Publications

Predicting chemical shifts: A method for the structure-based prediction of side-chain aromatic 1H chemical shifts of proteins is presented (see picture; blue structures: aromatic side chains, red spheres: aromatic hydrogen atoms). Its ability to differentiate correct structural models from incorrect ones is also demonstrated, together with its use to detect differences caused by cofactor or ligand binding, or by sequence alterations between ...

The protocols currently used for protein structure determination by nuclear magnetic resonance (NMR) depend on the determination of a large number of upper distance limits for proton-proton pairs. Typically, this task is performed manually by an experienced researcher rather than automatically by using a specific computer program. To assess whether it is indeed possible to generate in a fully automated manner NMR structures adequate for ...

In this paper we present a cohesive structural itemset miner aiming to discover interesting patterns in a set of data objects within a multidimensional spatial structure by combining the cohesion and the support of the pattern. We propose two ways to build the itemset miner, VertexOne and VertexAll, in an attempt to find a balance between accuracy and run-times. The experiments show that VertexOne performs better, and finds almost the same ...

In this paper we present a cohesive structural itemset miner aiming to discover interesting patterns in a set of data objects within a multidimensional spatial structure by combining the cohesion and the support of the pattern. The usefulness of this algorithm is demonstrated by applying it to find interesting patterns of amino acids in spatial proximity within a set of proteins based on their atomic coordinates in the protein molecular ...

The classical procedure for nuclear magnetic resonance structure calculation allocates empirical distance ranges and uses historical values for weighting factors. However, Bayesian analysis suggests that there are more optimal choices for potential shape (bounds-free log-harmonic shape) and restraints weights. We compare the classical protocol with the Bayesian approach for more than 300 protein structures. We analyze the conformation similarity ...

© 2019 Elsevier Ltd Gluten proteins play a crucial role in the properties and quality of intermediate and final wheat-based bakery products such as bread and crackers. Despite their importance, gluten protein structures and their interactions with other dough components have remained poorly understood due to the difficulty of studying these proteins in complex matrices without disturbing them. The present work reviews the principles, advantages, ...

Recent years have seen an increase in the development of computational proteins, including symmetric ones. A ninefold-symmetric β-propeller protein named Cake has recently been developed. Here, attempts were made to further engineer this protein into a threefold-symmetric nine-bladed propeller using computational design. Two nine-bladed propeller proteins were designed, named Scone-E and Scone-R. Crystallography, however, revealed the structure ...

Several major global diseases are caused by single-cell parasites called trypanosomatids. These organisms exhibit many unusual features including a unique and essential U-insertion/deletion RNA editing process in their single mitochondrion. Many key RNA editing steps occur in similar to 20S editosomes, which have a core of 12 proteins. Among these, the "interaction protein" KREPA6 performs a central role in maintaining the integrity of the ...

The Arabidopsis thaliana genome contains a small group of bipartite F-box proteins, consisting of an N-terminal F-box domain and a C-terminal domain sharing sequence similarity with Nictaba, the jasmonate-induced glycan-binding protein (lectin) from tobacco. Based on the high sequence similarity between the C-terminal domain of these proteins and Nictaba, the hypothesis was put forward that the so-called F-box-Nictaba proteins possess ...