Examination of the role of binding site water molecules in molecular recognition

Examination of the role of binding site water molecules in molecular recognition

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 entrop...

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Main Author: Orro Graña, Adolfo
Format: Others
Language:English
Published: SciLifeLab Stockholm 2012
Subjects:
Free energy of binding
enthalpy
entropy
ligand
hydration site
ligand-protein binding.
Online Access:http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164
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spelling ndltd-UPSALLA1-oai-DiVA.org-uu-2001642013-05-22T04:02:20ZExamination of the role of binding site water molecules in molecular recognitionengOrro Graña, AdolfoSciLifeLab Stockholm2012Free energy of bindingenthalpyentropyligandhydration siteligand-protein binding.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. Student thesisinfo:eu-repo/semantics/bachelorThesistexthttp://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164UPTEC X ; 12 026application/pdfinfo:eu-repo/semantics/openAccess
collection NDLTD
language English
format Others
sources NDLTD
topic Free energy of binding
enthalpy
entropy
ligand
hydration site
ligand-protein binding.
spellingShingle Free energy of binding
enthalpy
entropy
ligand
hydration site
ligand-protein binding.
Orro Graña, Adolfo
Examination of the role of binding site water molecules in molecular recognition
description 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.
author Orro Graña, Adolfo
author_facet Orro Graña, Adolfo
author_sort Orro Graña, Adolfo
title Examination of the role of binding site water molecules in molecular recognition
title_short Examination of the role of binding site water molecules in molecular recognition
title_full Examination of the role of binding site water molecules in molecular recognition
title_fullStr Examination of the role of binding site water molecules in molecular recognition
title_full_unstemmed Examination of the role of binding site water molecules in molecular recognition
title_sort examination of the role of binding site water molecules in molecular recognition
publisher SciLifeLab Stockholm
publishDate 2012
url http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-200164
work_keys_str_mv AT orrogranaadolfo examinationoftheroleofbindingsitewatermoleculesinmolecularrecognition
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