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Article
Open AccessPAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction
The specific recognition of a DNA locus by a given transcription factor is a widely studied issue. It is generally agreed that the recognition can be influenced not only by the binding motif but by the larger ...
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Article
Open AccessA comparison of approaches to accessing existing biological and chemical relational databases via SPARQL
Current biological and chemical research is increasingly dependent on the reusability of previously acquired data, which typically come from various sources. Consequently, there is a growing need for database ...
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Article
Open AccessIDSM ChemWebRDF: SPARQLing small-molecule datasets
The Resource Description Framework (RDF), together with well-defined ontologies, significantly increases data interoperability and usability. The SPARQL query language was introduced to retrieve requested RDF ...
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Article
Open AccessCorrection to: Interoperable chemical structure search service
It was highlighted that the original article [1] contained an error in the last paragraph of the section ‘Structure search using SPARQL’, specifically in the radius of the used fingerprint. This Correction art...
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Article
Open AccessThe bio.tools registry of software tools and data resources for the life sciences
Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge. We outline a pan-European...
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Article
Open AccessInteroperable chemical structure search service
The existing connections between large databases of chemicals, proteins, metabolites and assays offer valuable resources for research in fields ranging from drug design to metabolomics. Transparent search acro...
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Article
Open AccessSachem: a chemical cartridge for high-performance substructure search
Structure search is one of the valuable capabilities of small-molecule databases. Fingerprint-based screening methods are usually employed to enhance the search performance by reducing the number of calls to t...
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Article
Open AccessRandom protein sequences can form defined secondary structures and are well-tolerated in vivo
The protein sequences found in nature represent a tiny fraction of the potential sequences that could be constructed from the 20-amino-acid alphabet. To help define the properties that shaped proteins to stand...
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Article
Open AccessAdvanced SPARQL querying in small molecule databases
In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better...
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Article
Open AccessOn InChI and evaluating the quality of cross-reference links
There are many databases of small molecules focused on different aspects of research and its applications. Some tasks may require integration of information from various databases. However, determining which e...
