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Although numerous computational techniques have been applied to predict protein secondary structure (PSS), only limited studies have dealt with discovery of logic rules underlying the prediction itself. Such rules offer interesting links between the prediction model and the underlying biology. In addition, they enhance interpretability of PSS prediction by providing a degree of transparency to the...
Studies of intrinsically disordered proteins that lack a stable tertiary structure but still have important biological functions critically rely on computational methods that predict this property based on sequence information. Although a number of fairly successful models for prediction of protein disorder were developed over the last decade, the quality of their predictions is limited by available...
A challenging task is to understand the relationship between sequences and folding rates of proteins. Previous studies found that one of contact order (CO), long-range order (LRO), and total contact distance (TCD) has a significant correlation with folding rate of protein. The network concept is increasingly used to describe the topology and dynamics of complex systems. In this paper, the protein...
The amino acid sequence of a protein is the key to understanding its structure and ultimately its function in the cell. This paper addresses the fundamental issue of encoding amino acids in ways that the visualization of protein sequences facilitates the decoding of its information content. We show that a feature-based representation in a three-dimensional (3D) space derived from substitution matrices...
To infer protein function by matching local surface patterns, an effective scoring matrix for evaluating surface similarity is critical. In this study, we develop an evolution model of binding surfaces using a continuous time Markov process. We develop a Bayesian Markov chain Monte Carlo method to estimate the substitution rates of amino acid residues with specialized move sets. We then develop scoring...
A residue-residue interaction pseudo-potential has been developed specific for protein /spl beta/-sheets. The potential is derived by scoring the occurrence of all i-(j-2...J+2) residue-residue pairs between any two interacting /spl beta/-strands, subdividing according to 4 classes of hydrogen bond pattern. The potential can be useful in distinguishing between correct and incorrect alignments between...
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