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EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions

EzMechanism: an automated tool to propose catalytic mechanis...

引用

作者： Antonio J. Ribeiro Ioannis G. Riziotis Jonathan D. Tyzack Neera Borkakoti Janet M. Thornton

Over the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic catalytic *** the years, hundreds of enzyme reaction mechanisms have been studied using experimental and simulation methods. This rich literature on biological catalysis is now ripe for use as the foundation of new knowledge-based approaches to investigate enzyme mechanisms. Here, we present a tool able to automatically infer mechanistic paths for a given three-dimensional active site and enzyme reaction, based on a set of catalytic rules compiled from the Mechanism and Catalytic Site Atlas, a database of enzyme mechanisms. EzMechanism (pronounced as ‘Easy’ Mechanism) is available to everyone through a web user interface. When studying a mechanism, EzMechanism facilitates and improves the generation of hypotheses, by making sure that relevant information is considered, as derived from the literature on both related and unrelated enzymes. We validated EzMechanism on a set of 62 enzymes and have identified paths for further improvement, including the need for additional and more generic ca

关键词： Python programming language Cytoscape Computational models Software Protein function predictions Enzymes

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Proton Nuclear Magnetic Resonance (

Proton Nuclear Magnetic Resonance (

引用

作者： Niraj Kumar Srivastava

Proton nuclear magnetic resonance spectroscopy (1H NMR) is a useful tool for the analysis of lipid components in biofluids such as serum/plasma. Such tool is applied for the analysis of lipid components in serum/plasma of patients with Duchenne muscular dystrophy (DMD). The practical approach of sampling, storage, lipid extraction procedure, sample preparation before performing the 1H NMR spectroscopy experiments is presented. All the experimental parameters of NMR spectroscopy are also described. Details of the assignments of lipid components (qualitative analysis) and quantification of particular lipid components (quantitative analysis) are explained. less

关键词： NMR Metabolomics Proton NMR Sonication 1D NMR Spectroscopy Two dimensional correlation spectroscopy 1H--1H Correlation Spectroscopy High-field NMR programming language Data analysis Cholesterol Phospholipids Muscular dystrophy Triglycerides DMD

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Sequence Handling by Sequence Analysis Toolbox v1.0

Sequence Handling by Sequence Analysis Toolbox v1.0

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作者： Christian Ravnsborg Ingrell Rune Matthiesen Ole Nørregaard Jensen

The fact that mass spectrometry have become a high-throughput method calls for bioinformatic tools for automated sequence handling and prediction. For efficient use of bioinformatic tools, it is important that these tools are integrated or interfaced with each other. The purpose of sequence analysis toolbox v1.0 was to have a general purpose sequence analyzing tool that can import sequences obtained by high-throughput sequencing methods. The program includes algorithms for calculation or prediction of isoelectric point, hydropathicity index, transmembrane segments, and glycosylphosphatidyl inositol-anchored proteins. less

关键词： Sequence Analysis Mass Spectrometry High-Throughput Sequencing Structure Prediction Tandem Mass Spectrometry Swiss-Prot Expasy programming language Isoelectric point hydropathicity index transmembrane segments glycosylphosphatidyl inositol-anchored proteins

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A Beginner’s Guide to the COBRA Toolbox

A Beginner’s Guide to the COBRA Toolbox

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作者： Ali Navid

COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining characteristics of metabolism in the biosystems ranging in complexity from single cells to microbial communities and ultimately multicellular organisms. The toolbox has a number of different variants that can be used depending on a user’s choice of programming language. Here, I provide a basic tutorial for beginners that plan to use the original MATLAB version of the toolbox. less

关键词： MATLAB Gene Knockout Metabolic Engineering programming language Escherichia coli Systems biology, Genome-scale models, Constraint-based analysis, FBA, Metabolic networks, COBRA toolbox

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Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-Strand-Specific RNA-Seq Data

Long Intergenic Noncoding RNA (lincRNA) Discovery from Non-S...

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作者： A. A. Golicz

Long noncoding RNAs (lncRNAs) are transcripts over 200 base pairs in length without discernible protein coding potential. Long intergenic noncoding RNAs (lincRNAs) constitute a subset of lncRNAs, which do not overlap protein coding genes. Here we describe a detailed pipeline for lincRNA discovery from publicly available non-stranded RNA-Seq datasets. The pipeline presented can be applied to any plant species for which RNA-Seq data and a reference genome sequence are available. less

关键词： RNA-seq Genome Annotation Statistical Calculation Genome-Wide Association Study StringTie HISAT Python programming language Oryza sativa Transcriptome lincRNA Long intergenic noncoding RNA

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Implementation and Application of Pulsed Interleaved Excitation for Dual-Color FCS and RICS

Implementation and Application of Pulsed Interleaved Excitat...

