ConSole: using modularity of contact maps to locate solenoid domains in protein structures.

BackgroundPeriodic proteins, characterized by the presence of multiple repeats of short motifs, form an interesting and seldom-studied group. Due to often extreme divergence in sequence, detection and analysis of such motifs is performed more reliably on the structural level. Yet, few algorithms have been developed for the detection and analysis of structures of periodic proteins.ResultsConSole recognizes modularity in protein contact maps, allowing for precise identification of repeats in solenoid protein structures, an important subgroup of periodic proteins. Tests on benchmarks show that ConSole has higher recognition accuracy as compared to Raphael, the only other publicly available solenoid structure detection tool. As a next step of ConSole analysis, we show how detection of solenoid repeats in structures can be used to improve sequence recognition of these motifs and to detect subtle irregularities of repeat lengths in three solenoid protein families.ConclusionsThe ConSole algorithm provides a fast and accurate tool to recognize solenoid protein structures as a whole and to identify individual solenoid repeat units from a structure. ConSole is available as a web-based, interactive server and is available for download at http://console.sanfordburnham.org

Simple Irreducible Subgroups of Exceptional Algebraic Groups

A closed subgroup of a semisimple algebraic group is called irreducible if it lies in no proper parabolic subgroup. In this paper we classify all irreducible subgroups of exceptional algebraic groups $G$ which are connected, closed and simple of rank at least $2$. Consequences are given concerning the representations of such subgroups on various $G$-modules: for example, with one exception, the conjugacy classes of irreducible simple connected subgroups of rank at least $2$ are determined by their composition factors on the adjoint module for $G$.Comment: 46 pages; version to appear in J. Al

Capital Importers Pay More for their Imports

We examine the effects that a country’s net capital flows have on the (border) prices that a country pays for its imports of goods. Using data from 2000 to 2009 for 11 euro area countries we utilize a pricing-to-market specification to study exporters’ pricing behavior to the rest of the countries in the sample, at the industry level, for 900 goods disseminated at the 4- digit Standard International Trade Classification (SITC- revision 3) level. This allows us to construct a panel dataset which contains observations across exporters, importers, industries and time, ending up with a total of 594,327 observations. We find a strong influence of the importing country’s net capital inflows on the border prices of its imports of goods. This result is robust across different specifications of the underlying model, as well to different sample dis-aggregations across types of capital flows, product categories, and exporters.capital flows, import prices, pricing to market, globalization, euro area

Gradient boosting in Markov-switching generalized additive models for location, scale and shape

We propose a novel class of flexible latent-state time series regression models which we call Markov-switching generalized additive models for location, scale and shape. In contrast to conventional Markov-switching regression models, the presented methodology allows us to model different state-dependent parameters of the response distribution - not only the mean, but also variance, skewness and kurtosis parameters - as potentially smooth functions of a given set of explanatory variables. In addition, the set of possible distributions that can be specified for the response is not limited to the exponential family but additionally includes, for instance, a variety of Box-Cox-transformed, zero-inflated and mixture distributions. We propose an estimation approach based on the EM algorithm, where we use the gradient boosting framework to prevent overfitting while simultaneously performing variable selection. The feasibility of the suggested approach is assessed in simulation experiments and illustrated in a real-data setting, where we model the conditional distribution of the daily average price of energy in Spain over time

Complete Reducibility in Good Characteristic

Let $G$ be a simple algebraic group of exceptional type, over an algebraically closed field of characteristic $p \ge 0$. A closed subgroup $H$ of $G$ is called $G$-completely reducible ($G$-cr) if whenever $H$ is contained in a parabolic subgroup $P$ of $G$, it is contained in a Levi subgroup of $P$. In this paper we determine the $G$-conjugacy classes of non-$G$-cr simple connected subgroups of $G$ when $p$ is good for $G$. For each such subgroup $X$, we determine the action of $X$ on the adjoint module $L(G)$ and the connected centraliser of $X$ in $G$. As a consequence we classify all non-$G$-cr connected reductive subgroups of $G$, and determine their connected centralisers. We also classify the subgroups of $G$ which are maximal among connected reductive subgroups, but not maximal among all connected subgroups.Comment: 66 pages. To appear in Trans. Amer. Math. So

Irreducible A_1 Subgroups of Exceptional Algebraic Groups

A closed subgroup of a semisimple algebraic group is called irreducible if it lies in no proper parabolic subgroup. In this paper we classify all irreducible $A_1$ subgroups of exceptional algebraic groups $G$. Consequences are given concerning the representations of such subgroups on various $G$-modules: for example, the conjugacy classes of irreducible $A_1$ subgroups are determined by their composition factors on the adjoint module of $G$.Comment: 51 pages; published in J. Al

Finite subgroups of simple algebraic groups with irreducible centralizers

We determine all finite subgroups of simple algebraic groups that have irreducible centralizers - that is, centralizers whose connected component does not lie in a parabolic subgroup.Comment: 24 page