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A Computational Approach to Study Non-Synonymous Mutations

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datacite.subject.fosCiências Agrárias::Biotecnologia Agrária e Alimentar
datacite.subject.fosCiências Naturais::Ciências da Terra e do Ambiente
datacite.subject.sdg04:Educação de Qualidade
datacite.subject.sdg13:Ação Climática
datacite.subject.sdg15:Proteger a Vida Terrestre
dc.contributor.authorBashir, Sana
dc.contributor.authorLi, Fernanda
dc.contributor.authorShiraishi, Carlos S.H.
dc.contributor.authorYadró Garcia, Carlos A.
dc.contributor.authorBarbosa, Daniela
dc.contributor.authorAbreu, Rui M.V.
dc.contributor.authorRufino, José
dc.contributor.authorPinto, M. Alice
dc.contributor.authorHenriques, Dora
dc.date.accessioned2026-02-12T19:12:49Z
dc.date.available2026-02-12T19:12:49Z
dc.date.issued2025
dc.description.abstractNon-synonymous SNPs (Single Nucleotide Polymorphisms) result in amino acid substitutions within proteins. While some may have minimal impact on protein structure and function, others can significantly alter stability, conformation, and biological activity. Therefore, it is crucial to predict how SNP-induced changes affect protein structure and function. Here, we developed a novel pipeline that integrates bioinformatics and molecular modeling techniques to evaluate the structural and functional consequences of a non-synonymous SNP in a protein. Initially, Protein Plus was used to predict the potential active sites, which will help to determine whether a mutation is located within the functional binding regions. Identification of active sites is necessary to prioritize mutations that may alter protein structure and function. PolyPhen-2 and I-Mutant were used to evaluate the functional impact of mutations and the thermodynamic stability of the proteins. Next, to visualize the structural changes, AlphaFold3 was used to generate highconfidence 3D models for wild and mutant proteins. Finally, molecular dynamics (MD) simulations were conducted using YASARA to explore the dynamic behavior and stability of both mutant and wild-type proteins. MD simulations provide valuable insight into structural flexibility, potential conformational shifts, and the overall impact of the mutation on protein function. This computational pipeline provides a detailed framework to evaluate the structural and energetic consequences of non-synonymous mutations.eng
dc.identifier.citationBashir, Sana; Li, Fernanda; Shiraishi, Carlos S.H.; Yadró Garcia, Carlos A.; Barbosa, Daniela; Abreu, Rui M.V.; Rufino, José; Pinto, M. Alice; Henriques, Dora (2025). A Computational Approach to Study Non-Synonymous Mutations. VI International Conference of the Portuguese Society of Genetics. p. 74
dc.identifier.urihttp://hdl.handle.net/10198/35737
dc.language.isoeng
dc.peerreviewedyes
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectAmino acid
dc.subjectMolecular dynamics
dc.titleA Computational Approach to Study Non-Synonymous Mutationseng
dc.typeconference object
dspace.entity.typePublication
oaire.citation.conferenceDate2025
oaire.citation.conferencePlaceOeiras, Portugal
oaire.citation.startPage74
oaire.citation.titleVI International Conference of the Portuguese Society of Genetics
oaire.versionhttp://purl.org/coar/version/c_970fb48d4fbd8a85
person.familyNameLi
person.familyNameShiraishi
person.familyNameYadró Garcia
person.familyNameAbreu
person.familyNameRufino
person.familyNamePinto
person.familyNameHenriques
person.givenNameFernanda
person.givenNameCarlos S.H.
person.givenNameCarlos A.
person.givenNameRui M.V.
person.givenNameJosé
person.givenNameM. Alice
person.givenNameDora
person.identifier.ciencia-idF115-6760-0EBB
person.identifier.ciencia-id6C11-86D5-73AE
person.identifier.ciencia-idF71F-B08E-EC39
person.identifier.ciencia-id0F19-0DE2-12A2
person.identifier.ciencia-idC414-F47F-6323
person.identifier.ciencia-idF814-A1D0-8318
person.identifier.ciencia-id291F-986F-07DA
person.identifier.orcid0000-0003-0466-355X
person.identifier.orcid0000-0002-4174-8985
person.identifier.orcid0000-0002-6916-3647
person.identifier.orcid0000-0002-7745-8015
person.identifier.orcid0000-0002-1344-8264
person.identifier.orcid0000-0001-9663-8399
person.identifier.orcid0000-0001-7530-682X
person.identifier.scopus-author-id7003290613
person.identifier.scopus-author-id55947199100
person.identifier.scopus-author-id8085507800
person.identifier.scopus-author-id55761737300
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