Abstract

This diploma thesis is focused on searching of molecular surfaces using computational chemistry methods. Specifically, the thesis studies protein molecules, which have significant part in biochemistry of organisms. The aim of the thesis is finding amino acids, i. e. continual motifs, which are situated on the molecular surface. Before continual motifs searching, surface atoms are determined. Four approaches (NIN, SOV, Lattice and SAS) for searching of surface atoms are described in the thesis. Algorithms based on the approaches are implemented and tested on a group of proteins from Protein Data Bank. Further, an algorithm for recognizing surface continuous motifs (which utilizes results form previous approaches) is designed, implemented and tested on the above mentioned real proteins. Results of the tests are analyzed and the algorithms are compared with each other according to their accuracy and speed. …víceméně