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Motifs are overrepresented sequence or spatial patterns appearing in proteins. They often play important roles in maintaining protein stability and in facilitating protein function. When motifs are located in short sequence fragments, as in transmembrane domains that are only 6-20 residues in length, and when there is only very limited data, it is difficult to identify motifs. In this study, we introduce...
Proteins contain thousands or more atoms and have complex shapes. We discuss here the computation of protein packing defects, in the form of voids and pockets, from experimentally resolved protein structures, and the nature of their distribution and scaling behavior, as well as their origin. We further discuss how evolutionary selection pressure due to biological function unaltered by selection pressure...
Fixation of advantageous mutations is an important evolutionary force driving the accelerated protein diversification. However, the standard phylogenetic approach to infer positive selection is based on relative rate of nonsynonymous to synonymous substitutions, and requires the knowledge of DNA sequences, hence precludes its application to family of remotely related sequences where saturated substitution...
Locating functionally important protein surfaces and identifying the catalytic site residues are critical for studying enzyme functions. Here, we present methods for predicting and characterizing catalytic sites of enzymes at atomic level that is fold-independent. By extract atomic patterns of catalytic residues in surface pockets computed geometrically, we develop a library of atomic patterns on...
Locating functionally important protein surfaces and identifying the catalytic site residues are critical for studying enzyme functions. Here, we present methods for predicting and characterizing catalytic sites of enzymes at atomic level that is fold-independent. By extract atomic patterns of catalytic residues in surface pockets computed geometrically, we develop a library of atomic patterns on...
Protein design aims to identify sequences compatible with a given protein fold but incompatible to any alternative folds. To select the correct sequences and to guide the search process, a design scoring function is critically important. It is also important that a design scoring function can characterize the global fitness landscape of many proteins simultaneously. We describe how finding optimal...
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