Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets
Autor(a) principal: | |
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Data de Publicação: | 2023 |
Tipo de documento: | Dissertação |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10451/63291 |
Resumo: | Tese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de Ciências |
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Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targetsligação de hidrogénioligação de halogéneoσ-holeTeses de mestrado - 2023Departamento de Química e BioquímicaTese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de CiênciasThe characterization of protein-ligand complexes is essential for research in structural biochemistry, drug discovery, and biology. These protein–ligand interactions comprise hydrophobic interactions, hydrogen bonds, aromatic stacking, salt bridges, and even halogen bonds. There are several tools that automatically assign the presence of noncovalent protein–ligand interactions in PDB structures. This is extremely useful in drug design since in the initial stages, prior to library screening or molecule design, a comparative analysis of binding patterns in a target is often performed, thus helping to identify key residues. To assign the existence of a bond (such as hydrogen or a halogen bonds), these tools verify if certain geometric requirements are fulfilled, i.e., they use angle and distance thresholds. This might be problematic since the thresholds are empiric and might be excluding (or erroneously including) interactions. Therefore, the use of an energy-based criterion is a great advantage, as previously shown with the Define Secondary Structure of Proteins (DSSP) algorithm, which is a popular standard method for assigning the secondary structure to the amino acids of a protein. Based on previous work by our group which showed the existence of energy thresholds for the identification of these interactions, in this project, by using computational and modeling tools such as force field methods, a robust energy-based criterion to assign noncovalent interactions involving protein-ligand complexes was tested. The method was also tested in membrane-ligand systems thus hopefully contributing to the improvement of computational drug discovery tools.Costa, Paulo Jorge Ferreira de Matos, 1980-Victor, Bruno Lourenço da SilvaRepositório da Universidade de LisboaDias, Tiago Gonçalves2024-03-08T09:44:48Z202320232023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10451/63291engmetadata only accessinfo:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2024-03-11T01:20:23Zoai:repositorio.ul.pt:10451/63291Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-20T03:14:32.183457Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
title |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
spellingShingle |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets Dias, Tiago Gonçalves ligação de hidrogénio ligação de halogéneo σ-hole Teses de mestrado - 2023 Departamento de Química e Bioquímica |
title_short |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
title_full |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
title_fullStr |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
title_full_unstemmed |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
title_sort |
Improved drug discovery: towards an energy-based criterion to characterize ligand interactions with biomolecular targets |
author |
Dias, Tiago Gonçalves |
author_facet |
Dias, Tiago Gonçalves |
author_role |
author |
dc.contributor.none.fl_str_mv |
Costa, Paulo Jorge Ferreira de Matos, 1980- Victor, Bruno Lourenço da Silva Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Dias, Tiago Gonçalves |
dc.subject.por.fl_str_mv |
ligação de hidrogénio ligação de halogéneo σ-hole Teses de mestrado - 2023 Departamento de Química e Bioquímica |
topic |
ligação de hidrogénio ligação de halogéneo σ-hole Teses de mestrado - 2023 Departamento de Química e Bioquímica |
description |
Tese de mestrado, Bioquímica e Biomedicina, 2023, Universidade de Lisboa, Faculdade de Ciências |
publishDate |
2023 |
dc.date.none.fl_str_mv |
2023 2023 2023-01-01T00:00:00Z 2024-03-08T09:44:48Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/masterThesis |
format |
masterThesis |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10451/63291 |
url |
http://hdl.handle.net/10451/63291 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.rights.driver.fl_str_mv |
metadata only access info:eu-repo/semantics/openAccess |
rights_invalid_str_mv |
metadata only access |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.source.none.fl_str_mv |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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