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Molecular-Field-Based Three-Dimensional Similarity Studies on Quinoline-Based CNS Active Agents

Alka Bali
2011 ISRN Pharmaceutics  
A series of quinoline-based agents with CNS activity have been analyzed for their three-dimensional similarity with respect to a set of standard atypical antipsychotics.  ...  The method aligns the molecules based on their molecular fields represented as local extrema of electrostatic, van der Waals, and hydrophobic potentials of the molecule termed "field points."  ...  Quantification of chemical similarity is based on numerical representation of a chemical structure, and similarity comparisons are done based on 2D or 3D approaches. 2D approaches involve the calculation  ... 
doi:10.5402/2011/186943 pmid:22389844 pmcid:PMC3263725 fatcat:tvscvkntizhqzbxy552xp5ejfi

The Det.Belt Server: A Tool to Visualize and Estimate Amphipathic Solvent Belts around Membrane Proteins

Veronica Zampieri, Cécile Hilpert, Mélanie Garnier, Yannick Gestin, Sébastien Delolme, Juliette Martin, Pierre Falson, Guillaume Launay, Vincent Chaptal
2021 Membranes  
Detergents wrap around membrane proteins to form a belt covering the hydrophobic part of the protein serving for membrane insertion and interaction with lipids.  ...  The number of detergent monomers forming this belt is usually unknown to investigators, unless dedicated detergent quantification is undertaken, which for many projects is difficult to setup.  ...  Acknowledgments: The authors wish to thank Andrei Lomize for sharing the source code of the PPM server (https://opm.phar.umich.edu/ppm_server) (accessed on 15 December 2020).  ... 
doi:10.3390/membranes11070459 fatcat:x2pahyb4x5c2dcid2u4nymv2fu

Molecular challenges in modern chemometrics

R. Wehrens, R.de Gelder, G.J. Kemperman, B. Zwanenburg, L.M.C. Buydens
1999 Analytica Chimica Acta  
One of the main obstacles is the definition of an appropriate representation of a molecule. Although a variety of different representations are used, none are generally applicable.  ...  Despite the huge quantities of data that are available nowadays, it is often difficult to recognise and extract relevant chemical information for the problem at hand.  ...  Acknowledgements DSM Life Science Products and the Dutch Ministry of Economic Affairs are kindly acknowledged for their financial support.  ... 
doi:10.1016/s0003-2670(99)00621-2 fatcat:g4iawb2knneylaetljaqrhprmu

Multivariate analysis of hyperspectral stimulated Raman scattering microscopy images

Imaiyan Chitra Ragupathy, Volker Schweikhard, Andreas Zumbusch
2021 Journal of Raman Spectroscopy  
In this work, we report a quantitative comparison of the performance of different multivariate methods used for the analysis of hyperspectral SRS data from different model samples.  ...  We show that the combination with a selection of essential components based on first-order autocorrelation, gives a simple workflow for the MCR-based analysis of hyperspectral coherent Raman imaging data  ...  ACKNOWLEDGMENTS We thank Anayat Bhat and Franziska Rabold for help with the cell culture, Dr. Mustafa Kocademir for assisting in spontaneous Raman data collection, and Dr.  ... 
doi:10.1002/jrs.6184 fatcat:iktab527nfbgrj3jpbxaqy2yse

Quantitative NMR-Based Biomedical Metabolomics: Current Status and Applications

Alexandra A. Crook, Robert Powers
2020 Molecules  
While qNMR is limited by sensitivity and dynamic range, the simple method development, minimal sample derivatization, and the simultaneous qualitative and quantitative information provide a unique landscape  ...  In this review of quantitative NMR-based metabolomics, the advancements and limitations of current techniques for metabolite quantification will be evaluated as well as the applications of qNMR in biomedical  ...  of a few select chemical classes or compounds.  ... 
doi:10.3390/molecules25215128 pmid:33158172 fatcat:w4tr5z327fcdfllniluiqs77we

Appreciation of the Chemical Ingredients of Black Grapes Structures Vitis vinifera L. and Identify the Impact Against oxidation

