Examination of the role of binding site water molecules in molecular recognition
Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
A set of algorithms were designed, implemented and evaluated in order to, first, identifyclusters of conserved waters in binding pockets, i.e. hydration sites. Then, their contributionto the free energy of binding in a ligand-protein association was quantified by calculatingtheir enthalpy and entropy. The information obtained by using these algorithms couldcontribute to the development of new drugs by generating new ligands that target specifichigh-energy, unfavorable waters. Evaluation tests show that our algorithms can indeedprovide relevant data about how hydration sites influence ligand-protein binding.
Place, publisher, year, edition, pages
2012. , 35 p.
UPTEC X, 12 026
Free energy of binding, enthalpy, entropy, ligand, hydration site, ligand-protein binding.
Other Biological Topics
IdentifiersURN: urn:nbn:se:uu:diva-200164OAI: oai:DiVA.org:uu-200164DiVA: diva2:622350
Molecular Biotechnology Engineering Programme