Abstract

This thesis is focused on the algorithms searching for discontinuous motifs on the surface of protein molecules. A surface is the most important part of a molecule, because all reactions between molecules take place on the surface. Therefore, it is favourable to know which atoms or motifs (continuous or discontinuos groups of amino acids) occur on the surface and which lie buried in the internal part of the molecule. From the algorithms for identification of the surface atoms three suitable ones were chosen and studied in detail: NIN approach (a classical simple approach for identifying surface atoms), UCSF approach (which uses heuristics) and a sophisticated SAS approach. The algorithms are described within this thesis and analysed from many points of view. Using the basis of these algorithms, an algorithm searching for discontinuous motifs on surface of protein molecules was developed. Described algorithms were implemented and successfully tested for searching surface atoms and discontinuous motifs (specifically biologically important motifs from the ELM database). These atoms and motifs were searched on the the surfaces of real protein molecules from the PDB~database. The programs samie (for surface motifs) and sad (for surface atoms) were created by the implementation of the above mentioned algorithms. For the calculation of the solvent-accessible surface was designed a script sasa. The developed programs will be used in a larger bioinformatics project realised in co-operation between University College Dublin and ANF Data company. This project is focused on determining geometrically similar motifs in molecules of drugs and proteins. Specifically, the identification of the surface protein motifs will help to reduce the amount of studied data. …moreless