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Pan-cancer proteogenomics connects oncogenic drivers to functional states.
Cell. 2023 Aug 31;186(18):3921-3944.e25. doi: 10.1016/j.cell.2023.07.014. Epub 2023 Aug 14.
Cell. 2023.
PMID: 37582357
Free article.
The structural coverage of the human proteome before and after AlphaFold.
Porta-Pardo E, Ruiz-Serra V, Valentini S, Valencia A.
Porta-Pardo E, et al. Among authors: ruiz serra v.
PLoS Comput Biol. 2022 Jan 24;18(1):e1009818. doi: 10.1371/journal.pcbi.1009818. eCollection 2022 Jan.
PLoS Comput Biol. 2022.
PMID: 35073311
Free PMC article.
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Unraveling the molecular basis of host cell receptor usage in SARS-CoV-2 and other human pathogenic β-CoVs.
Pontes C, Ruiz-Serra V, Lepore R, Valencia A.
Pontes C, et al. Among authors: ruiz serra v.
Comput Struct Biotechnol J. 2021;19:759-766. doi: 10.1016/j.csbj.2021.01.006. Epub 2021 Jan 12.
Comput Struct Biotechnol J. 2021.
PMID: 33456724
Free PMC article.
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Frustraevo: a web server to localize and quantify the conservation of local energetic frustration in protein families.
Parra RG, Freiberger MI, Poley-Gil M, Fernandez-Martin M, Radusky LG, Ruiz-Serra V, Wolynes PG, Ferreiro DU, Valencia A.
Parra RG, et al. Among authors: ruiz serra v.
Nucleic Acids Res. 2024 Apr 8:gkae244. doi: 10.1093/nar/gkae244. Online ahead of print.
Nucleic Acids Res. 2024.
PMID: 38587198
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3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures.
Ruiz-Serra V, Valentini S, Madroñero S, Valencia A, Porta-Pardo E.
Ruiz-Serra V, et al.
Bioinformatics. 2024 Mar 29;40(4):btae171. doi: 10.1093/bioinformatics/btae171.
Bioinformatics. 2024.
PMID: 38565273
Free PMC article.
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Local energetic frustration conservation in protein families and superfamilies.
Freiberger MI, Ruiz-Serra V, Pontes C, Romero-Durana M, Galaz-Davison P, Ramírez-Sarmiento CA, Schuster CD, Marti MA, Wolynes PG, Ferreiro DU, Parra RG, Valencia A.
Freiberger MI, et al. Among authors: ruiz serra v.
Nat Commun. 2023 Dec 16;14(1):8379. doi: 10.1038/s41467-023-43801-2.
Nat Commun. 2023.
PMID: 38104123
Free PMC article.
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Assessing the accuracy of contact and distance predictions in CASP14.
Ruiz-Serra V, Pontes C, Milanetti E, Kryshtafovych A, Lepore R, Valencia A.
Ruiz-Serra V, et al.
Proteins. 2021 Dec;89(12):1888-1900. doi: 10.1002/prot.26248. Epub 2021 Oct 3.
Proteins. 2021.
PMID: 34595772
Free PMC article.
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