2018 Advances in Environmental Biology  
Alcohol extraction process was conducted for the Structures of black grapes as well as testing the Effect of extracted antireductionist us anti oxidation and iron binding force.  ...  You had estimated the chemical composition of grape Vitis vinifera L. black structures and humidity were 10.65 and 8.04% and protein 5.63 and 5.87% and carbs 80.43 82.21% fat ratio and 0.36 and 0.39% And  ...  The possibility of eating it year round in mushy or dried, and grape fruits a Fast digestion with high nutritional value, and his aptitude for calculating representation during any body.  ... 
doi:10.22587/aeb.2018.12.6.2 fatcat:yc25lgtpn5bi7czavbywytwuwq

High-Resolution Quantitative Metabolome Analysis of Urine by Automated Flow Injection NMR

Laeticia Da Silva, Markus Godejohann, François-Pierre J. Martin, Sebastiano Collino, Alexander Bürkle, María Moreno-Villanueva, Jürgen Bernhardt, Olivier Toussaint, Beatrix Grubeck-Loebenstein, Efstathios S. Gonos, Ewa Sikora, Tilman Grune (+5 others)
2013 Analytical Chemistry  
This method includes the acquisition of nuclear Overhauser effect spectroscopy one-dimensional and J-resolved two-dimensional (J-Res-2D) (1)H NMR spectra obtained on a 600 MHz spectrometer, equipped with  ...  With the aim to describe an overall metabolomics workflow, the quantification of 36 metabolites, mainly related to central carbon metabolism and gut microbial host cometabolism, was obtained, as well as  ...  Metabolite quantifiability was tested for the established FIA-NMR method using a standard addition and a calibration curve method for four chemically different compounds: a sugar ((±)-glucose), an aromatic  ... 
doi:10.1021/ac4004776 pmid:23718684 pmcid:PMC3690541 fatcat:6xu7wfx5fjexxeo4vfepq6m7fi

Comprehensive Chemical Characterization of the Pistacia vera Fruits through Original NMR Quantification Methods

Archimede Rotondo, Francesca Rigano, Luigi Mondello
2020 Applied Sciences  
a blessed touch for gourmet dishes; (2) Methods: The simultaneous NMR profiles concerning the hydrophilic and hydrophobic phases, enabled by a specific throughput over grinded pistachio seeds, led to  ...  The chemical quantification takes advantage from the innovative multi-assignment recovered analysis (MARA-NMR) technique able to provide experimentally robust panels for both hydrophobic and hydrophilic  ...  (LC × LC), thus obtaining a bidimensional map usable for a direct comparison.  ... 
doi:10.3390/app10165523 fatcat:jjnra7lafzf3teraqvgsndsn6u

Databases and Software for NMR-Based Metabolomics

James J. Ellinger, Roger A. Chylla, Eldon L. Ulrich, John L. Markley
2012 Current Metabolomics  
Public and commercial databases now contain experimental 1D 1H, 13C and 2D 1H-13C spectra and extracted spectral parameters for over a thousand compounds and theoretical data for thousands more.  ...  In this review we focus on database and software tools that support a quantitative NMR approach to the analysis of 1D and 2D NMR spectra of complex biological mixtures.  ...  Acknowledgments Supported by National Institutes of Health Grants P41 LM05799 and P41 GM103399.  ... 
doi:10.2174/2213235x11301010028 pmid:24260723 pmcid:PMC3832261 fatcat:umhinkhvavfsjeyhkpqylbjnly

SCISSORS: Practical Considerations

Steven M. Kearnes, Imran S. Haque, Vijay S. Pande
2013 Journal of Chemical Information and Modeling  
The SCISSORS method rapidly approximates measures of pairwise molecular similarity such as ROCS and LINGO Tanimotos, acting as a filter to quickly reduce the size of a problem.  ...  We show that SCISSORS can accurately predict multiconformer similarity and suggest a method for estimating optimal SCISSORS parameters in a data set-specific manner.  ...  We also acknowledge the following award for providing computing resources: MRI-R2: Acquisition of a Hybrid CPU/GPU and Visualization Cluster for Multidisciplinary Studies in Transport Physics with Uncertainty  ... 
doi:10.1021/ci400264f pmid:24289274 pmcid:PMC4207653 fatcat:mgq5q6encfh6dkangfkbog7s2e

