PDBe-KB: a community-driven resource for structural and functional annotations.

The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional annotations of macromolecular structure data, contained in the Protein Data Bank (PDB). The goal of PDBe-KB is two-fold: (i) to increase the visibility and reduce the fragmentation of annotations contributed by specialist data resources, and to make these data more findable, accessible, interoperable and reusable (FAIR) and (ii) to place macromolecular structure data in their biological context, thus facilitating their use by the broader scientific community in fundamental and applied research. Here, we describe the guidelines of this collaborative effort, the current status of contributed data, and the PDBe-KB infrastructure, which includes the data exchange format, the deposition system for added value annotations, the distributable database containing the assembled data, and programmatic access endpoints. We also describe a series of novel web-pages-the PDBe-KB aggregated views of structure data-which combine information on macromolecular structures from many PDB entries. We have recently released the first set of pages in this series, which provide an overview of available structural and functional information for a protein of interest, referenced by a UniProtKB accession

Measuring structural similarity of semistructured data based on information-theoretic approaches

We propose and experimentally evaluate different approaches for measuring the structural similarity of semistructured documents based on information-theoretic concepts. Common to all approaches is a two-step procedure: first, we extract and linearize the structural information from documents, and then, we use similarity measures that are based on, respectively, Kolmogorov complexity and Shannon entropy to determine the distance between the documents. Compared to other approaches, we are able to achieve a linear run-time complexity and demonstrate in an experimental evaluation that the results of our technique in terms of clustering quality are on a par with or even better than those of other, slower approaches

DNA Barcoding of <i>Trichobilharzia</i> (Trematoda: Schistosomatidae) Species and Their Detection in eDNA Water Samples

We designed and tested species-specific PCR primers to detect Trichobilharzia species via environmental DNA (eDNA) barcoding in selected Austrian water bodies. Tests were performed with eDNA samples from the field as well as with artificial samples from the lab, where snails releasing cercariae were kept in aquariums. From two localities, Trichobilharzia was documented based on the release of cercariae from snails, enabling morphological species identification. In both cases, the corresponding species were detected via eDNA: Trichobilharzia szidati and Trichobilharzia physellae. Nonetheless, the stochasticity was high in the replicates. PCR tests with aquarium water into which the cercariae had been released allowed eDNA detection even after 44 days. As in the PCRs with eDNA samples from the field, positive results of these experiments were not obtained for all samples and replicates. PCR sensitivity tests with dilution series of T. szidati genomic DNA as well as of PCR amplification products yielded successful amplification down to concentrations of 0.83 pg/µL and 0.008 pg/µL, respectively. Our results indicate that the presumed species specificity of PCR primers may not be guaranteed, even if primers were designed for specific species. This entails misidentification risks, particularly in areas with incomplete species inventories

First Record of Trichobilharzia physellae (Talbot, 1936) in Europe, a Possible Causative Agent of Cercarial Dermatitis

Several species of avian schistosomes are known to cause dermatitis in humans worldwide. In Europe, this applies above all to species of the genus Trichobilharzia. For Austria, a lot of data are available on cercarial dermatitis and on the occurrence of Trichobilharzia, yet species identification of trematodes in most cases is doubtful due to the challenging morphological determination of cercariae. During a survey of trematodes in freshwater snails, we were able to detect a species in the snail Physella acuta (Draparnaud, 1805) hitherto unknown for Austria, Trichobilharzia physellae; this is also the first time this species has been reported in Europe. Species identification was performed by integrative taxonomy combining morphological investigations with molecular genetic analyses. The results show a very close relationship between the parasite found in Austria and North American specimens (similarity found in CO1 ≥99.57%). Therefore, a recent introduction of T. physellae into Europe can be assumed

PDBe-KB: collaboratively defining the biological context of structural data

none71: The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive.noneVaradi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, Mandar; Nadzirin, Nurul; Nair, Sreenath S; Pravda, Lukas; Tanweer, Ahsan; Al-Lazikani, Bissan; Andreini, Claudia; Barton, Geoffrey J; Bednar, David; Berka, Karel; Blundell, Tom; Brock, Kelly P; Carazo, Jose Maria; Damborsky, Jiri; David, Alessia; Dey, Sucharita; Dunbrack, Roland; Recio, Juan Fernandez; Fraternali, Franca; Gibson, Toby; Helmer-Citterich, Manuela; Hoksza, David; Hopf, Thomas; Jakubec, David; Kannan, Natarajan; Krivak, Radoslav; Kumar, Manjeet; Levy, Emmanuel D; London, Nir; Macias, Jose Ramon; Srivatsan, Madhusudhan M; Marks, Debora S; Martens, Lennart; McGowan, Stuart A; McGreig, Jake E; Modi, Vivek; Parra, R Gonzalo; Pepe, Gerardo; Piovesan, Damiano; Prilusky, Jaime; Putignano, Valeria; Radusky, Leandro G; Ramasamy, Pathmanaban; Rausch, Atilio O; Reuter, Nathalie; Rodriguez, Luis A; Rollins, Nathan J; Rosato, Antonio; Rubach, Paweł; Serrano, Luis; Singh, Gulzar; Skoda, Petr; Sorzano, Carlos Oscar S; Stourac, Jan; Sulkowska, Joanna I; Svobodova, Radka; Tichshenko, Natalia; Tosatto, Silvio C E; Vranken, Wim; Wass, Mark N; Xue, Dandan; Zaidman, Daniel; Thornton, Janet; Sternberg, Michael; Orengo, Christine; Velankar, SameerVaradi, Mihaly; Anyango, Stephen; Armstrong, David; Berrisford, John; Choudhary, Preeti; Deshpande, Mandar; Nadzirin, Nurul; Nair, Sreenath S; Pravda, Lukas; Tanweer, Ahsan; Al-Lazikani, Bissan; Andreini, Claudia; Barton, Geoffrey J; Bednar, David; Berka, Karel; Blundell, Tom; Brock, Kelly P; Carazo, Jose Maria; Damborsky, Jiri; David, Alessia; Dey, Sucharita; Dunbrack, Roland; Recio, Juan Fernandez; Fraternali, Franca; Gibson, Toby; Helmer-Citterich, Manuela; Hoksza, David; Hopf, Thomas; Jakubec, David; Kannan, Natarajan; Krivak, Radoslav; Kumar, Manjeet; Levy, Emmanuel D; London, Nir; Macias, Jose Ramon; Srivatsan, Madhusudhan M; Marks, Debora S; Martens, Lennart; Mcgowan, Stuart A; Mcgreig, Jake E; Modi, Vivek; Parra, R Gonzalo; Pepe, Gerardo; Piovesan, Damiano; Prilusky, Jaime; Putignano, Valeria; Radusky, Leandro G; Ramasamy, Pathmanaban; Rausch, Atilio O; Reuter, Nathalie; Rodriguez, Luis A; Rollins, Nathan J; Rosato, Antonio; Rubach, Paweł; Serrano, Luis; Singh, Gulzar; Skoda, Petr; Sorzano, Carlos Oscar S; Stourac, Jan; Sulkowska, Joanna I; Svobodova, Radka; Tichshenko, Natalia; Tosatto, Silvio C E; Vranken, Wim; Wass, Mark N; Xue, Dandan; Zaidman, Daniel; Thornton, Janet; Sternberg, Michael; Orengo, Christine; Velankar, Samee