Search results for " Complexity"
showing 10 items of 623 documents
Disentangling the complexity of low complexity proteins
2020
Abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichot…
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 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…
Analyticity of a restricted formality
2020
International audience; The Kontsevich formality can be viewed as a non-linear map ℱ from the L∞ algebra of poly-vector fields on ℝd to the space of poly-differential operators. The space of the half-homogenous poly-vector fields is a sub-L∞ algebra. We prove here that the restriction of ℱto this subspace is weakly analytic.