965 research outputs found
Implementation of a Bayesian secondary structure estimation method for the SESCA circular dichroism analysis package
Get PDFCircular dichroism spectroscopy is a structural biology technique frequently applied to determine the secondary structure composition of soluble proteins. Our recently introduced computational analysis package SESCA aids the interpretation of protein circular dichroism spectra and enables the validation of proposed corresponding structural models. To further these aims, we present the implementation and characterization of a new Bayesian secondary structure estimation method in SESCA, termed SESCA_bayes. SESCA_bayes samples possible secondary structures using a Monte Carlo scheme, driven by the likelihood of estimated scaling errors and non-secondary-structure contributions of the measured spectrum. SESCA_bayes provides an estimated secondary structure composition and separate uncertainties on the fraction of residues in each secondary structure class. It also assists efficient model validation by providing a posterior secondary structure probability distribution based on the measured spectrum. Our presented study indicates that SESCA_bayes estimates the secondary structure composition with a significantly smaller uncertainty than its predecessor, SESCA_deconv, which is based on spectrum deconvolution. Further, the mean accuracy of the two methods in our analysis is comparable, but SESCA_bayes provides more accurate estimates for circular dichroism spectra that contain considerable non-SS contributions
How accurate is circular dichroism-based model validation?
Get PDFCircular dichroism (CD) spectroscopy is highly sensitive to the secondary structure (SS) composition of proteins. Several methods exist to either estimate the SS composition of a protein or to validate existing structural models using its CD spectrum. The accuracy and precision of these methods depend on the quality of both the measured CD spectrum and the used reference structure. Using a large reference protein set with high-quality CD spectra and synthetic data derived from this set, we quantified deviations from both ideal spectra and reference structures due to experimental limitations. We also determined the impact of these deviations on SS estimation, CD prediction, and SS validation methods of the SESCA analysis package. With regard to the CD spectra, our results suggest intensity scaling errors and non-SS contributions as the main causes of inaccuracies. These factors also can lead to overestimated model errors during validation. The errors of the used reference structures combine non-additively with errors caused by the CD spectrum, which increases the uncertainty of model validation. We have further shown that the effects of scaling errors in the CD spectrum can be nearly eliminated by appropriate re-scaling, and that the accuracy of model validation methods can be improved by accounting for typical non-SS contributions. These improvements have now been implemented within the SESCA package and are available at: https://www.mpibpc.mpg.de/sesca
From Helmut Jürgensen’s former students: The game of informatics
No full textPersonal reflections are given on being students of Helmut Jürgensen. Then, we attempt
to address his hypothesis that informatics follows trend-like behaviours through the
use of a content analysis of university job advertisements, and then via simulation
techniques from the area of quantitative economics
Smalltalk Interpreter in Java
No full textAuthor Helmut Rohregger, BSc.Kurzfassungen in deutscher und englischer SpracheMasterarbeit Universität Linz 201
Smalltalk Interpreter in Java
No full textAuthor Helmut Rohregger, BSc.Kurzfassungen in deutscher und englischer SpracheMasterarbeit Universität Linz 201
HELMUT E. LUCK JAKO HISTORYK PSYCHOLOGII
Get PDFThe article presents the figure of Helmut E. Luck, well-known scientist in the world of historians of psychology. Helmut E. Luck also is well-known in Poland, as the author or the scientific editor of several books in the field of history of psychology. In the first part of the article the short presentation of his scientific career and his scientific achievements are demonstrated. The second part comprises the analysis of his opinions in the scope of social psychology. Helmut E. Luck was the one of pioneers in psychology, who paid attention to social positive phenomena or social positive behaviors. In the field of history of psychology, H.E.Luck made the contribution to methodological analysis of psychological ideas in history, preferring the model which underlines connection of psychology with culture and at the same time creates the opportunity to analysis of biographical plots. The article also shows unquestionable and unusually merits of Luck’s in popularization of knowledge about history of psychology.The article presents the figure of Helmut E. Luck, well-known scientist in the world of historians of psychology. Helmut E. Luck also is well-known in Poland, as the author or the scientific editor of several books in the field of history of psychology. In the first part of the article the short presentation of his scientific career and his scientific achievements are demonstrated. The second part comprises the analysis of his opinions in the scope of social psychology. Helmut E. Luck was the one of pioneers in psychology, who paid attention to social positive phenomena or social positive behaviors. In the field of history of psychology, H.E.Luck made the contribution to methodological analysis of psychological ideas in history, preferring the model which underlines connection of psychology with culture and at the same time creates the opportunity to analysis of biographical plots. The article also shows unquestionable and unusually merits of Luck’s in popularization of knowledge about history of psychology
Die IPrA, Helmut und ich
Get PDFThis contribution describes the beginning and the development of the professional and personal relationship between Helmut and the author which has been highly influenced by our joint membership in the International Pragmatics Association and by our activities in and for the IPrA
Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models
Get PDFCircular dichroism (CD) spectroscopy is an analytical technique that measures the wavelength-dependent differential absorbance of circularly polarized light and is applicable to most biologically important macromolecules, such as proteins, nucleic acids, and carbohydrates. It serves to characterize the secondary structure composition of proteins, including intrinsically disordered proteins, by analyzing their recorded spectra. Several computational tools have been developed to interpret protein CD spectra. These methods have been calibrated and tested mostly on globular proteins with well-defined structures, mainly due to the lack of reliable reference structures for disordered proteins. It is therefore still largely unclear how accurately these computational methods can determine the secondary structure composition of disordered proteins. Here, we provide such a required reference data set consisting of model structural ensembles and matching CD spectra for eight intrinsically disordered proteins. Using this set of data, we have assessed the accuracy of several published CD prediction and secondary structure estimation tools, including our own CD analysis package, SESCA. Our results show that for most of the tested methods, their accuracy for disordered proteins is generally lower than for globular proteins. In contrast, SESCA, which was developed using globular reference proteins, but was designed to be applicable to disordered proteins as well, performs similarly well for both classes of proteins. The new reference data set for disordered proteins should allow for further improvement of all published methods.Alexander von Humboldt-Stiftung https://doi.org/10.13039/100005156Max Plank Societ
Helmut E. Luck and history of psychology
No full textThe article presents the figure of Helmut E. Luck, well-known scientist in the world of historians of psychology. Helmut E. Luck also is well-known in Poland, as the author or the scientific editor of several books in the field of history of psychology. In the first part of the article the short presentation of his scientific career and his scientific achievements are demonstrated. The second part comprises the analysis of his opinions in the scope of social psychology. Helmut E. Luck was the one of pioneers in psychology, who paid attention to social positive phenomena or social positive behaviors. In the field of history of psychology, H.E.Luck made the contribution to methodological analysis of psychological ideas in history, preferring the model which underlines connection of psychology with culture and at the same time creates the opportunity to analysis of biographical plots. The article also shows unquestionable and unusually merits of Luck’s in popularization of knowledge about history of psychology
Mauersegler weiter Wege. Mathias Enard: Kompass
No full textAnalysis of the peculiar scientific narrative in the novel of the Prix-Goncourt winning author Mathias Enard
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