Irene Nobeli

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Molecular recognition between proteins and their interacting partners underlies the biochemistry of living organisms. Specificity in this recognition is thought to be essential, whereas promiscuity is often associated with unwanted side effects, poor catalytic properties and errors in biological function. Recent experimental evidence suggests that(More)
Voltage-gated sodium channels are important targets for the development of pharmaceutical drugs, because mutations in different human sodium channel isoforms have causal relationships with a range of neurological and cardiovascular diseases. In this study, functional electrophysiological studies show that the prokaryotic sodium channel from Magnetococcus(More)
Here, we present an automatic assignment of potential cognate ligands to domains of enzymes in the CATH and SCOP protein domain classifications on the basis of structural data available in the wwPDB. This procedure involves two steps; firstly, we assign the binding of particular ligands to particular domains; secondly, we compare the chemical similarity of(More)
The Escherichia coli metabolome has been characterised using the two-dimensional structures of 745 metabolites, obtained from the EcoCyc and KEGG databases. Physicochemical properties of the metabolome have been calculated to provide an overview of this set of cognate ligands. A library of fragments commonly found among these molecules has been employed to(More)
The molecular recognition and discrimination of adenine and guanine ligand moieties in complexes with proteins have been studied using empirical observations on carefully selected crystal structures. The distribution of protein folds that bind these purines has been found to differ significantly from that across the whole PDB, but the most populated(More)
In a cell, there are many possibilities for cross interactions between enzymes and small molecules, arising from the similarities in the structures of the metabolites and the flexibility in binding of protein active sites. Despite this promiscuity, the cognate partners must be able to recognize each other in vivo, for the cell to function efficiently. This(More)
PROCOGNATE is a database of protein cognate ligands for the domains in enzyme structures as described by CATH, SCOP and Pfam, and is available as an interactive website or a flat file. This article gives an overview of the database and its generation and presents a new website front end, as well as recent increased coverage in our dataset via inclusion of(More)
Increasingly biological text mining research is focusing on the extraction of complex relationships relevant to the construction and curation of biological networks and pathways. However, one important category of pathway — metabolic pathways — has been largely neglected. Here we present a relatively simple method for extracting metabolic reaction(More)
Protein structures provide a valuable resource for rational drug design. For a protein with no known ligand, computational tools can predict surface pockets that are of suitable size and shape to accommodate a complementary small-molecule drug. However, pocket prediction against single static structures may miss features of pockets that arise from proteins'(More)