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Mutations in EGFR kinase domain can cause non-small-cell lung cancer, which is one of the most lethal diseases in the world. However, current therapy is limited by the drug resistance effect in different EGFR mutants. There is an urgent demand for developing computational methods to predict drug resisted mutations. In this study, we use quantum mechanics and molecular mechanics models to generate...
Protein-ligand interaction is important in drug development and protein design. Previous studies focused on the detection of the potential ligand binding sites but lack of analysis of the true binding sites on the protein. In this work, we use alpha shape models to represent the surface of the protein structure and extract surface patches to study the ligand binding sites. Analysis is performed on...
Previous studies about protein-DNA interaction focused on the bound structure of DNA-binding proteins and provided good but not practical results. In our work, we apply an alpha shape model to represent the surface structure of the protein-DNA complex and use structural alignment to develop an interface-atom curvature-dependent conditional probability discriminatory function for the prediction of...
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