String kernels and high-quality data set for improved prediction of kinked helices in α-helical membrane proteins.
The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. For the particular case of kink prediction, we generated a data set of 132 membrane proteins containing 1014 manually labeled helices and examined the environment of kinks. Our sequence analysis confirms the great relevance of proline and reveals disproportionately high occurrences of glycine and serine at kink positions. The structural analysis shows significantly different solvent accessible surface area mean values for kinked and nonkinked helices. More important, …
SKINK: a web server for string kernel based kink prediction in α-helices
Abstract Motivation: The reasons for distortions from optimal α-helical geometry are widely unknown, but their influences on structural changes of proteins are significant. Hence, their prediction is a crucial problem in structural bioinformatics. Here, we present a new web server, called SKINK, for string kernel based kink prediction. Extending our previous study, we also annotate the most probable kink position in a given α-helix sequence. Availability and implementation: The SKINK web server is freely accessible at http://biows-inf.zdv.uni-mainz.de/skink. Moreover, SKINK is a module of the BALL software, also freely available at www.ballview.org. Contact: benny.kneissl@roche.com
ProteinScanAR - An Augmented Reality Web Application for High School Education in Biomolecular Life Sciences
Understanding protein structures is a crucial step in creating molecular insight for researchers as well as students and pupils. The enormous scaling gap between an atomic point of view and objects in daily life hampers developing an intuitive relation between them. Especially for high school students, it can be difficult to understand the spatial relations of a protein structure. Due to lack of direct imaging techniques, molecules can only be explored by studying abstract molecular models. Here, the use of Augmented reality (AR) techniques has proven to strongly improve structural perception. In this work we present ProteinScanAR, an augmented reality framework for biomolecular education t…
Evaluation of auditory development in infants and toddlers who received cochlear implants under the age of 24 months with the LittlEARS® Auditory Questionnaire
Abstract Background and Aims Newborn hearing screening and early intervention for congenital hearing loss have created a need for tools assessing the hearing development of very young children. A multidisciplinary evaluation of children's development is now becoming standard in clinical practice, though not many reliable diagnostic instruments exist. For this reason, the LittlEARS ® Auditory Questionnaire (LEAQ) was created to assess the auditory skills of a growing population of infants and toddlers who receive hearing instruments. The LEAQ relies on parent report, which has been shown to be a reliable way of assessing child development. Results with this tool in a group of children who re…