Automated scoring of AFLPs using RawGeno v 2.0, a free R CRAN library.

Amplified Fragment Length Polymorphisms (AFLPs) are a cheap and efficient protocol for generating large sets of genetic markers. This technique has become increasingly used during the last decade in various fields of biology, including population genomics, phylogeography, and genome mapping. Here, we present RawGeno, an R library dedicated to the automated scoring of AFLPs (i.e., the coding of electropherogram signals into ready-to-use datasets). Our program includes a complete suite of tools for binning, editing, visualizing, and exporting results obtained from AFLP experiments. RawGeno can either be used with command lines and program analysis routines or through a user-friendly graphical user interface. We describe the whole RawGeno pipeline along with recommendations for (a) setting the analysis of electropherograms in combination with PeakScanner, a program freely distributed by Applied Biosystems; (b) performing quality checks; (c) defining bins and proceeding to scoring; (d) filtering nonoptimal bins; and (e) exporting results in different formats.

Blind docking of 260 protein-ligand complexes with EADock 2.0.

Molecular docking softwares are one of the important tools of modern drug development pipelines. The promising achievements of the last 10 years emphasize the need for further improvement, as reflected by several recent publications (Leach et al., J Med Chem 2006, 49, 5851; Warren et al., J Med Chem 2006, 49, 5912). Our initial approach, EADock, showed a good performance in reproducing the experimental binding modes for a set of 37 different ligand-protein complexes (Grosdidier et al., Proteins 2007, 67, 1010). This article presents recent improvements regarding the scoring and sampling aspects over the initial implementation, as well as a new seeding procedure based on the detection of cavities, opening the door to blind docking with EADock. These enhancements were validated on 260 complexes taken from the high quality Ligand Protein Database [LPDB, (Roche et al., J Med Chem 2001, 44, 3592)]. Two issues were identified: first, the quality of the initial structures cannot be assumed and a manual inspection and/or a search in the literature are likely to be required to achieve the best performance. Second the description of interactions involving metal ions still has to be improved. Nonetheless, a remarkable success rate of 65% was achieved for a large scale blind docking assay, when considering only the top ranked binding mode and a success threshold of 2 A RMSD to the crystal structure. When looking at the five-top ranked binding modes, the success rate increases up to 76%. In a standard local docking assay, success rates of 75 and 83% were obtained, considering only the top ranked binding mode, or the five top binding modes, respectively.

Ein digitales Kulturobjekt. Der Fall der »Restaurierung« des Ecce homo von Borja

Im August 2012 brachte der Heimatverein von Borja, in Spanien, auf seinem Blog seine »tiefe Betroffenheit« über einen, wie es hieß, »unbeschreiblichen Vorgang« zum Ausdruck: Ein Wandgemälde in der Iglesia del Santuario de la Misericordia war in einer Form restauriert worden, die das ursprüngliche Motiv - den Schmerzensmann - fast unkenntlich machte. Die Affäre ging in kürzester Zeit durch die internationale Presse und durch das Internet. Sie schlug dabei unerwartet hohe Wellen, mit denen sich Hohn und Spott über den in fast allen Kommentaren als »misslungen« bezeichneten Restaurierungsakt ergoss. Im Web 2.0 hingegen gab das dergestalt »restaurierte« Antlitz des Ecce homo Anlass zu einer Vielzahl von Neuinterpretationen, es avancierte zu einem regelrechten Internet-Phänomen, das in der vorliegenden Studie in Hinblick auf den Umgang mit und die Aneignung von Bildern im digitalen Zeitalter untersucht werden soll.