)...
To help the biomedical scientist pre-confirm the disease-related genes, we considered these gene as a whole research set and analyzed the topological features of their interaction network. Two strategies had been proposed to construct the disease-related gene network from the OMIM database. Using these two constructed sets, we trained two support vector machine prediction models, the accuracy of which...
Three different protein fractions were isolated from barley bran and flour. Electrophoretic properties, including molecular weight and fraction patterns of barley protein isolates (BPIs), were characterized and examined by Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). The functional properties of BPIs also were investigated, and then compared with soy, and zein protein. SDS-PAGE...
De novo peptide sequencing is one of the most challenging topics in the field of computational proteomics. In this manuscript, a novel method based on virtual database searching is presented to improve the performance of de novo sequencing for the data from high resolution LTQ-FT mass spectrometry. Our method directly generates a virtual database from each spectrum and applies a search engine to match...
Functioning as an “address tag” that directs nascent proteins to their proper sub-cellular localizations, signal peptides have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. In the past twenty years, many algorithms have been proposed for predicting signal peptides. In spite of pioneering algorithms based on “scaled window” or “benchmark window”, similarity as...
Biodegradable materials of soybean protein have been considered as the potential substitution for petroleum-based plastics. It is an effective way to alleviate the shortage of resources and the environmental pollution, and ensure the sustainable development of resources and environment. The objective of this work was to characterize the material performance of soybean protein components. Two major...
Identifying calcium-binding sites in proteins help acknowledge protein functions. We thus developed a graph theory and geometry approach to improve the accuracy for predicting calcium-binding sites, we enhance our previous approach at a high level to find biggest local oxygen clusters with a graph algorithm to find maximal cliques and propose a new geometric criterion embedding the bidentate property...
Aligning protein sequences using a score matrix has became a routine but valuable method in modern biological research. However, alignment in "Twilight Zone" is still a challenging issue. New score matrices such as Position Specific Score Matrix and structural context-based matrix have been issued to deal with it, whereas generalized matrices are still useful in pairwise alignment and/or...
Signal peptides are short regions of amino acid residues, which have become a crucial tool in finding new drugs or reprogramming cells for gene therapy. Owing to the rapidly increasing number of protein, it is highly demanded to develop the automated algorithm to identify the signal peptides. Recently, we had adopted a new alignment kernel function to identify secretory proteins. Compared with previous...
Sequence alignment has been a most commonly used method in modern biological research. However, sequence alignment in "Twilight Zone" is still a challenging issue. Three protein class-specific matrices are constructed to investigate whether alignment in "Twilight Zone" can be improved by using class-specific matrices and gap penalties. The substitution pattern differences between...
Disulfide connectivity prediction from protein sequence helps determine protein three dimensional structure. The methods for predicting disulfide connectivity generally fall into two categories: pair-wise and pattern-wise methods. Previously, the accuracy rates of the predictions were up to 52%, because (1) pair-wise methods feature mainly on each individual bond but neglect the global influence among...
Potassium channels are membrane proteins that allow the passage of potassium ions at near diffusion rates while severely limiting the flux of the slightly smaller sodium ions. Based on the three dimensional structure of KcsA with a D- alanine at position 77 (KcsAD-Ala77), the authors use a hierarchical model of K channel selectivity permeability process involving ab initio quantum calculations and...
Base on new experimental results, we give a dynamical model to study the dynamical mechanism of the negative feedback loop composed of p53 and Mdm2 proteins regulated by p14/19ARR The oscillatory behaviors for the activities of p53 and Mdm2 proteins regulated by p14/19ARF in individual of cells are described in our dynamical model. The results help us build a basal network about oscillatory behaviors...
The sliding window method will cause the severe unbalanced dataset problem. In this paper, under-sample the majority class method is adopted to solve this problem, and SVM is used to classify the processed data. The better prediction result of minority class (that is, the signal peptides positive sample set) is observed. Besides, we discover that the (-3,-1) rule is helpful to the prediction. So Information...
Identifying protein calcium-binding sites is an important problem in proteomics. To this end, we construct a graph containing only oxygen information to represent protein partial structures. In this graph, each vertex represents an oxygen atom. Edges are given to any two vertex-atoms based on a simple distance threshold between contact atoms. Applying a clique-finding algorithm to a set of graphs...
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