We used our newly developed tools for the detection of protein binding sites, which are available on the ProBiS web server (http://probis.cmm.ki.si), in a project entitled "Modeling of biopharmaceutical molecules" carried out in cooperation with the Lek pharmaceutical company.
F.17 Transfer of existing technologies, know-how, methods and procedures into practice
The work described in this thesis builds upon ProBiS algorithm for comparison of protein structures. Such comparisons can be very time consuming. The main goal of our project was their pre-computation and development of the ProBiS database. Thesis begins with a description of ProBiS algorithm and a web page, through which it operates. Our main contribution is construction of appropriate architecture of the system and its implementation using distributed computation, and construction of a database and its further optimization through denormalization. We have also implemented the user interface for searching the database. Our newly developed ProBiS database is a novel resource for protein structural comparisons and greatly improves the user experience of ProBiS web server.
D.10 Educational activities
COBISS.SI-ID: 8691028A computer method for local structure comparison of proteins and its use for the detection of binding sites was presented.
D.10 Educational activities
COBISS.SI-ID: 4505626I had an invited lecture on conference "VII Joint Meeting on Medicinal Chemistry" (invitation attached). I presented the web server, ProBiS, freely available at http://probis.cmm.ki.si. This provides access to the program ProBiS (Protein Binding Sites), which detects binding sites on proteins based on local structural alignments. Given a structure of a protein with unknown binding sites, ProBiS suggests the regions on its surface which may be involved in binding with small ligands, proteins, or DNA/RNA. Alternatively, given a protein with an identified binding site, ProBiS finds other proteins with structurally or physicochemically similar binding sites. If used as a pairwise structure alignment program, ProBiS detects and superimposes similar functional sites ina pair of submitted protein structures, even when these do not have similar folds.
B.04 Guest lecture
COBISS.SI-ID: 4717082In this lecture I presented our recently developed ProBiS web server at http://probis.cmm.ki.si, for the detection of structurally similar protein binding sites. I also discussed the use of the server for the detection of protein, nucleic, and small molecule binding sites.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 4440346