FRINK Linked Data Fragments server

Matches in SemOpenAlex for { <https://semopenalex.org/work/W4308685963> ?p ?o ?g. }

• W4308685963 abstract "Abstract Motivation Protein structure prediction has been greatly improved by deep learning, but the contribution of different information is yet to be fully understood. This article studies the impacts of two kinds of information for structure prediction: template and multiple sequence alignment (MSA) embedding. Templates have been used by some methods before, such as AlphaFold2, RoseTTAFold and RaptorX. AlphaFold2 and RosetTTAFold only used templates detected by HHsearch, which may not perform very well on some targets. In addition, sequence embedding generated by pre-trained protein language models has not been fully explored for structure prediction. In this article, we study the impact of templates (including the number of templates, the template quality and how the templates are generated) on protein structure prediction accuracy, especially when the templates are detected by methods other than HHsearch. We also study the impact of sequence embedding (generated by MSATransformer and ESM-1b) on structure prediction. Results We have implemented a deep learning method for protein structure prediction that may take templates and MSA embedding as extra inputs. We study the contribution of templates and MSA embedding to structure prediction accuracy. Our experimental results show that templates can improve structure prediction on 71 of 110 CASP13 (13th Critical Assessment of Structure Prediction) targets and 47 of 91 CASP14 targets, and templates are particularly useful for targets with similar templates. MSA embedding can improve structure prediction on 63 of 91 CASP14 (14th Critical Assessment of Structure Prediction) targets and 87 of 183 CAMEO targets and is particularly useful for proteins with shallow MSAs. When both templates and MSA embedding are used, our method can predict correct folds (TMscore &gt; 0.5) for 16 of 23 CASP14 FM targets and 14 of 18 Continuous Automated Model Evaluation (CAMEO) targets, outperforming RoseTTAFold by 5% and 7%, respectively. Availability and implementation Available at https://github.com/xluo233/RaptorXFold. Supplementary information Supplementary data are available at Bioinformatics online." @default.
• W4308685963 created "2022-11-14" @default.
• W4308685963 creator A5019398608 @default.
• W4308685963 creator A5025240664 @default.
• W4308685963 creator A5067265615 @default.
• W4308685963 creator A5081693954 @default.
• W4308685963 date "2022-11-10" @default.
• W4308685963 modified "2023-10-15" @default.
• W4308685963 title "Improving protein structure prediction using templates and sequence embedding" @default.
• W4308685963 cites W2051210555 @default.
• W4308685963 cites W2069458148 @default.
• W4308685963 cites W2102245393 @default.
• W4308685963 cites W2102461176 @default.
• W4308685963 cites W2151581834 @default.
• W4308685963 cites W2557595285 @default.
• W4308685963 cites W2949867299 @default.
• W4308685963 cites W2950954328 @default.
• W4308685963 cites W2953008890 @default.
• W4308685963 cites W2971733377 @default.
• W4308685963 cites W2972411752 @default.
• W4308685963 cites W2980789587 @default.
• W4308685963 cites W2980805969 @default.
• W4308685963 cites W2987090428 @default.
• W4308685963 cites W2995514860 @default.
• W4308685963 cites W2997234557 @default.
• W4308685963 cites W2999044305 @default.
• W4308685963 cites W3159634588 @default.
• W4308685963 cites W3163965514 @default.
• W4308685963 cites W3177828909 @default.
• W4308685963 cites W3198789071 @default.
• W4308685963 cites W3209492740 @default.
• W4308685963 doi "https://doi.org/10.1093/bioinformatics/btac723" @default.
• W4308685963 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/36355462" @default.
• W4308685963 hasPublicationYear "2022" @default.
• W4308685963 type Work @default.
• W4308685963 citedByCount "1" @default.
• W4308685963 crossrefType "journal-article" @default.
• W4308685963 hasAuthorship W4308685963A5019398608 @default.
• W4308685963 hasAuthorship W4308685963A5025240664 @default.
• W4308685963 hasAuthorship W4308685963A5067265615 @default.
• W4308685963 hasAuthorship W4308685963A5081693954 @default.
• W4308685963 hasBestOaLocation W43086859631 @default.
• W4308685963 hasConcept C124101348 @default.
• W4308685963 hasConcept C154945302 @default.
• W4308685963 hasConcept C18051474 @default.
• W4308685963 hasConcept C199360897 @default.
• W4308685963 hasConcept C2778112365 @default.
• W4308685963 hasConcept C41008148 @default.
• W4308685963 hasConcept C41608201 @default.
• W4308685963 hasConcept C47701112 @default.
• W4308685963 hasConcept C54355233 @default.
• W4308685963 hasConcept C55493867 @default.
• W4308685963 hasConcept C82714645 @default.
• W4308685963 hasConcept C86803240 @default.
• W4308685963 hasConceptScore W4308685963C124101348 @default.
• W4308685963 hasConceptScore W4308685963C154945302 @default.
• W4308685963 hasConceptScore W4308685963C18051474 @default.
• W4308685963 hasConceptScore W4308685963C199360897 @default.
• W4308685963 hasConceptScore W4308685963C2778112365 @default.
• W4308685963 hasConceptScore W4308685963C41008148 @default.
• W4308685963 hasConceptScore W4308685963C41608201 @default.
• W4308685963 hasConceptScore W4308685963C47701112 @default.
• W4308685963 hasConceptScore W4308685963C54355233 @default.
• W4308685963 hasConceptScore W4308685963C55493867 @default.
• W4308685963 hasConceptScore W4308685963C82714645 @default.
• W4308685963 hasConceptScore W4308685963C86803240 @default.
• W4308685963 hasFunder F4320306076 @default.
• W4308685963 hasFunder F4320321001 @default.
• W4308685963 hasFunder F4320332161 @default.
• W4308685963 hasIssue "1" @default.
• W4308685963 hasLocation W43086859631 @default.
• W4308685963 hasLocation W43086859632 @default.
• W4308685963 hasLocation W43086859633 @default.
• W4308685963 hasOpenAccess W4308685963 @default.
• W4308685963 hasPrimaryLocation W43086859631 @default.
• W4308685963 hasRelatedWork W1503053695 @default.
• W4308685963 hasRelatedWork W2055709700 @default.
• W4308685963 hasRelatedWork W2064451414 @default.
• W4308685963 hasRelatedWork W2091737559 @default.
• W4308685963 hasRelatedWork W2317873522 @default.
• W4308685963 hasRelatedWork W2356466110 @default.
• W4308685963 hasRelatedWork W2966686650 @default.
• W4308685963 hasRelatedWork W3023334178 @default.
• W4308685963 hasRelatedWork W3088295674 @default.
• W4308685963 hasRelatedWork W4308685963 @default.
• W4308685963 hasVolume "39" @default.
• W4308685963 isParatext "false" @default.
• W4308685963 isRetracted "false" @default.
• W4308685963 workType "article" @default.