0000000000207802

AUTHOR

Gustavo Parisi

showing 2 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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PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

2020

Abstract The Protein Ensemble Database (PED) (https://proteinensemble.org), which holds structural ensembles of intrinsically disordered proteins (IDPs), has been significantly updated and upgraded since its last release in 2016. The new version, PED 4.0, has been completely redesigned and reimplemented with cutting-edge technology and now holds about six times more data (162 versus 24 entries and 242 versus 60 structural ensembles) and a broader representation of state of the art ensemble generation methods than the previous version. The database has a completely renewed graphical interface with an interactive feature viewer for region-based annotations, and provides a series of descriptor…

MESH: Databases ProteinMESH: Search EngineAcademicSubjects/SCI00010[SDV.BBM.BS] Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM][SDV]Life Sciences [q-bio]media_common.quotation_subjectBiologycomputer.software_genreIntrinsically disordered proteins03 medical and health sciencesDatabases0302 clinical medicineInformation and Computing SciencesGeneticsFeature (machine learning)Database IssueHumansDatabases ProteinRepresentation (mathematics)Function (engineering)MESH: Tumor Suppressor Protein p53ComputingMilieux_MISCELLANEOUS030304 developmental biologymedia_commonGraphical user interfaceStructure (mathematical logic)MESH: Intrinsically Disordered Proteins0303 health sciencesMESH: HumansDatabase[SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry Molecular Biology/Structural Biology [q-bio.BM]business.industryProteinBiological Sciences[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]MetadataSearch EngineIntrinsically Disordered ProteinsState (computer science)Generic health relevanceTumor Suppressor Protein p53businesscomputer030217 neurology & neurosurgeryEnvironmental SciencesDevelopmental Biology
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