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作者： Jelle Hendrix Don C. Lamb

Pulsed interleaved excitation (PIE) employs pulsed laser sources that are interleaved such that differentially colored fluorophores can be measured or imaged quasi-simultaneously in the absence of spectral crosstalk. PIE improves the robustness and reduces data analysis complexity of many fluorescence techniques, such as fluorescence cross-correlation spectroscopy (FCCS) and raster image cross-correlation spectroscopy (ccRICS), two methods used for quantitative investigation of molecular interactions in vitro and in living cells. However, as PIE is most often used for fluorescence fluctuation spectroscopy and burst analysis experiments and utilizes time-correlated single-photon counting detection and advanced optoelectronics, it has remained a technique that is mostly used by specialized single-molecule research groups. This protocols chapter provides an accessible overview of PIE for anyone considering implementing the method on a homebuilt or commercial microscope. We give details on the instrumentation, data collection and analysis software, on how to properly set up and align a PIE microscope, and finally, on how to perform proper dual-color FCS and RICS experiments. less

关键词： Raster Image Correlation Spectroscopy Fluorescence Cross-correlation Spectroscopy Fluorescence Correlation Spectroscopy (FCS) Confocal Microscopy Fluorescence Fluctuation Spectroscopy FRET Scanning Fluorescence Correlation Spectroscopy Fluorescence Detection Image Analysis Data analysis programming language Lens CLSM FCS Time-correlated single-photon counting FCCS Pulsed interleaved excitation RICS ccRICS

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Peripheral Nervous System Responses to Food Stimuli:

Peripheral Nervous System Responses to Food Stimuli:

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作者： Maelle Moranges Marc Plantevit Moustafa Bensafi

In the field of food, as in other fields, the measurement of emotional responses to food and their sensory properties is a major challenge. In the present protocol, we propose a step-by-step procedure that allows a physiological description of odors, aromas, and their hedonic properties. The method rooted in subgroup discovery belongs to the field of data science and especially data mining. It is still little used in the field of food and is based on a descriptive modeling of emotions on the basis of human physiological responses.

关键词： Data Mining Python programming language Emotions Pleasantness Odors Aromas Food stimuli Subgroup discovery

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Interfering Peptides Targeting Protein–Protein Interactions in the Ethylene Plant Hormone Signaling Pathway as Tools to Delay Plant Senescence

Interfering Peptides Targeting Protein–Protein Interactions...

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作者： Alexander Hofmann Alexander Minges Georg Groth

Interfering peptides (iPs) have been recognized as valuable substances to specifically target protein–protein interactions (PPIs) in senescence and disease. Although the concept of iPs has been validated for several PPIs in medical and pharmaceutical research, little attention so far has been paid to the enormous potential iPs that may provide to target and control plant growth and developmental processes or plant environmental responses. However, recent research on PPIs in the ethylene signaling pathway has identified the synthetic peptide NOP-1 derived from the nuclear localization signal of ethylene regulator EIN2 as an efficient inhibitor of typical ethylene responses such as ripening, aging, and senescence. Biophysical and biochemical studies on purified recombinant proteins of the ethylene receptor family from various plant species demonstrate that the synthetic peptide binds in the nM-μM range at the plant target. Here, we describe methods to evaluate and quantify the effect of the NOP-1 peptide on flower senescence as a typical ethylene response in the intact plant system. This approach will help to systematically advance our technological capability to delay plant ethylene responses and to expand shelf-life or vase life of fruits and flowers. less

关键词： Spectroscopy HPLC Python Data analysis programming language Rubus idaeus Protein–protein interactions Interfering peptides Ethylene signaling Plant senescence

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Efficient XML usage within wireless sensor networks 08

Efficient XML usage within wireless sensor networks

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Proceedings of the 4th Annual International Conference on Wireless Internet

作者： Nils Hoeller Christoph Reinke Jana Neumann Sven Groppe Daniel Boeckmann Volker Linnemann Institute of Information Systems Luebeck Germany

ISBN: (纸本)9789639799363

Integrating wireless sensor networks in heterogeneous networks is a complex task. A reason is the absence of a standardized data exchange format that is supported in all participating sub networks. XML has evolved to the de facto standard data exchange format between heterogeneous networks and systems. However, XML usage within sensor networks has not been introduced because of the limited hardware resources. In this paper, we introduce XML template objects making XML usage applicable within sensor networks. This new XML data binding technique provides significant high compression results while still allowing dynamic XML processing and XML navigation. This is a step towards more complex but exchangeable data management in sensor networks and the extension of the service-oriented paradigm to sensor network application engineering.

关键词： database management programming language wireless sensor networks XML

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Syntax and Semantics of Coding in Python

Syntax and Semantics of Coding in Python

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作者： Jeremy Meulemans Tonya Ward Dan Knights

Python is a dynamically typed programming language providing a unique blend of power, simplicity and expressiveness that has quickly established itself as a major player in technical fields. The language is built around a very natural syntax, making it an ideal language for both beginners to programming and scientists looking for rapid research implementation. Usage cases from simple file formatting to determining the impact of oil degradation in obtained metagenomic sequence data are facilitated by features of the language. For example, the study of oil breakdown by bacterial communities is likely to involve handling very high-dimensional data, including both the metabolites present in oil and the hundreds of bacterial species often present in environmental communities. The ease of incorporating existing Python modeling packages and the solid frameworks provided by python for scientific computing make this an ideal language for analyzing these types of data. less

关键词： Python programming language Introduction Coding language Problem solving

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