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Understanding gene regulatory networks has become one of the central research problems in bioinformatics. More than thirty algorithms have been proposed to identify DNA regulatory sites during the past thirty years. However, the prediction accuracy of these algorithms is still quite low. Ensemble algorithms have emerged as an effective strategy in(More)
Protein-protein interactions are a pivotal component of many biological processes and mediate a variety of functions. Knowing the tertiary structure of a protein complex is therefore essential for understanding the interaction mechanism. However, experimental techniques to solve the structure of the complex are often found to be difficult. To this end,(More)
The tertiary structures of protein complexes provide a crucial insight about the molecular mechanisms that regulate their functions and assembly. However, solving protein complex structures by experimental methods is often more difficult than single protein structures. Here, we have developed a novel computational multiple protein docking algorithm,(More)
Computational protein tertiary structure prediction has made significant progress over the last decade due to the advancement of techniques and the growth of sequence and structure databases. However, it is still not very easy to predict the accuracy of a given predicted structure. Predicting the accuracy, or quality assessment of a prediction model, is(More)
Computational protein tertiary structure prediction has made significant progress over the past years. However, most of the existing structure prediction methods are not equipped with functionality to predict accuracy of constructed models. Knowing the accuracy of a structure model is crucial for its practical use since the accuracy determines potential(More)
Optimizing weighting factors for a linear combination of terms in a scoring function is a crucial step for success in developing a threading algorithm. Usually weighting factors are optimized to yield the highest success rate on a training dataset, and the determined constant values for the weighting factors are used for any target sequence. Here we explore(More)
The immensely popular fields of cancer research and bioinformatics overlap in many different areas, e.g. large data repositories that allow for users to analyze data from many experiments (data handling, databases), pattern mining, microarray data analysis, and interpretation of proteomics data. There are many newly available resources in these areas that(More)
The tertiary structure of proteins provides rich source of information for understanding protein function and evolution. Computational protein tertiary structure prediction has made significant progress over more than a decade due to the advancement of the techniques and the growth of sequence and structure databases. However, methods for assessing quality(More)
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