Search results for "complexi"

Efficient computation of root mean square deviations under rigid transformations

2013

The computation of root mean square deviations (RMSD) is an important step in many bioinformatics applications. If approached naively, each RMSD computation takes time linear in the number of atoms. In addition, a careful implementation is required to achieve numerical stability, which further increases runtimes. In practice, the structural variations under consideration are often induced by rigid transformations of the protein, or are at least dominated by a rigid component. In this work, we show how RMSD values resulting from rigid transformations can be computed in constant time from the protein's covariance matrix, which can be precomputed in linear time. As a typical application scenar…

A reduction of protein specific motions in co-ligated myoglobin embedded in a trehalose glass

2000

A Stevedore's protein knot.

2009

Protein knots, mostly regarded as intriguing oddities, are gradually being recognized as significant structural motifs. Seven distinctly knotted folds have already been identified. It is by and large unclear how these exceptional structures actually fold, and only recently, experiments and simulations have begun to shed some light on this issue. In checking the new protein structures submitted to the Protein Data Bank, we encountered the most complex and the smallest knots to date: A recently uncovered α-haloacid dehalogenase structure contains a knot with six crossings, a so-called Stevedore knot, in a projection onto a plane. The smallest protein knot is present in an as yet unclassified …

RepeatsDB

2015

Database of annotated tandem repeat protein structures.

Assessing the low complexity of protein sequences via the low complexity triangle.

2020

Background Proteins with low complexity regions (LCRs) have atypical sequence and structural features. Their amino acid composition varies from the expected, determined proteome-wise, and they do not follow the rules of structural folding that prevail in globular regions. One way to characterize these regions is by assessing the repeatability of a sequence, that is, calculating the local propensity of a region to be part of a repeat. Results We combine two local measures of low complexity, repeatability (using the RES algorithm) and fraction of the most frequent amino acid, to evaluate different proteomes, datasets of protein regions with specific features, and individual cases of proteins…

The Conservation of Low Complexity Regions in Bacterial Proteins Depends on the Pathogenicity of the Strain and Subcellular Location of the Protein

2021

Low complexity regions (LCRs) in proteins are characterized by amino acid frequencies that differ from the average. These regions evolve faster and tend to be less conserved between homologs than globular domains. They are not common in bacteria, as compared to their prevalence in eukaryotes. Studying their conservation could help provide hypotheses about their function. To obtain the appropriate evolutionary focus for this rapidly evolving feature, here we study the conservation of LCRs in bacterial strains and compare their high variability to the closeness of the strains. For this, we selected 20 taxonomically diverse bacterial species and obtained the completely sequenced proteomes of t…

REP2

2021

REP2 is a web server to detect common tandem repeats in protein sequences.

A Dynamic Distributed Algorithm for Multicast Path Setup

2005

In the past few years, there has been a considerable work on multicast route selection techniques, with the aim to design scalable protocols which can guarantee an efficient use of network resources. Steiner tree-based multicast algorithms produce optimal trees, but they are prohibitively expensive. For this reason, heuristic methods are generally employed. Conventional centralized Steiner heuristics provide effective solutions, but they are unpractical for large networks, since they require a complete knowledge of the network topology. In this paper, we propose a new distributed approach that is efficient and suitable for real network adoption. Performance evaluation indicates that it outp…

Occupational cognitive complexity and episodic memory in old age

2021

The aim of this study was to investigate occupational cognitive complexity of main lifetime occupation in relation to level and 15-year change in episodic memory recall in a sample of older adults (≥ 65 years, n = 780). We used latent growth curve modelling with occupational cognitive complexity (O*NET indicators) as independent variable. Subgroup analyses in a sample of middle-aged (mean: 49.9 years) men (n = 260) were additionally performed to investigate if a general cognitive ability (g) factor at age 18 was predictive of future occupational cognitive complexity and cognitive performance in midlife. For the older sample, a higher level of occupational cognitive complexity was related to…

Teaching Public Administration Abroad through the Fulbright Specialist Program

2011

The purpose of this article is to promote the benefits of the Fulbright Specialist Program—which was created in 2001 as a short-term complement to the Fulbright Scholar Program—and to encourage more public administration scholars to consider teaching abroad. After providing an overview of the Fulbright Specialist Program and the collaborative teaching approach we used for the preparation and delivery of instructional materials, it presents a number of lessons learned from the perspective of the Fulbright Specialist and the host institution for maximizing the experience of teaching abroad. This article also is dedicated to the work of Fulbright, which has pursued its mission to increase mutu…