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The progress in experimental and computational structural biology has led to a rapid growth of experimentally resolved structures and computational models of protein-protein interactions. However, distinguishing between the physiological and non-physiological interactions remains a challenging problem. In this work, two related problems of interface classification have been addressed. The first problem...
Protein-protein interactions are important for the prediction of protein functions since two interacting proteins usually have similar functions in a cell. In this work, our aim is to predict protein-protein interactions with a known portion of the interaction network when there are large numbers of protein interactions in the data set. Phylogenetic profiles of proteins form the feature vectors for...
A single mass spectrometry experiment could produce hundreds of thousands of tandem mass spectra. Several search engines have been developed to interpret tandem mass spectra. All search engines need to determine the masses of peptide ions from their mass/charge ratios. Unfortunately, mass spectrometers do not detect the charges of ions. A current strategy is to search candidate peptides multiple times,...
Relationship extraction (RE) from biomedical literature is an important and challenging problem in both text mining and bioinformatics. Although various approaches have been proposed to extract protein-protein interaction types, their accuracy rates leave a large room for further exploration of more effective methods. In this paper, two supervised learning algorithms based on newly-defined ldquobio-semantic...
This paper presents a novel method to extract Protein-Protein Interaction (PPI) information from biomedical literatures based on Support Vector Machine (SVM) and K Nearest Neighbors (KNN). The two protein names, words between two proteins, words surrounding two proteins, keyword between or among the surrounding words of two protein names, ExpDistance based on word distance of two proteins, ProDistance...
Analysis of protein-protein recognition is a popular issue recently, which plays a crucial role in regulation of biochemical pathways and signaling transmittal. A protein is recognized with the other protein by combining a transient complex, otherwise which will become a permanent complex. Therefore, understanding physico-chemical properties of the protein interface can offer important clues for biological...
Due to the heightened concern about bioterrorism and emerging/reemerging infectious diseases, a flood of molecular data about human pathogens has been generated and maintained in disparate databases. However, scientific findings regarding these pathogens and their host responses are buried in the growing volume of biomedical literature and there is an urgent need to mine information pertaining to...
In computational proteomics, inferring the peptide sequence from its MS/MS data is an important issue and many algorithms have been proposed. Ions classification aiming at determining the type of ions provides a basis for most of the existing algorithms. However, no report on ions classification methods have been found to our knowledge. In this paper, a method extracting ion feature is first presented...
Nowadays, protein-protein interaction (PPI) extraction has become a research focus. Many methods have been applied to this domain, such as supervised learning approaches. This paper applied support vector machine (SVM) to extract PPI, which bases on several lexical features and one syntactic feature achieved through link grammar parser. Due to syntax's complexity different sentence structure can not...
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