Abstract：
:G-protein-coupled receptors (GPCRs) initiate signaling pathways via trimetric guanine nucleotide-binding proteins. GPCRs are classified based on their ligand-binding properties and molecular phylogenetic analyses. Nonetheless, these later analyses are in most case dependent on multiple sequence alignments, themselves dependent on human intervention and expertise. Alignment-free classifications of GPCR sequences, in addition to being unbiased, present many applications uncovering hidden physicochemical parameters shared among specific groups of receptors, to being used in automated workflows for large-scale molecular modeling applications. Current alignment-free classification methods, however, do not reach a full accuracy. This chapter discusses how GPCRs amino acid sequences can be classified using pseudo amino acid composition and multiscale energy representation of different physiochemical properties of amino acids. A hybrid feature extraction strategy is shown to be suitable to represent GPCRs and to be able to exploit GPCR amino acid sequence discrimination capability in spatial as well as transform domain. Classification strategies such as support vector machine and probabilistic neural network are then discussed in regards to GPCRs classification. The work of GPCR-Hybrid web predictor is also discussed.
journal_name
Methods Enzymoljournal_title
Methods in enzymologyauthors
Rehman ZU,Mirza MT,Khan A,Xhaard Hdoi
10.1016/B978-0-12-407865-9.00004-2subject
Has Abstractpub_date
2013-01-01 00:00:00pages
61-79eissn
0076-6879issn
1557-7988pii
B978-0-12-407865-9.00004-2journal_volume
522pub_type
杂志文章abstract：:The above methodology has been used to prepare a variety of PE-immunotoxins. These reagents are potent cytotoxic agents for cells in culture that bind the appropriate antibody and nontoxic when cells do not bind the antibody. PE-immunotoxins can be used to select for mutant cultured cells which lack the target of the ...
journal_title：Methods in enzymology
pub_type： 杂志文章
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更新日期：1987-01-01 00:00:00
abstract：:Respiration is widely used for evaluation of the metabolic capabilities or physiological state of the microbial culture. This chapter describes novel approaches for characterization of respiration at a single cell level: (1) flow cytometry-based redox sensing (FCRS) of actively metabolizing microbes; (2) respiration r...
journal_title：Methods in enzymology
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更新日期：2011-01-01 00:00:00
abstract：:Hsp70 chaperones and their obligatory J-protein cochaperones function together in many cellular processes. Via cycles of binding to short stretches of exposed amino acids on substrate proteins, Hsp70/J-protein chaperones not only facilitate protein folding but also drive intracellular protein transport, biogenesis of ...
journal_title：Methods in enzymology
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abstract：:It is widely acknowledged that mitochondria are highly active structures that rapidly respond to cellular and environmental perturbations by changing their shape, number, and distribution. Mitochondrial remodeling is a key component of diverse biological processes, ranging from cell cycle progression to autophagy. In ...
journal_title：Methods in enzymology
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doi：10.1016/bs.mie.2016.09.080
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abstract：:Protein kinases transfer a phosphoryl group from ATP onto target proteins and play a critical role in signal transduction and other cellular processes. Here, we review the kinase kinetic and chemical mechanisms and their application in understanding kinase structure and function. Aberrant kinase activity has been impl...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
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更新日期：2014-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章,评审
doi：10.1016/S0076-6879(09)63040-8
更新日期：2009-01-01 00:00:00
abstract：:5-FOA is an extremely useful reagent for the selection of Ura- cells amid a population of Ura+ cells. The selection is effective in transformation and recombination studies where loss of URA3+ is desired. A new plasmid shuffling procedure based on the 5-FOAR selection permits the recovery of conditional lethal mutatio...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/0076-6879(87)54076-9
更新日期：1987-01-01 00:00:00
abstract：:Histone acetylation is a dynamic epigenetic modification that functions in the regulation of DNA-templated reactions, such as transcription. This lysine modification is reversibly controlled by histone (lysine) acetyltransferases and deacetylases. Here, we present methods employing isotopic labeling and mass spectrome...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.01.007
更新日期：2016-01-01 00:00:00
abstract：:Autophagy is a major intracellular catabolic pathway induced in response to amino acid starvation. Recent findings implicate it in diverse physiological/pathophysiological events, such as protein and organelle turnover, development, aging, pathogen infection, cell death, and neurodegeneration. However, experimental me...
