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Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can

Many studies have demonstrated that shape string is an extremely important structure representation, since it is more complete than the classical secondary structure. The shape string provides detailed information also in the regions denoted random coil. But few services are provided for systematic analysis of protein shape string. To fill this gap, we have developed an accurate shape string predi

Conformal prediction has been proposed as a more rigorous way to define prediction confidence compared to other application domain concepts that have earlier been used for QSAR modeling. One main advantage of such a method is that it provides a prediction region potentially with multiple predicted labels, which contrasts to the single valued (regression) or single label (classification) output pre

Chemogenomics data generally refers to the activity data of chemical compounds on an array of protein targets and represents an important source of information for building in silico target prediction models. The increasing volume of chemogenomics data offers exciting opportunities to build models based on Big Data. Preparing a high quality data set is a vital step in realizing this goal and this

The volume of high throughput screening data has considerably increased since the beginning of the automated biochemical and cell-based assays era. This information-rich data source provides tremendous repurposing opportunities for data mining. It was recently shown that biochemical or cell-based assay results can be compiled into so-called high-throughput fingerprints (HTSFPs) as a new type of de

Motivation: The precise prediction of protein secondary structure is of key importance for the prediction of 3D structure and biological function. Although the development of many excellent methods over the last few decades has allowed the achievement of prediction accuracies of up to 80%, progress seems to have reached a bottleneck, and further improvements in accuracy have proven difficult. Resu

After World War II and prior to the financial deregulation of the 1980s, monetary policy in Sweden as well as in other western European countries rested chiefly on a system of far- reaching non-market-oriented controls of credit flows and interest rates. How was monetary policy conducted in such an environment of financial repression, where the central bank was unable to rely on traditional moneta

Numerous methods for predicting c-turns in proteins have been developed. However, the results they generally provided are not very good, with a Matthews correlation coefficient (MCC) ≤0.18. Here, an attempt has been made to develop a method to improve the accuracy of γ-turn prediction. First, we employ the geometric mean metric as optimal criterion to evaluate the performance of support vector mac

The β-turn is a secondary protein structure type that plays an important role in protein configuration and function. Development of accurate prediction methods to identify β-turns in protein sequences is valuable. Several methods for β-turn prediction have been developed; however, the prediction quality is still a challenge and there is infstantial room for improvement. Innovations of the proposed

Non-negative matrix approximation (NNMA) has been used in diverse scientific fields, but it still has some major limitations. In the present study a novel trilinear decomposition method, termed three-way NNMA (TWNNMA), was developed. The method decomposes three-way arrays directly without unfolding and overcomes the restriction of locking zero elements in the deduced multiplicative update rules by

Previous studies have shown that the C57 and 129 strains of mice display marked differences in behavioural performance, neuroanatomy, neurochemistry and synaptic plasticity. However, few metabolomic studies of their biofluids have been performed. As part of a series of metabolic phenotyping, the effects of gender and strain upon serum metabolite composition and variation are examined in this study

Mycobacterium, the most common disease-causing genus, infects billions of people and is notoriously difficult to treat. Understanding the subcellular localization of mycobacterial proteins can provide essential clues for protein function and drug discovery. In this article, we present a novel approach that focuses on local sequence information to identify localization motifs that are generated by

Amyloid-β (Aβ) is hypothesized to facilitate the spread of tau pathology beyond the medial temporal lobe. However, there is evidence that, independently of Aβ, age-related tau pathology might be present outside of the medial temporal lobe. We therefore aimed to study age-related Aβ-independent tau deposition outside the medial temporal lobe in two large cohorts and to investigate potential downstr

Stricter regulations on emissions and higher demands on engine performance drive automotive industries to replace conventional gray cast iron with compacted graphite iron (CGI). CGI has a higher wear resistance, strength, elastic modulus, and almost double fatigue strength as to gray cast iron, yet the same positive properties make CGI more difficult to machine. This study focuses on finish millin

There is a high demand to design and develop recyclable biobased polymers using eco-friendly synthetic approaches. In this work, we present the facile synthesis of two dicarboxylate monomers with a central non-cyclic acetal unit (dimethyl 4,4'(methylenebis(oxy))dibenzoate and dimethyl 4,4'-(methylenebis(oxy))bis(3-methoxybenzoate)), using potentially biosourced methyl paraben and methyl vanillate.