Before and after AlphaFold2: An overview of protein structure prediction

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dc.contributorSistema FMUSP-HC: Faculdade de Medicina da Universidade de São Paulo (FMUSP) e Hospital das Clínicas da FMUSP
dc.contributor.authorBERTOLINE, Leticia M. F.
dc.contributor.authorLIMA, Angelica N.
dc.contributor.authorKRIEGER, Jose E.
dc.contributor.authorTEIXEIRA, Samantha K.
dc.date.accessioned2023-12-15T18:45:26Z
dc.date.available2023-12-15T18:45:26Z
dc.date.issued2023
dc.description.abstractThree-dimensional protein structure is directly correlated with its function and its determination is critical to understanding biological processes and addressing human health and life science problems in general. Although new protein structures are experimentally obtained over time, there is still a large difference between the number of protein sequences placed in Uniprot and those with resolved tertiary structure. In this context, studies have emerged to predict protein structures by methods based on a template or free modeling. In the last years, different methods have been combined to overcome their individual limitations, until the emergence of AlphaFold2, which demonstrated that predicting protein structure with high accuracy at unprecedented scale is possible. Despite its current impact in the field, AlphaFold2 has limitations. Recently, new methods based on protein language models have promised to revolutionize the protein structural biology allowing the discovery of protein structure and function only from evolutionary patterns present on protein sequence. Even though these methods do not reach AlphaFold2 accuracy, they already covered some of its limitations, being able to predict with high accuracy more than 200 million proteins from metagenomic databases. In this mini-review, we provide an overview of the breakthroughs in protein structure prediction before and after AlphaFold2 emergence.eng
dc.description.indexPubMed
dc.description.indexWoS
dc.description.indexScopus
dc.description.sponsorshipFundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) [INCT-2014/50889-7]
dc.description.sponsorshipConselho Nacional de Desenvolvimento Cientifico e Tecnologico-CNPq [INCT-465586/2014-7]
dc.description.sponsorshipCoordenacao de Aperfeicoamento de Pessoal de Nivel Superior-CAPES [PROEX-169192/2018-0]
dc.description.sponsorshipZerbini Foundation
dc.description.sponsorshipFoxconn Brazil
dc.identifier.citationFRONTIERS IN BIOINFORMATICS, v.3, article ID 1120370, 8p, 2023
dc.identifier.doi10.3389/fbinf.2023.1120370
dc.identifier.eissn2673-7647
dc.identifier.urihttps://observatorio.fm.usp.br/handle/OPI/57375
dc.language.isoeng
dc.publisherFRONTIERS MEDIA SAeng
dc.relation.ispartofFrontiers in Bioinformatics
dc.rightsopenAccesseng
dc.rights.holderCopyright FRONTIERS MEDIA SAeng
dc.subjectprotein structure predictioneng
dc.subjectAlphaFoldeng
dc.subjecttemplate-based modelingeng
dc.subjectfree modelingeng
dc.subjectprotein language modeleng
dc.subject.otherfold recognitioneng
dc.subject.wosMathematical & Computational Biologyeng
dc.titleBefore and after AlphaFold2: An overview of protein structure predictioneng
dc.typearticleeng
dc.type.categoryrevieweng
dc.type.versionpublishedVersioneng
dspace.entity.typePublication
hcfmusp.citation.scopus29
hcfmusp.contributor.author-fmusphcLETICIA MACHADO FAVERY BERTOLINE
hcfmusp.contributor.author-fmusphcANGELICA NAKAGAWA LIMA
hcfmusp.contributor.author-fmusphcJOSE EDUARDO KRIEGER
hcfmusp.contributor.author-fmusphcSAMANTHA KUWADA TEIXEIRA
hcfmusp.description.articlenumber1120370
hcfmusp.description.volume3
hcfmusp.origemWOS
hcfmusp.origem.pubmed36926275
hcfmusp.origem.scopus2-s2.0-85153708123
hcfmusp.origem.wosWOS:001087603700001
hcfmusp.publisher.cityLAUSANNEeng
hcfmusp.publisher.countrySWITZERLANDeng
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Artigos e Materiais de Revistas Científicas - HC/InCor
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