Virtually all processes in living organisms are conducted by proteins. Proteins perform their function by binding to other proteins (protein-protein interactions) or small molecules - so called ligands (protein-ligand interactions). Active sites for protein-ligand interactions are pockets in protein structure where ligand can bind. Predicting of ligand binding sites is the first step to study and predict protein functions and structure based drug-design. In this thesis we reviewed current approaches for binding site prediction and proposed our own improvement. We have developed a novel pocket ranking function based on prediction model that predicts ligandability (ability to bind a ligand) of a given point inside of a pocket. Prediction is done considering only a local physicochemical and geometric properties derived from neighbourhood.
| Identifer | oai:union.ndltd.org:nusl.cz/oai:invenio.nusl.cz:321000 |
| Date | January 2013 |
| Creators | Krivák, Radoslav |
| Contributors | Neruda, Roman, Mráz, František |
| Source Sets | Czech ETDs |
| Language | English |
| Detected Language | English |
| Type | info:eu-repo/semantics/masterThesis |
| Rights | info:eu-repo/semantics/restrictedAccess |
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