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pub_type： 杂志文章
doi：10.1016/S0076-6879(08)03609-4
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)03049-1
更新日期：2005-01-01 00:00:00
abstract：:A simple and convenient method is described to determine primary deuterium kinetic isotope effects (1°DKIEs) on reactions where the hydron incorporated into the reaction product is derived from solvent water. The 1°DKIE may be obtained by 1H NMR analyses as the ratio of the yields of H- and D-labeled products from a r...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2017.06.043
更新日期：2017-01-01 00:00:00
abstract：:In the near future, computational tools and methods based on the mathematical modeling of biomedically relevant networks and pathways will be necessary for the design of therapeutic strategies that fight complex multifactorial diseases. Beyond the use of pharmacokinetic and pharmacodynamic approaches, we propose here ...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-381270-4.00011-1
更新日期：2011-01-01 00:00:00
abstract：:Dicer is a multidomain ribonuclease that processes double-stranded RNAs (dsRNAs) to 21-nt small interfering RNAs (siRNAs) during RNA interference and excises microRNAs (miRNAs) from precursor hairpins. PAZ and PIWI domain (PPD) proteins, also involved in RNAi and miRNA function, are the best-characterized proteins kno...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(04)92019-8
更新日期：2005-01-01 00:00:00
abstract：:Changes in chromatin structure emanating from DNA breaks are among the most initiating events in the damage response of the cell. In higher eukaryotes, poly(ADP-ribose) polymerase-1 (PARP-1) translates the occurrence of DNA breaks detected by its zinc-finger domain into a signal, poly ADP-ribose, synthesized and ampli...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)09029-4
更新日期：2006-01-01 00:00:00
abstract：:Microfluidic devices have very broad applications in biological assays from simple chemotaxis assays to much more complicated 3D bioreactors. In this chapter, we describe the design and methods for performing chemotaxis assays using simple microfluidic chemotaxis chambers. With these devices, using real-time video mic...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2015.09.023
更新日期：2016-01-01 00:00:00
abstract：:Bispecific antibodies may be used to improve clinical efficacy by targeting two disease mechanisms for the treatment of complex human diseases in a single agent. Bispecific antibodies also hold promise for certain therapeutic applications difficult to achieve by single-targeting monospecific antibodies, such as immune...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-416039-2.00002-1
更新日期：2012-01-01 00:00:00
abstract：:Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were d...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2016.11.009
更新日期：2017-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(07)38014-2
更新日期：2008-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2018.04.002
更新日期：2018-01-01 00:00:00
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journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(05)07052-7
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abstract：:Cholestatic syndromes are inborn or acquired disorders of bile formation. In recent years, several inherited cholestatic syndromes were characterized at the molecular level: progressive familial intrahepatic cholestasis (PFIC) and benign recurrent intrahepatic cholestasis (BRIC). Both PFIC and BRIC were divided phenot...
journal_title：Methods in enzymology
pub_type： 杂志文章,评审
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更新日期：2005-01-01 00:00:00
abstract：:There is a great need for practicing scientists to volunteer their time and expertise in the K-12th grade science classroom. We have found that bioluminescence is a fun and exciting way to teach basic science concepts and is an excellent tool for the volunteering scientist. We have had very positive reactions from bot...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/s0076-6879(00)05517-8
更新日期：2000-01-01 00:00:00
abstract：:The Duffy blood group antigen is a serpentine protein with seven transmembrane domains that is not coupled to G-proteins or other known intracellular effectors. In addition to erythrocytes, it is also expressed in endothelial cells and neurons. In recent years the Duffy antigen has received much attention because of i...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(09)05409-3
更新日期：2009-01-01 00:00:00
abstract：:Undiluted cytoplasmic extract prepared from unfertilized Xenopus laevis eggs by low-speed centrifugation (CSF extracts) is useful for reconstitution of egg microtubule dynamics and meiosis-II spindle organization, but it suffers limitations for biochemical analysis due to abundant particulates. Here, we describe prepa...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-397924-7.00023-6
更新日期：2014-01-01 00:00:00
abstract：:A genetic interaction occurs when the combination of two mutations leads to an unexpected phenotype. Screens for synthetic genetic interactions have been used extensively to identify genes whose products are functionally related. In particular, synthetic lethal genetic interactions often identify genes that buffer one...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/S0076-6879(10)70007-0
更新日期：2010-01-01 00:00:00
abstract：:Pulsed electron double resonance technique, also known as double electron-electron resonance, jointly with site-directed spin labeling (SDSL) have been used extensively for studying structures and structural change. During the last decades, significant enhancements have been made by optimization of the experimental pr...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2015.05.027
更新日期：2015-01-01 00:00:00
abstract：:Gas chromatography-mass spectrometry (GC-MS) is one of the three most popular analytical platforms for metabolomics and is largely employed for the study of oncometabolism. Large volumes of data are usually generated in a GC-MS experiment, and many analytical steps are required to extract biologically relevant informa...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-801329-8.00016-7
更新日期：2014-01-01 00:00:00
abstract：:Family 3 carbohydrate-binding modules (CBM3s) are among the most distinctive, diverse, and robust. CBM3s, which are numerous components of both free cellulases and cellulosomes, bind tightly to crystalline cellulose, and thus play a key role in cellulose degradation through their substrate targeting capacity. In addit...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/B978-0-12-415931-0.00013-6
更新日期：2012-01-01 00:00:00
abstract：:Synthetic hydrogen sulfide (H2S) donors are useful research tools as well as potential therapeutic agents. In this chapter, we report the detailed protocols for the synthesis and evaluation of a series of phosphorodithioate-based H2S donors. Fluorescence assays were used to determine H2S release from the donors in bot...
journal_title：Methods in enzymology
pub_type： 杂志文章
doi：10.1016/bs.mie.2014.11.032
更新日期：2015-01-01 00:00:00
