Visualization of pharmacophoric interaction potentials
Praktikum / Diplomarbeit
Gerhard Wolber, Alois Dornhofer,
Description
Inte:Ligand is a young company which specializes in optimizing the
(in-silico) drug discovery process by using specific interaction models. These
models are then used to screen virtual compound libraries so that risks of side
effects can be assessed in an early stage of the discovery process and drug
candidates can be filtered.
Proteins are quite large organic molecules
conisting of some hundred atoms whereas drug candidates are relatively small
organic molecules composed of up to 50 atoms. The biological activity of a new
potential drug candidate depends on a drug-receptor-interaction model, a
so-called pharmacophore which is a collection of chemical features in 3D space
within the small molecule. Hence, if the pharmacophore matches its protein
couterpart this provides evidence of activity. Chemical features are, for
example, hydrogen bond acceptors (HBA), hydrogen bond donors (HBD), positive and
negative ionizable areas as well as hydrophilic and lipophilic areas. The task
to be solved is to improve the current visualization (vectors indicating HBA/HBD
and spheres indicating hydrophilic, lipophilic, and ionizable areas) of the
pharmacophore.
Task
- create an improved visualization of the previously mentioned point and vector features of the interaction model based on a specific potential distribution and/or
- a surface visualization which maps the potential distribution onto the surface.
Requirements
- Java and Java3D
- Knowledge in computer graphics and visualization
- Interest in biochemistry (no knowledge required)
- Readiness to work in a unix-centric
environment
Additional Information
- www.inteligand.com, praktika@inteligand.com
- 1-2 persons
