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Small-Molecule Library Screening by Docking with PyRx

Small-Molecule Library Screening by Docking with PyRx

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作者： Sargis Dallakyan Arthur J. Olson

Virtual molecular screening is used to dock small-molecule libraries to a macromolecule in order to find lead compounds with desired biological function. This in silico method is well known for its application in computer-aided drug design. This chapter describes how to perform small-molecule virtual screening by docking with PyRx, which is open-source software with an intuitive user interface that runs on all major operating systems (Linux, Windows, and Mac OS). Specific steps for using PyRx, as well as considerations for data preparation, docking, and data analysis, are also described. less

关键词： Molecular Docking AutoDock Docking Method Virtual Screening Data analysis Python programming language PubChem Computer-aided drug design Virtual molecular screening Vina Open Babel

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Identification and Validation of miRNA Target Sites Within Nontraditional miRNA Targets

Identification and Validation of miRNA Target Sites Within N...

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作者： Scott T. Younger David R. Corey

miRNAs are endogenous small RNAs that regulate gene expression through recognition of complementary RNA sequences. While miRNAs have generally been understood to repress gene expression posttranscriptionally through recognition of 3′-untranslated regions (3′-UTRs) of mRNA transcripts, they have the potential to target additional classes of RNAs. Understanding the expanding pool of potential miRNA targets has been hindered by the lack of tools for predicting target sites within these RNAs. Here, the principles for developing computational algorithms for identifying putative miRNA target sites outside of mRNA are discussed. Laboratory techniques for validating computational miRNA target predictions are described. less

关键词： Transfection Genome Visualization Gene Prediction Cell And Tissue Culture RNA Extraction Real-time PCR Quantitative Reverse Transcription PCR programming language microRNA Noncoding RNA Duplex RNA

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Methods for RNA Profiling of Gravi-Responding Plant Tissues

Methods for RNA Profiling of Gravi-Responding Plant Tissues

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作者： Jyoti Dalal Eric Land Naresh Vasani Luyan He Caroline Smith Maria Rodriguez-Welsh Imara Y. Perera Heike Sederoff

Plant transcriptional responses to gravity stimulation by reorientation are among the fastest measured in any tissue or species. Upon reorientation, changes in abundance of specific mRNAs can be measured within seconds or minutes, for plastid or nuclear encoded genes, respectively. Identifying fast gravity-induced transcripts has been made possible by the development of high-throughput technology for qualitative and quantitative RNA analysis. RNA profiling has undergone further rapid development due to its enormous potential in basic sciences and medical applications. We describe here the current and most widely used methods to profile the changes in an entire transcriptome by high-throughput sequencing of RNA fractions (RNAseq) and single gene transcript analysis using real-time quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR). less

关键词： PCR RNA-seq Total RNA Extraction Next Generation Sequencing Reverse Transcription PCR Real-time PCR Transcription Profiling RNA Extraction Library Preparation High-Throughput Sequencing Homogenization Quantitative Reverse Transcription PCR RNA Quality Analysis RNA Electrophoresis Fractionation Size-exclusion Chromatography Nucleic Acid Microarray Agarose Gel Electrophoresis Trinity Sterilization Data analysis DNA Ligation programming language Sequencing RNA miRNA Transcriptome Transcript sRNA

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In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

In Silico HLA Typing Using Standard RNA-Seq Sequence Reads

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作者： Sebastian Boegel Jelle Scholtalbers Martin Löwer Ugur Sahin John C. Castle

Next-generation sequencing (NGS) enables high-throughput transcriptome profiling using the RNA-Seq assay, resulting in billions of short sequence reads. Worldwide adoption has been rapid: many laboratories worldwide generate transcriptome sequence reads daily. Here, we describe methods for obtaining a sample’s human leukocyte antigen (HLA) class I and II types and HLA expression using standard NGS RNA-Seq sequence reads. We demonstrate the application using our algorithm, seq2HLA, and a publicly available RNA-Seq dataset from the Burkitt lymphoma cell line Raji. less

关键词： RNA-seq Major Histocompatibility Typing Assay Bowtie Python programming language Homo sapiens Raji NGS In silico Immunoinformatics HLA expression HLA type

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Computational Cardiac Electrophysiology: Implementing Mathematical Models of Cardiomyocytes to Simulate Action Potentials of the Heart

Computational Cardiac Electrophysiology: Implementing Mathem...

