Search results for "Computational biology"
showing 10 items of 1237 documents
The Role of Self-Assembling Lipid Molecules in Vaccination
2018
Abstract The advent of vaccines represents one of the most significant advances in medical history. The protection provided by vaccines has greatly contributed in reducing the number of cases of infections and most notably to the eradication of small pox. A large number of new technologies and approaches in vaccine development are currently being investigated with the goal of providing the basis for the next generation of prophylactics against an ever-expanding list of emerging and reemerging pathogens. In this chapter, we will focus on the role of lipids and lipid self-assembling vesicles in new and promising vaccination approaches. We will start by describing how lipids can induce activat…
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the de…
A Molecular Dynamics-Shared Pharmacophore Approach to Boost Early-Enrichment Virtual Screening: A Case Study on Peroxisome Proliferator-Activated Rec…
2016
Molecular dynamics (MD) simulations can be used, prior to virtual screening, to add flexibility to proteins and study them in a dynamic way. Furthermore, the use of multiple crystal structures of the same protein containing different co-crystallized ligands can help elucidate the role of the ligand on a protein's active conformation, and then explore the most common interactions between small molecules and the receptor. In this work, we evaluated the contribution of the combined use of MD on crystal structures containing the same protein but different ligands to examine the crucial ligand-protein interactions within the complexes. The study was carried out on peroxisome proliferator-activat…
An approach to identify new antihypertensive agents using Thermolysin as model: In silico study based on QSARINS and docking
2019
Thermolysin is a bacterial proteolytic enzyme, considered by many authors as a pharmacological and biological model of other mammalian enzymes, with similar structural characteristics, such as angiotensin converting enzyme and neutral endopeptidase. Inhibitors of these enzymes are considered therapeutic targets for common diseases, such as hypertension and heart failure. In this report, a mathematical model of Multiple Linear Regression, for ordinary least squares, and genetic algorithm, for selection of variables, are developed and implemented in QSARINS software, with appropriate parameters for its fitting. The model is extensively validated according to OECD standards, so that its robust…
Applying pattern recognition methods plus quantum and physico-chemical molecular descriptors to analyze the anabolic activity of structurally diverse…
2008
The great cost associated with the development of new anabolic-androgenic steroid (AASs) makes necessary the development of computational methods that shorten the drug discovery pipeline. Toward this end, quantum, and physicochemical molecular descriptors, plus linear discriminant analysis (LDA) were used to analyze the anabolic/androgenic activity of structurally diverse steroids and to discover novel AASs, as well as also to give a structural interpretation of their anabolic-androgenic ratio (AAR). The obtained models are able to correctly classify 91.67% (86.27%) of the AASs in the training (test) sets, respectively. The results of predictions on the 10% full-out cross-validation test al…
In Silico Prediction of Caco-2 Cell Permeability by a Classification QSAR Approach
2011
In the present study, 21 validated QSAR models that discriminate compounds with high Caco-2 permeability (Papp ≥8×10(-6) cm/s) from those with moderate-poor permeability (Papp <8×10(-6) cm/s) were developed on a novel large dataset of 674 compounds. 20 DRAGON descriptor families were used. The global accuracies of obtained models were ranking between 78-82 %. A general model combining all types of molecular descriptors was developed and it classified correctly 81.56 % and 83.94 % for training and test sets, respectively. An external set of 10 compounds was predicted and 80 % was correctly assessed by in vitro Caco-2 assays. The potential use of the final model was evaluated by a virtual s…
Modeling anti-allergic natural compounds by molecular topology.
2013
Molecular topology has been applied to the search of QSAR models able to identify the anti-allergic activity of a wide group of heterogeneous compounds. Through the linear discriminant analysis and artificial neural networks, correct classification percentages above 85% for both the training set and the test set have been obtained. After carrying out a virtual screening with a natural product library, about thirty compounds with theoretical anti-allergic activity have been selected. Among them, hesperidin, naringin, salinomycin, sorbitol, curcumol, myricitrin, diosmin and kinetin stand out. Some of these compounds have already been referenced as having anti-allergic activity.
ViR: a tool to account for intrasample variability in the detection of viral integrations
2020
ABSTRACTLateral gene transfer (LT) from viruses to eukaryotic cells is a well-recognized phenomenon. Somatic integrations of viruses have been linked to persistent viral infection and genotoxic effects, including various types of cancer. As a consequence, several bioinformatic tools have been developed to identify viral sequences integrated into the human genome. Viral sequences that integrate into germline cells can be transmitted vertically, be maintained in host genomes and be co-opted for host functions. Endogenous viral elements (EVEs) have long been known, but the extent of their widespread occurrence has only been recently appreciated. Modern genomic sequencing analyses showed that e…
Deciphering the role of insertion sequences in the evolution of bacterial epidemic pathogens with panISa software
2020
Next-generation sequencing (NGS) is now widely used in microbiology to explore genome evolution and the structure of pathogen outbreaks. Bioinformatics pipelines readily detect single-nucleotide polymorphisms or short indels. However, bacterial genomes also evolve through the action of small transposable elements called insertion sequences (ISs), which are difficult to detect due to their short length and multiple repetitions throughout the genome. We designed panISa software for the ab initio detection of IS insertions in the genomes of prokaryotes. PanISa has been released as open source software (GPL3) available from https://github.com/bvalot/panISa. In this study, we assessed the utilit…
Genomic and Proteomic Analysis of Wine Yeasts
2011
Publisher Summary Saccharomyces cerevisiae is the main microorganism involved in wine fermentation. It has been used as a model organism in molecular biology for many years and is the only wine yeast species for which abundant genomic and proteomic information is available. Most of the techniques currently used in functional genomics and proteomics were initially developed in this yeast. The fact that S. cerevisiae was the first microorganism to be widely used in the development of genome technology allowed other phylogenetically related yeasts to be analyzed subsequently in global sequencing projects, and the use of comparative genomics has since led to important conclusions regarding gene…