1,721,168 research outputs found
Waggawagga-CLI: A command-line tool for predicting stable single α-helices (SAH-domains), and the SAH-domain distribution across eukaryotes
No full textStable single-alpha helices (SAH-domains) function as rigid connectors and constant force springs between structural domains, and can provide contact surfaces for protein-protein and protein-RNA interactions. SAH-domains mainly consist of charged amino acids and are monomeric and stable in polar solutions, characteristics which distinguish them from coiled-coil domains and intrinsically disordered regions. Although the number of reported SAH-domains is steadily increasing, genome-wide analyses of SAH-domains in eukaryotic genomes are still missing. Here, we present Waggawagga-CLI, a command-line tool for predicting and analysing SAH-domains in protein sequence datasets. Using Waggawagga-CLI we predicted SAH-domains in 24 datasets from eukaryotes across the tree of life. SAH-domains were predicted in 0.5 to 3.5% of the protein-coding content per species. SAH-domains are particularly present in longer proteins supporting their function as structural building block in multi-domain proteins. In human, SAH-domains are mainly used as alternative building blocks not being present in all transcripts of a gene. Gene ontology analysis showed that yeast proteins with SAH-domains are particular enriched in macromolecular complex subunit organization, cellular component biogenesis and RNA metabolic processes, and that they have a strong nuclear and ribonucleoprotein complex localization and function in ribosome and nucleic acid binding. Human proteins with SAH-domains have roles in all types of RNA processing and cytoskeleton organization, and are predicted to function in RNA binding, protein binding involved in cell and cell-cell adhesion, and cytoskeletal protein binding. Waggawagga-CLI allows the user to adjust the stabilizing and destabilizing contribution of amino acid interactions in i,i+3 and i,i+4 spacings, and provides extensive flexibility for user-designed analyses
The widespread prevalence and functional significance of silk-like structural proteins in metazoan biological materials
No full textIn nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of biological materials with diverse morphologies. The SilkSlider predictor software developed here is available at https://github.com/wwood/SilkSlider
Recent Developments on Protein–Ligand Interactions
No full textProtein–ligand interactions play a fundamental role in most major biological functions. The number and diversity of small molecules that interact with proteins, whether naturally or not, can quickly become overwhelming. They are as essential as amino acids, nucleic acids or membrane lipids, enabling a large number of essential functions. One need only think of carbohydrates or even just ATP to be certain. They are also essential in drug discovery. With the increasing structural information of proteins and protein–ligand complexes, molecular modelling, molecular dynamics, and chemoinformatics approaches are often required for the efficient analysis of a large number of such complexes and to provide insights. Similarly, numerous computational approaches have been developed to characterize and use the knowledge of such interactions, which can lead to drug candidates. "Recent Developments on Protein–Ligand Interactions: From Structure, Function to Applications" was dedicated to the different aspect of protein–ligand analysis and/or prediction using computational approaches, as well as new developments dedicated to these tasks. It will interest both specialists and non-specialists, as the presented studies cover a very large spectra in terms of methodologies and applications. It underlined the variety of scientific area linked to these questions, i.e., chemistry, biology, physics, informatics, bioinformatics, structural bioinformatics and chemoinformatics
Recent Developments on Protein–Ligand Interactions
No full textProtein–ligand interactions play a fundamental role in most major biological functions. The number and diversity of small molecules that interact with proteins, whether naturally or not, can quickly become overwhelming. They are as essential as amino acids, nucleic acids or membrane lipids, enabling a large number of essential functions. One need only think of carbohydrates or even just ATP to be certain. They are also essential in drug discovery. With the increasing structural information of proteins and protein–ligand complexes, molecular modelling, molecular dynamics, and chemoinformatics approaches are often required for the efficient analysis of a large number of such complexes and to provide insights. Similarly, numerous computational approaches have been developed to characterize and use the knowledge of such interactions, which can lead to drug candidates. "Recent Developments on Protein–Ligand Interactions: From Structure, Function to Applications" was dedicated to the different aspect of protein–ligand analysis and/or prediction using computational approaches, as well as new developments dedicated to these tasks. It will interest both specialists and non-specialists, as the presented studies cover a very large spectra in terms of methodologies and applications. It underlined the variety of scientific area linked to these questions, i.e., chemistry, biology, physics, informatics, bioinformatics, structural bioinformatics and chemoinformatics
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines
Full text linkThe secondary structures approximate badly the 3D protein structures. A new method have been developped to create a more complex and precise structural alphabet (called Protein Blocks) which could be used in a local prediction method. The analysis of the specificity and stability of this alphabet has been performed. This alphabet is composed of 16 prototypes of 5 Cα length. The local prediction of PBs from the sequence gives correct results.The prediction is based on Bayesian statistics which is efficient to understand the meaning and influences of every amino acids. To improve this prediction, we have used two concepts : (i) 1 local fold is associated with a set of sequences and (ii) 1 sequence could give different folds. The first point is associated with the splitting of occurrence matrices associated with the most common PBs. The second point is based upon a confidence index and allow the location of well-predicted residues. Some succession of Protein Blocks are over-represented. So, we have define a network describing most of the protein topology.Finally, we propose a method called Hybrid Protein Model which allow the compaction of succession of Protein Blocks in a fuzzy manner and create structurally dependant cluster. This approach has been extended to the research of structural homology.Caractériser la structure tridimensionnelle des protéines avec les structures secondaires classiques est assez pauvre structurellement. Nous avons donc développé une nouvelle méthodologie pour concevoir des séries de petits prototypes moyens nommés Blocs Protéiques (BPs) qui permettent une bonne approximation des structures protéiques. L'analyse de la spécificité des blocs protéiques a montré leur stabilité et leur spécificité sur le plan structural. Le choix final du nombre de BPs est associé a une prédiction locale correcte.Cette prédiction se base avec une méthode bayésienne qui permet de comprendre l'importance des acides aminés de maniè;re simple. Pour améliorer cette prédiction, nous nous sommes bases sur deux concepts : (i) 1 repliement local -> n séquences et (ii) 1 séquence -> n repliements. Le premier concept signifie que plusieurs types de séquences peuvent être associes a la même structure et le second qu'une séquence peut-être associée a plusieurs type de repliements. Ces deux aspects sont développés en se basant sur la recherche d'un indice de fiabilité lie a la prédiction locale, pour trouver des zones de fortes probabilités. Certains mots, i.e. successions de blocs protéiques apparaissent plus fréquemment que d'autres. Nous avons donc défini au mieux quelle est l'architecture de ces successions, les liens existants entre ces différents mots.Du fait de cette redondance qui peut apparaìtre dans la structure protéique, une méthode de compactage qui permet d'associer des structures structurellement proches sur le plan local a été mise au point. Cette approche appelée "protéine hybride" de conception simple permet de catégoriser en classes "structurellement dépendantes" l'ensemble des structures de la base de données protéiques. Cette approche, en plus du compactage, peut être utilisée dans une optique différente, celle de la recherche d'homologie structurale et de la caractérisation des dépendances entre structures et séquences
Compartimentation chromosomique: Compartimentation chromosomique
No full textDu fait du nombre importants de génomes complets actuellement disponibles, il devient possible de les comparer directement. La méthode de chromosome hybride (HXM) permet, en découpant ces génomes en longues zones similaires, cette comparaison
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