Applicants for this position will improve and develop algorithms for constrained 3D-structure modeling of proteins as well as docking processes. The successful modeling of G-protein coupled receptors (GPCR) without experimental knowledge is still a very challenging task.
However, recently solved structures of G-protein coupled receptors (GPCR) allow to derive general structural properties of this protein family, to formulate these as constraints and, hence, to include them in the modeling procedure of unknown GPCRs.
The applicant will also investigate to what extent information derived from various ligands can be used to improve the models. The second part focuses on the inuence of electrostatics in the docking process of small ligands. Both, the electrostatic potential of the ligand and the surrounding water molecules will be examined. Former studies prove that the water network aects the electrostatics in the direct surrounding of the protein.
Based on the concepts to describe the water network in a macroscopic theory, the so called nonlocal response theory, an extensive application to biological processes such as the protonation of proteins and the binding process of ligands is planned for the PhD studies.
PhD Student Position in the Field of Structural Bioinformatics
