SUMMARY Structural analysis of long DNA fragments, including chromosomes and whole genomes, is one of the main challenges in modern bioinformatics. Here, we propose an original approach based on spectral methods and its implementation called SBARS (Spectral-Based Approach for Repeats Search. The main idea of our approach is that repeated DNA structures are recognized not within the nucleotide s...

To facilitate flexible and efficient structural bioinformatics analyses, new functionality for three-dimensional structure processing and analysis has been introduced into PyCogent - a popular feature-rich framework for sequence-based bioinformatics, but one which has lacked equally powerful tools for handling stuctural/coordinate-based data. Extensible Python modules have been developed, which...

Each year the International Society for Computational Biology (ISCB; http:// www.iscb.org) honors a young scientist who has already achieved a significant and lasting impact on our field. The ISCB Awards Committee, comprised of current and former directors of the society and chaired by Søren Brunak, director of the Center for Biological Sequence Analysis at the Technical University of Denmark, ...

Motivation Ebola viruses are not pathogenic but can be adapted to replicate and cause disease in rodents. Here, we used a structural bioinformatics approach to analyze the mutations associated with Ebola virus adaptation to rodents to elucidate the determinants of host-specific Ebola virus pathogenicity. Results We identified 33 different mutations associated with Ebola virus adaptation to ro...

Motivation: Large-scale computational docking will be increasingly used in future years to discriminate protein–protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein–protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. ...

Motivation: A sizeable fraction of eukaryotic proteins contain intrinsically disordered regions (IDRs), which act in unfolded states or by undergoing transitions between structured and unstructured conformations. Over time, sequence-based classifiers of IDRs have become fairly accurate and currently a major challenge is linking IDRs to their biological roles from the molecular to the systems le...

SUMMARY The application of protein-protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of >97% strong scaling. AVAILABILITY AND IMPL...

We present examples from our research in the fields of immunophysics, structural bioinformatics, design of proteins with tailored activities, and rational drug design. Our aim is to understand the function of the complement system, which is part of innate immunity, and to design regulators and inhibitors against illregulated activation of the complement system. We use atomic resolution computat...

Co-evolution techniques were originally conceived to assist in protein structure prediction by inferring pairs of residues that share spatial proximity. However, the functional relationships that can be extrapolated from co-evolution have also proven to be useful in a wide array of structural bioinformatics applications. These techniques are a powerful way to extract structural and functional i...

Bioinformatics education can be broadly defined as the teaching and learning of the use of computer and information technology, along with mathematical and statistical analysis for gathering, storing, analyzing, interpreting, and integrating data to solve biological problems. The recent surge of genomics, proteomics, and structural biology in the potential advancement of research and developmen...