Structural alphabets derived from attractors in conformational space

Background: The hierarchical and partially redundant nature of protein structures justifies the definition of frequently occurring conformations of short fragments as 'states'. Collections of selected representatives for these states define Structural Alphabets, describing the most typical local conformations within protein structures. These alphabets form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.Results: A Structural Alphabet has been derived by clustering all four-residue fragments of a high-resolution subset of the protein data bank and extracting the high-density states as representative conformational states. Each fragment is uniquely defined by a set of three independent angles corresponding to its degrees of freedom, capturing in simple and intuitive terms the properties of the conformational space. The fragments of the Structural Alphabet are equivalent to the conformational attractors and therefore yield a most informative encoding of proteins. Proteins can be reconstructed within the experimental uncertainty in structure determination and ensembles of structures can be encoded with accuracy and robustness.Conclusions: The density-based Structural Alphabet provides a novel tool to describe local conformations and it is specifically suitable for application in studies of protein dynamics. © 2010 Pandini et al; licensee BioMed Central Ltd

The role of bot squads in the political propaganda on Twitter

Social Media are nowadays the privileged channel for information spreading and news checking. Unexpectedly for most of the users, automated accounts, also known as social bots, contribute more and more to this process of news spreading. Using Twitter as a benchmark, we consider the traffic exchanged, over one month of observation, on a specific topic, namely the migration flux from Northern Africa to Italy. We measure the significant traffic of tweets only, by implementing an entropy-based null model that discounts the activity of users and the virality of tweets. Results show that social bots play a central role in the exchange of significant content. Indeed, not only the strongest hubs have a number of bots among their followers higher than expected, but furthermore a group of them, that can be assigned to the same political tendency, share a common set of bots as followers. The retwitting activity of such automated accounts amplifies the presence on the platform of the hubs' messages.Comment: Under Submissio

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform