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DNA-binding proteins plays important role in a variety of vital biology processes. In this study, we apply a machine learning method for classify DNA-binding proteins from non-binding proteins based on sequence information. Using an evolutionary feature and residue composition feature extracted from primary structure, we have trained a support vector machine(SVM) to distinguish DNA-binding proteins...
Due to the large number of protein structures whose functions are unknown, it becomes increasing important to study the structural characteristics of catalytic residues. Here, we use a novel method to calculate the local structural rigidity (LSR) of protein. Based on a dataset of 760 proteins, the results show that catalytic residues have distinct structural properties. They are shown to be extremely...
An epitope activates B cells to amplify and induce antibodies which can neutralize the foreign molecules, particles and pathogens. It also plays a crucial role in developing synthetic peptides for vaccination. Identification of epitopes using biological screening approaches is time consuming and high cost. Therefore, bioinformatics approaches are developed to enhance the speed of identifying the epitopes...
Identification of protein-ligand binding site is an important task in structure-based drug design and docking algorithms. In these two decades, many different approaches have been developed to predict the binding site, such as geometric, energetic and sequence-based methods. We present the binding site prediction algorithm that takes advantage of both sequence conservation and geometric methods for...
Given the essential role of protein in life processes, computational assignment of protein functions has become one of the most important tasks in the area of bioinformatics. While Gene Ontology (GO) has been widely used in functional annotation, new approaches to address the problem of annotation incompleteness, which can leverage the support of the GO framework, are imminently required. In this...
Proteins function through interactions with other proteins, compounds, RNA and DNA. Prediction of protein interface sites is the key process for providing clues to the function of a protein, and is becoming increasing relevant to drug discovery. In this paper, combining the protein features with the theory of granular computing of quotient space based on protein-protein interaction sites classification...
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