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Paula Nazarena Arrías

dblp:426/5560 · DBLP profile ↗
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1ranked-venue papers
0as first author
1since 2021 · last 2024
0000-0001-5668-768XORCID · reported

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Interdisciplinary, comprehensive, and emerging computing
1 paper
Bioinformatics and computational biology · 100%

Topics — the 3 heaviest of 4, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › protein structure analysis
protein structure alignment
0.812024
STRPsearch: fast detection of structured tandem repeat proteins · Bioinform. 2024
Bioinformatics and computational biology
protein structure analysis
0.812024
STRPsearch: fast detection of structured tandem repeat proteins · Bioinform. 2024
Bioinformatics and computational biology › structural bioinformatics › structural motif analysis
structural motif search
0.812024
STRPsearch: fast detection of structured tandem repeat proteins · Bioinform. 2024

Methods — techniques the papers use, named apart from their topics

structural alignment · 0.8TM-score profile · 0.8
YearPublicationVenuePosition
2024 STRPsearch: fast detection of structured tandem repeat proteins
abstract
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. AVAILABILITY AND IMPLEMENTATION: STRPsearch is coded in Python. All scripts and associated documentation are available from: https://github.com/BioComputingUP/STRPsearch.
Soroush Mozaffari, Paula Nazarena Arrías, Damiano Clementel, Damiano Piovesan, Carlo Ferrari, Silvio C. E. Tosatto, Alexander Miguel Monzon
Bioinform.2