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Examination of the role of binding site water molecules in molecular recognition
SciLifeLab Stockholm. (Computational structural and chemical biology)
2012 (English)Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
Abstract [en]

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.
Series
UPTEC X, 12 026
Keyword [en]
Free energy of binding, enthalpy, entropy, ligand, hydration site, ligand-protein binding.
National Category
Other Biological Topics
Identifiers
URN: urn:nbn:se:uu:diva-200164OAI: oai:DiVA.org:uu-200164DiVA: diva2:622350
Educational program
Molecular Biotechnology Engineering Programme
Supervisors
Examiners
Available from: 2013-05-21 Created: 2013-05-21 Last updated: 2013-05-21Bibliographically approved

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CiteExportLink to record
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Citation style
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