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Arrías, Paula NazarenaORCID iD iconorcid.org/0000-0001-5668-768X
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Publikasjoner (3 av 3) Visa alla publikasjoner
Arrías, P. N., Esnal, M. R. & Malm, M. (2025). Imaging the rAAV manufacturing process: assessing the subcellular localisation of capsids during production. Human Gene Therapy, 36(3-4), E187-E188
Åpne denne publikasjonen i ny fane eller vindu >>Imaging the rAAV manufacturing process: assessing the subcellular localisation of capsids during production
2025 (engelsk)Inngår i: Human Gene Therapy, ISSN 1043-0342, E-ISSN 1557-7422, Vol. 36, nr 3-4, s. E187-E188Artikkel i tidsskrift, Meeting abstract (Annet vitenskapelig) Published
sted, utgiver, år, opplag, sider
Mary Ann Liebert, 2025
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-366118 (URN)001418811501134 ()
Merknad

QC 20250707

Tilgjengelig fra: 2025-07-07 Laget: 2025-07-07 Sist oppdatert: 2025-07-07bibliografisk kontrollert
Esnal, M. R., Arrías, P. N., Rockberg, J. & Malm, M. (2025). Understanding recombinant AAV production kinetics in HEK293 cells. Human Gene Therapy, 36(3-4), E189-E189
Åpne denne publikasjonen i ny fane eller vindu >>Understanding recombinant AAV production kinetics in HEK293 cells
2025 (engelsk)Inngår i: Human Gene Therapy, ISSN 1043-0342, E-ISSN 1557-7422, Vol. 36, nr 3-4, s. E189-E189Artikkel i tidsskrift, Meeting abstract (Annet vitenskapelig) Published
sted, utgiver, år, opplag, sider
Mary Ann Liebert, 2025
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-366119 (URN)001418811501138 ()
Merknad

QC 20250707

Tilgjengelig fra: 2025-07-07 Laget: 2025-07-07 Sist oppdatert: 2025-07-07bibliografisk kontrollert
Mozaffari, S., Arrías, P., Clementel, D., Piovesan, D., Ferrari, C., Tosatto, S. C. .. & Monzon, A. M. (2024). STRPsearch: fast detection of structured tandem repeat proteins. Bioinformatics, 40(12), Article ID btae690.
Åpne denne publikasjonen i ny fane eller vindu >>STRPsearch: fast detection of structured tandem repeat proteins
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2024 (engelsk)Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 40, nr 12, artikkel-id btae690Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Motivation: Structured Tandem Repeats Proteins (STRPs) constitute a subclass of tandem repeats characterized by repetitive structural motifs. These proteins exhibit distinct secondary structures that form repetitive tertiary arrangements, often resulting in large molecular assemblies. Despite highly variable sequences, STRPs can perform important and diverse biological functions, maintaining a consistent structure with a variable number of repeat units. With the advent of protein structure prediction methods, millions of 3D models of proteins are now publicly available. However, automatic detection of STRPs remains challenging with current state-of-the-art tools due to their lack of accuracy and long execution times, hindering their application on large datasets. In most cases, manual curation remains the most accurate method for detecting and classifying STRPs, making it impracticable to annotate millions of structures. Results: We introduce STRPsearch, a novel tool for the rapid identification, classification, and mapping of STRPs. Leveraging manually curated entries from RepeatsDB as the known conformational space of STRPs, STRPsearch uses the latest advances in structural alignment for a fast and accurate detection of repeated structural motifs in proteins, followed by an innovative approach to map units and insertions through the generation of TM-score profiles. STRPsearch is highly scalable, efficiently processing large datasets, and can be applied to both experimental structures and predicted models. In addition, it demonstrates superior performance compared to existing tools, offering researchers a reliable and comprehensive solution for STRP analysis across diverse proteomes.

sted, utgiver, år, opplag, sider
Oxford University Press (OUP), 2024
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-358172 (URN)10.1093/bioinformatics/btae690 (DOI)001377102900001 ()39558588 (PubMedID)2-s2.0-85211966531 (Scopus ID)
Merknad

QC 20250114

Tilgjengelig fra: 2025-01-07 Laget: 2025-01-07 Sist oppdatert: 2025-02-20bibliografisk kontrollert
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ORCID-id: ORCID iD iconorcid.org/0000-0001-5668-768X