UniProtKB/Swiss-Prot

Boutet, Emmanuel; Lieberherr, Damien; Tognolli, Michael; Schneider, Michel; Bairoch, Amos Marc

doi:10.1007/978-1-59745-535-0_4

Cited by 563 publications

(486 citation statements)

References 14 publications

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“…PPR sequences obtained using PSI-BLAST from the UniProtKB database 50 . Multiple identical sequences were removed and sequences were aligned using ClustalW 51 .…”

Section: Methodsmentioning

confidence: 99%

An artificial PPR scaffold for programmable RNA recognition

et al. 2014

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Pentatricopeptide repeat (PPR) proteins control diverse aspects of RNA metabolism in eukaryotic cells. Although recent computational and structural studies have provided insights into RNA recognition by PPR proteins, their highly insoluble nature and inconsistencies between predicted and observed modes of RNA binding have restricted our understanding of their biological functions and their use as tools. Here we use a consensus design strategy to create artificial PPR domains that are structurally robust and can be programmed for sequence-specific RNA binding. The atomic structures of these artificial PPR domains elucidate the structural basis for their stability and modelling of RNA-protein interactions provides mechanistic insights into the importance of RNA-binding residues and suggests modes of PPR-RNA association. The modular mode of RNA binding by PPR proteins holds great promise for the engineering of new tools to target RNA and to understand the mechanisms of gene regulation by natural PPR proteins.

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“…PPR sequences obtained using PSI-BLAST from the UniProtKB database 50 . Multiple identical sequences were removed and sequences were aligned using ClustalW 51 .…”

Section: Methodsmentioning

confidence: 99%

An artificial PPR scaffold for programmable RNA recognition

et al. 2014

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“…The associations between object descriptions and the elements (concepts) of an ontology form a so-called annotation mapping. For instance, the protein objects of Ensembl [11] and Swiss-Prot [3] are associated with concepts of the popular Gene Ontology [9] to describe the molecular functions and biological processes in which the proteins are involved. Annotation mappings are utilized in different analysis scenarios and applications.…”

Section: Introductionmentioning

confidence: 99%

Estimating the Quality of Ontology-Based Annotations by Considering Evolutionary Changes

Groß

Hartung

Kirsten

et al. 2009

Lecture Notes in Computer Science

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Abstract. Ontology-based annotations associate objects, such as genes and proteins, with well-defined ontology concepts to semantically and uniformly describe object properties. Such annotation mappings are utilized in different applications and analysis studies whose results strongly depend on the quality of the used annotations. To study the quality of annotations we propose a generic evaluation approach considering the annotation generation methods (provenance) as well as the evolution of ontologies, object sources, and annotations. Thus, it facilitates the identification of reliable annotations, e.g., for use in analysis applications. We evaluate our approach for functional protein annotations in Ensembl and Swiss-Prot using the Gene Ontology.

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“…According to the UniportKB database, only 17 of the identified methylation sites were known to exist. 23 As a positive control, eight known histone methylation sites were determined in this work, including H3K27 mono-, di-and trimethylation, K36 mono-and di-methylation and H4K20 mono-, di-and tri-methylation. Intriguingly, we also seemed to identify a novel monomethylation site at H2BK6.…”

mentioning

confidence: 99%