3D-Beacons: decreasing the gap between protein sequences and structures through a federated network of protein structure data resources

While scientists can often infer the biological function of proteins from their 3-dimensional quaternary structures, the gap between the number of known protein sequences and their experimentally determined structures keeps increasing. A potential solution to this problem is presented by ever more sophisticated computational protein modeling approaches. While often powerful on their own, most methods have strengths and weaknesses. Therefore, it benefits researchers to examine models from various model providers and perform comparative analysis to identify what models can best address their specific use cases. To make data from a large array of model providers more easily accessible to the broader scientific community, we established 3D-Beacons, a collaborative initiative to create a federated network with unified data access mechanisms. The 3D-Beacons Network allows researchers to collate coordinate files and metadata for experimentally determined and theoretical protein models from state-of-the-art and specialist model providers and also from the Protein Data Bank

Comprehensive Collection and Prediction of ABC Transmembrane Protein Structures in the AI Era of Structural Biology

The number of unique transmembrane (TM) protein structures doubled in the last four years, which can be attributed to the revolution of cryo-electron microscopy. In addition, AlphaFold2 (AF2) also provided a large number of predicted structures with high quality. However, if a specific protein family is the subject of a study, collecting the structures of the family members is highly challenging in spite of existing general and protein domain-specific databases. Here, we demonstrate this and assess the applicability and usability of automatic collection and presentation of protein structures via the ABC protein superfamily. Our pipeline identifies and classifies transmembrane ABC protein structures using the PFAM search and also aims to determine their conformational states based on special geometric measures, conftors. Since the AlphaFold database contains structure predictions only for single polypeptide chains, we performed AF2-Multimer predictions for human ABC half transporters functioning as dimers. Our AF2 predictions warn of possibly ambiguous interpretation of some biochemical data regarding interaction partners and call for further experiments and experimental structure determination. We made our predicted ABC protein structures available through a web application, and we joined the 3D-Beacons Network to reach the broader scientific community through platforms such as PDBe-KB

LOCALMULTIDEM and MDE Discursive Political Opportunity Structures (WP1) Dataset, 2004-2006

This study contains the data collected through Workpackage 1 relating to Discursive Political Opportunity Structures of the Localmultide m project and through other related sister projects that formed part of the Multicultural Democracy in Europe (MDE) research network. It also contains the documentation (questionnaires, codebook, etc.) required to understand and analyze the data. This workpackage involved collecting information at the aggregate (or macro) level through a claims-making analysis of the discursive opportunities relating to migrants in each of the cities and countries studied. It contains data for 9 cities: Barcelona, Budapest, Geneva, London, Lyon, Madrid, Milan, Stockholm and Zurich

Resource and Service Centres as the Backbone for a Sustainable Service Infrastructure

Currently, research infrastructures are being designed and established in manydisciplines since they all suffer from an enormous fragmentation of theirresources and tools. In the domain of language resources and tools the CLARINinitiative has been funded since 2008 to overcome many of the integration andinteroperability hurdles. CLARIN can build on knowledge and work from manyprojects that were carried out during the last years and wants to build stableand robust services that can be used by researchers. Here service centres willplay an important role that have the potential of being persistent and thatadhere to criteria as they have been established by CLARIN. In the last year ofthe so-called preparatory phase these centres are currently developing four usecases that can demonstrate how the various pillars CLARIN has been working oncan be integrated. All four use cases fulfil the criteria of beingcross-national

Designing the ELEXIS Parallel Sense-Annotated Dataset in 10 European Languages

Over the course of the last few years, lexicography has witnessed the burgeoning of increasingly reliable automatic approaches supporting the creation of lexicographic resources such as dictionaries, lexical knowledge bases and annotated datasets. In fact, recent achievements in the field of Natural Language Processing and particularly in Word Sense Disambiguation have widely demonstrated their effectiveness not only for the creation of lexicographic resources, but also for enabling a deeper analysis of lexical-semantic data both within and across languages. Nevertheless, we argue that the potential derived from the connections between the two fields is far from exhausted. In this work, we address a serious limitation affecting both lexicography and Word Sense Disambiguation, i.e. the lack of high-quality sense-annotated data and describe our efforts aimed at constructing a novel entirely manually annotated parallel dataset in 10 European languages. For the purposes of the present paper, we concentrate on the annotation of morpho-syntactic features. Finally, unlike many of the currently available sense-annotated datasets, we will annotate semantically by using senses derived from high-quality lexicographic repositories

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

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 descriptors of the qualitative and quantitative properties of the ensembles. High quality of the data is guaranteed by a new submission process, which combines both automatic and manual evaluation steps. A team of biocurators integrate structured metadata describing the ensemble generation methodology, experimental constraints and conditions. A new search engine allows the user to build advanced queries and search all entry fields including cross-references to IDP-related resources such as DisProt, MobiDB, BMRB and SASBDB. We expect that the renewed PED will be useful for researchers interested in the atomic-level understanding of IDP function, and promote the rational, structure-based design of IDP-targeting drugs