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作者： Michael M. Bell Elizabeth M. Cherry

Mathematical models are now an important tool for studying cardiac electrophysiology and arrhythmias. Utilizing these models to quantify behavior and make predictions requires solving the models computationally using numerical schemes. We discuss different solution methods and other computational considerations for simulating cardiac action potentials in single cells and multicellular preparations. less

关键词： Electrophysiology MATLAB programming language Python Computational methods Computer simulation Mathematical models Cardiac action potential Numerical integration

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Exploring the RNA Editing Potential of RNA-Seq Data by ExpEdit

Exploring the RNA Editing Potential of RNA-Seq Data by ExpEd...

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作者： Mattia D’Antonio Ernesto Picardi Tiziana Castrignanò Anna Maria D’Erchia Graziano Pesole

Revealing the impact of A-to-I RNA editing in RNA-Seq experiments is relevant in humans because RNA editing can influence gene expression. In addition, its deregulation has been linked to a variety of human diseases. Exploiting the RNA editing potential in complete RNA-Seq datasets, however, is a challenging task. Indeed, no dedicated software is available, and sometimes deep computational skills and appropriate hardware resources are required. To explore the impact of known RNA editing events in massive transcriptome sequencing experiments, we developed the ExpEdit web service application. In the present work, we provide an overview of ExpEdit as well as methodologies to investigate known RNA editing in human RNA-Seq datasets. less

关键词： Deep Sequencing Genomics RNA-seq Illumina Sequencing Genome Alignment TopHat Bowtie Genome Assembly Statistical Calculation Transcriptome sequencing Python programming language SAMtools Homo sapiens Bioinformatics RNA editing A-to-I editing

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Genome-Scale Metabolic Network Reconstruction

Genome-Scale Metabolic Network Reconstruction

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作者： Marco Fondi Pietro Liò

Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process. less

关键词： Genome Annotation Genomics Extrusion Text Mining Sequence Comparison Genome Sequencing Python programming language Escherichia coli Flux balance analysis Metabolic modeling Metabolic model reconstruction

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Annotation of Glycomics MS and MS/MS Spectra Using the GlycoWorkbench Software Tool

Annotation of Glycomics MS and MS/MS Spectra Using the Glyco...

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作者： David Damerell Alessio Ceroni Kai Maass René Ranzinger Anne Dell Stuart M. Haslam

The GlycoWorkbench software tool allows users to semiautomatically annotate glycomics MS and MS/MS spectra and MS glycoproteomics spectra. The GlycanBuilder software tool is embedded within GlycoWorkbench allowing users to draw glycan structures and export images of the drawn structures. This chapter demonstrates to users how to draw glycan structures within GlycoWorkbench using the GlycanBuilder software tool. This chapter also demonstrates how to use GlycoWorkbench to import MS and MS/MS glycomics spectra and use the cascading annotation feature to annotate both the MS and MS/MS spectra with a single command. less

关键词： Mass Spectrometry Tandem Mass Spectrometry Glycoproteomics programming language Bioinformatics Glycomics Glycobiology Glycoinformatics

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Measurements of Rhodopsin Diffusion Within Signaling Membrane Microcompartments in Live Photoreceptors

Measurements of Rhodopsin Diffusion Within Signaling Membran...

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作者： Mehdi Najafi Peter D. Calvert

High-resolution multiphoton imaging of live cells has become an invaluable method to study protein dynamics in highly compartmentalized subcellular environments. Here we describe procedures that we recently developed to quantify rhodopsin mobility within and between retinal rod photoreceptor light signaling microcompartments, the disc membrane lobules, using multiphoton fluorescence relaxation after photoconversion. less

关键词： Live Cell Imaging FRAP Dissection Image Processing Decapitation Multiphoton Microscopy Transillumination MATLAB programming language Xenopus laevis Bos taurus Lens Xenopus G protein-coupled receptors Cell signaling Rhodopsin diffusion Microcompartments

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Using Deep Sequencing Data for Identification of Editing Sites in Mature miRNAs

Using Deep Sequencing Data for Identification of Editing Sit...

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作者： Shahar Alon Eli Eisenberg

Deep sequencing has many possible applications; one of them is the identification and quantification of RNA editing sites. The most common type of RNA editing is adenosine to inosine (A-to-I) editing. A prerequisite for this editing process is a double-stranded RNA (dsRNA) structure. Such dsRNAs are formed as part of the microRNA (miRNA) maturation process, and it is therefore expected that miRNAs are affected by A-to-I editing. Indeed, tens of editing sites were found in miRNAs, some of which change the miRNA binding specificity. Here, we describe a protocol for the identification of RNA editing sites in mature miRNAs using deep sequencing data. less

关键词： Deep Sequencing Genomics Statistical Calculation Bowtie Illumina Sequencing programming language Mus musculus Bioinformatics miRNA A-to-I editing

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