0000000000207791

AUTHOR

Marco Necci

showing 3 related works from this author

RepeatsDB in 2021: improved data and extended classification for protein tandem repeat structures

2020

The RepeatsDB database (URL: https://repeatsdb.org/) provides annotations and classification for protein tandem repeat structures from the Protein Data Bank (PDB). Protein tandem repeats are ubiquitous in all branches of the tree of life. The accumulation of solved repeat structures provides new possibilities for classification and detection, but also increasing the need for annotation. Here we present RepeatsDB 3.0, which addresses these challenges and presents an extended classification scheme. The major conceptual change compared to the previous version is the hierarchical classification combining top levels based solely on structural similarity (Class > Topology > Fold) with two new lev…

Repetitive Sequences Amino AcidAcademicSubjects/SCI00010BiologíaStatistics as TopicProtein Data Bank (RCSB PDB)Computational biologyBiologyRepetitive SequencesGene Ontology; HEK293 Cells; HeLa Cells; Humans; Proteins; Reproducibility of Results; Statistics as Topic; User-Computer Interface; Databases Protein; Repetitive Sequences Amino Acid; Tandem Repeat SequencesDatabases03 medical and health sciencesAnnotationUser-Computer InterfaceProtein structureSimilarity (network science)Tandem repeatGeneticsDatabase IssueHumansDatabases ProteinCiencias Exactasdatabase030304 developmental biology0303 health sciencesHierarchy (mathematics)Protein030302 biochemistry & molecular biologyProteinsReproducibility of Resultscomputer.file_formatProtein Data BankClass (biology)proteinsAmino AcidComputingMethodologies_PATTERNRECOGNITIONGene OntologyHEK293 CellsclassificationTandem Repeat Sequencesprotein tandem repeat structures[INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM]computerHeLa CellsNucleic Acids Research
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A novel approach to investigate the evolution of structured tandem repeat protein families by exon duplication.

2020

Tandem Repeat Proteins (TRPs) are ubiquitous in cells and are enriched in eukaryotes. They contributed to the evolution of organism complexity, specializing for functions that require quick adaptability such as immunity-related functions. To investigate the hypothesis of repeat protein evolution through exon duplication and rearrangement, we designed a tool to analyze the relationships between exon/intron patterns and structural symmetries. The tool allows comparison of the structure fragments as defined by exon/intron boundaries from Ensembl against the structural element repetitions from RepeatsDB. The all-against-all pairwise structural alignment between fragments and comparison of the t…

Protein familyStructural alignmentBiological data visualizationExonComputational biologyBiologyEvolution Molecular03 medical and health sciencesExonProtein structureTandem repeatStructural BiologyGene duplicationAnimalsHumans030304 developmental biology0303 health sciences030302 biochemistry & molecular biologyIntronProteinsExonsProtein superfamilyClassificationIntronsBiological data visualization; Classification; Exon; Protein evolution; Protein structure; Repeat proteinTandem Repeat SequencesRepeat proteinProtein structureProtein evolutionJournal of structural biology
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PlaToLoCo: the first web meta-server for visualization and annotation of low complexity regions in proteins

2020

Abstract Low complexity regions (LCRs) in protein sequences are characterized by a less diverse amino acid composition compared to typically observed sequence diversity. Recent studies have shown that LCRs may co-occur with intrinsically disordered regions, are highly conserved in many organisms, and often play important roles in protein functions and in diseases. In previous decades, several methods have been developed to identify regions with LCRs or amino acid bias, but most of them as stand-alone applications and currently there is no web-based tool which allows users to explore LCRs in protein sequences with additional functional annotations. We aim to fill this gap by providing PlaToL…

Sequence analysisAcademicSubjects/SCI00010Protein domainComputational biologyBiologyDomain (software engineering)Computer graphics03 medical and health sciencesAnnotationProtein DomainsSequence Analysis ProteinGeneticsComputer GraphicsHumansAmino Acids030304 developmental biology0303 health sciencesIntersection (set theory)030302 biochemistry & molecular biologyMembrane ProteinsProteinsMolecular Sequence AnnotationVisualizationMolecular Sequence AnnotationWeb Server IssueSoftwareNucleic Acids Research
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