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

On the discrete logarithm problem in finite fields of fixed characteristic

For $q$ a prime power, the discrete logarithm problem (DLP) in $\mathbb{F}_{q}$ consists in finding, for any $g \in \mathbb{F}_{q}^{\times}$ and $h \in \langle g \rangle$, an integer $x$ such that $g^x = h$. We present an algorithm for computing discrete logarithms with which we prove that for each prime $p$ there exist infinitely many explicit extension fields $\mathbb{F}_{p^n}$ in which the DLP can be solved in expected quasi-polynomial time. Furthermore, subject to a conjecture on the existence of irreducible polynomials of a certain form, the algorithm solves the DLP in all extensions $\mathbb{F}_{p^n}$ in expected quasi-polynomial time.Comment: 15 pages, 2 figures. To appear in Transactions of the AM

GSATools: Analysis of allosteric communication and functional local motions using a structural alphabet

Motivation: GSATools is a free software package to analyze conformational ensembles and to detect functional motions in proteins by means of a structural alphabet. The software integrates with the widely used GROMACS simulation package and can generate a range of graphical outputs. Three applications can be supported: (i) investigation of the conformational variability of local structures; (ii) detection of allosteric communication; and (iii) identification of local regions that are critical for global functional motions. These analyses provide insights into the dynamics of proteins and allow for targeted design of functional mutants in theoretical and experimental studies. Availability: The C source code of the GSATools, along with a set of pre-compiled binaries, is freely available under GNU General Public License from http://mathbio.nimr.mrc.ac.uk/wiki/GSATools. Contact: alessandro.pandini@kcl. ac.uk or [email protected] Supplementary information: Supplementary data are available at Bioinformatics online. © 2013 The Author 2013. Published by Oxford University Press

Der magische Geldbeutel und der unaufhaltsame Siegeszug des Ausgebens : der erste deutschsprachige Wirtschaftsroman ; ein Bestseller der Frühen Neuzeit

Grenzenloser Reichtum und schier unerschöpfliche Geldquellen – diese Träume sind der Stoff, aus dem unzählige Geschichten narratives Kapital schlagen. Der Mythos von König Midas oder die Comics mit Dagobert Duck gehören zu den prominentesten Vertretern solcher Erzählungen. Der Fortunatus hingegen, in dem ein Geld produzierender Zauberbeutel die Geschicke bestimmt, ist weitgehend in Vergessenheit geraten. Dabei kann gerade dieser Roman, der 1509 in Augsburg anonym veröffentlicht wurde, in doppelter Hinsicht als ein Pionier der Literaturgeschichte gelten

Finding ECM-friendly curves through a study of Galois properties

In this paper we prove some divisibility properties of the cardinality of elliptic curves modulo primes. These proofs explain the good behavior of certain parameters when using Montgomery or Edwards curves in the setting of the elliptic curve method (ECM) for integer factorization. The ideas of the proofs help us to find new families of elliptic curves with good division properties which increase the success probability of ECM

Tinnitus and Coxsackie B infections: A case series

Tinnitus is a frequent and often debilitating condition. There is consensus in the scientific community that there exist various forms of tinnitus, which differ in their pathogenesis. Here we report a series of five cases where the onset of tinnitus was associated with viral infections. In all five patients elevated antibodies against Coxsackie B have been detected. This observation suggests that Coxsackie B Virus infections might be involved in the development of some cases of tinnitus and indicate that further systematic investigations are warranted.Fil: Langguth, Berthold. Universitat Regensburg; AlemaniaFil: Stadtlaender, Hans. An der Zuckerfabrik 2; AlemaniaFil: Landgrebe, Michael. Universitat Regensburg; AlemaniaFil: Elgoyhen, Ana Belen. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Coors, Hermann. Gaußstr 10; AlemaniaFil: Vielsmeier, Veronika. Universitat Regensburg; AlemaniaFil: Kleinjung, Tobias. Universitat Regensburg; Alemani

Leap-dynamics: efficient sampling of conformational space of proteins and peptides in solution

AbstractA molecular simulation scheme, called Leap-dynamics, that provides efficient sampling of protein conformational space in solution is presented. The scheme is a combined approach using a fast sampling method, imposing conformational ‘leaps’ to force the system over energy barriers, and molecular dynamics (MD) for refinement. The presence of solvent is approximated by a potential of mean force depending on the solvent accessible surface area. The method has been successfully applied to N-acetyl-L-alanine-N-methylamide (alanine dipeptide), sampling experimentally observed conformations inaccessible to MD alone under the chosen conditions. The method predicts correctly the increased partial flexibility of the mutant Y35G compared to native bovine pancreatic trypsin inhibitor. In particular, the improvement over MD consists of the detection of conformational flexibility that corresponds closely to slow motions identified by nuclear magnetic resonance techniques

Discrete logarithms in quasi-polynomial time in finite fields of fixed characteristic

We prove that the discrete logarithm problem can be solved in quasi-polynomial expected time in the multiplicative group of finite fields of fixed characteristic. More generally, we prove that it can be solved in the field of cardinality pn in expected time (pn)2log2(n)+O(1)