1,720,988 research outputs found
Predicting protein-ligand and protein-peptide interfaces
No full textThe paper deals with the identification of binding sites and concentrates on interactions involving small interfaces. In particular we focus our attention on two major interface types, namely protein-ligand and protein-peptide interfaces. As concerns protein-ligand binding site prediction, we classify the most interesting methods and approaches into four main categories: (a) shape-based methods, (b) alignment-based methods, (c) graph-theoretic approaches and (d) machine learning methods. Class (a) encompasses those methods which employ, in some way, geometric information about the protein surface. Methods falling into class (b) address the prediction problem as an alignment problem, i.e. finding protein-ligand atom pairs that occupy spatially equivalent positions. Graph theoretic approaches, class (c), are mainly based on the definition of a particular graph, known as the protein contact graph, and then apply some sophisticated methods from graph theory to discover subgraphs or score similarities for uncovering functional sites. The last class (d) contains those methods that are based on the learn-from-examples paradigm and that are able to take advantage of the large amount of data available on known protein-ligand pairs. As for protein-peptide interfaces, due to the often disordered nature of the regions involved in binding, shape similarity is no longer a determining factor. Then, in geometry-based methods, geometry is accounted for by providing the relative position of the atoms surrounding the peptide residues in known structures. Finally, also for protein-peptide interfaces, we present a classification of some successful machine learning methods. Indeed, they can be categorized in the way adopted to construct the learning examples. In particular, we envisage three main methods: distance functions, structure and potentials and structure alignment
Computing Orthogonal Drawings with the Minimum Number of Bends
No full textWe describe a branch-and-bound algorithm for computing an orthogonal grid drawing with the minimum number of bends of a biconnected planar graph. Such an algorithm is based on an efficient enumeration schema of the embeddings of a planar graph and on several new methods for computing lower bounds of the number of bends. We experiment with such algorithm on a large test suite and compare the results with the state-of-the-art. The experiments show the feasibility of the approach and also its limitations. Further, the experiments show how minimizing the number of bends has positive effects on other quality measures of the effectiveness of the drawing. We also present a new method for dealing with vertices of degree larger than four
Continuous global optimization for protein structure analysis
Full text linkOptimization methods are a powerful tool in protein structure analysis. In this paper we show that they can be profitably used to solve relevant problems in drug design such as the comparison and recognition of protein binding
sites and the protein-peptide docking. Binding sites recognition is generally based on geometry often combined with physico-chemical properties of the site whereas the search for correct protein-peptide docking is often based on the minimization of an interaction energy model. We show that continuous global optimization methods can be used to solve the above problems and show some computational results
Clustering and Classification Techniques for Gene Expression Profile Pattern Analysis
No full textThe analysis of gene expression profiles from microarray/RNA sequencing (RNA-Seq) experimental samples demands new efficient methods from statistics and computer science. This chapter considers two main types of gene expression data analysis such as gene clustering and experiment classification. It introduces the transcriptome analysis, highlighting the widespread approaches to handle it. The chapter provides an overview of the microarray and RNA-Seq technologies. In addition, the integrated software packages GenePattern, Gene Expression Logic Analyzer (GELA), TM4 software suite, and other common analysis tools are illustrated. For gene expression profile pattern discovery and experiment classification, the software packages are tested on four real case studies: Alzheimer's disease versus healthy mice; multiple sclerosis samples; psoriasis tissues; and breast cancer patients. The performed experiments and the described techniques provide an effective overview to the field of gene expression profile classification and clustering through pattern analysis
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
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