The shape of porphyrins

Christopher J. Kingsbury, Mathias O. Senge
2021 Coordination chemistry reviews  
This method has been used previously for comparison of small data sets of synthetic and biological porphyrins.  ...  This quantification allows for assessment of predicted structures and forms the basis of a symmetry-by-design motif for a range of porphyrinoids.  ...  This work was prepared with the support of the Technical University of Munich -Institute for Advanced Study through a Hans Fischer Senior Fellowship. Appendix A.  ... 
doi:10.1016/j.ccr.2020.213760 fatcat:k5ccrxt6t5eihc2uhzpjenrgcm

A correction method for systematic error in 1H-NMR time-course data validated through stochastic cell culture simulation

Stanislav Sokolenko, Marc G. Aucoin
2015 BMC Systems Biology  
In contrast to the established use of 13 C-NMR for targeted elucidation of intracellular metabolic flux (reviewed in [1]), the quantification of a  ...  Trend shapes were simulated from generic functions corresponding to each classification. The resulting shapes were then scaled to simulated compound concentrations.  ...  The authors thank Marco Quattrociocchi for his assistance with cell culturing, Sandi Yen for her critical review of the manuscript, and Larry Campbell for discussion of MS techniques.  ... 
doi:10.1186/s12918-015-0197-4 pmid:26335002 pmcid:PMC4558828 fatcat:epoyfirg65h2xlc5ockadxlybi

A simple and fast sampling method for assessing chemical and nutritional characteristics of pumpkins

Bruno Trindade Cardoso, Semíramis Rabelo Ramalho Ramos, Ricardo Elesbão A lves, Carlos Alberto da Silva Ledo, Antonina dos Santos, Hister Maria Matias dos Santos
2020 Horticultura Brasileira  
In the chemical and nutritional analyses of pumpkin, the size of bulk sample recommended by the method of reference, makes the process time consuming and difficult to execute.  ...  The cylinder method was rapid, efficient, reliable and exhibited the greatest suitability for replacing the reference method.  ...  The authors were solely responsible for experimental design, data collection and analysis, preparation and submission of the manuscript.  ... 
doi:10.1590/s0102-053620200304 fatcat:4cq7k7auk5cd5pdpmf454dll2y

Determination of Three Organochlorine Pesticides in Aqueous Samples by Solid-Phase Extraction Based on Natural Nano Diatomite in Packed Syringe Coupled to Gas Chromatography–Mass Spectrometry

Abdollah TAGHANI, Nasser GOUDARZI, Ghadamali BAGHERIAN, Mansour Arab CHAMJANGALI
2017 Analytical Sciences  
A rapid, simple, and sensitive technique is proposed based on a miniaturized solid-phase extraction method named mictroextraction in a packed syringe coupled with gas chromatography-mass spectrometry for  ...  The reproducibility of this method was found to be in the range of 3.5 -11.1% for the understudied pesticides.  ...  Acknowledgements The authors wish to acknowledge the support of Rural Water and Wastewater Company in the Golestan province, Iran.  ... 
doi:10.2116/analsci.33.1135 pmid:28993587 fatcat:razv6v7mz5am3baqogm5ul6ope

Development of a Highly Sensitive Methodology for Quantitative Determination of Fexofenadine in a Microdose Study by Multiple Injection Method Using Ultra-High Performance Liquid Chromatography with Tandem Mass Spectrometry

Yukari Tanaka, Yutaka Yoshikawa, Hiroyuki Yasui
2012 Biological and Pharmaceutical Bulletin  
We suggest that this method might be beneficial for the quantification of fexofenadine concentrations in a microdose clinical study.  ...  In this study, MIM involved continuous injections of multiple samples containing the single compound into a column of the ultra-HPLC (UHPLC) system, and then, temporary trapping of the analyte at the column  ...  was selected as a model compound, and we developed and validated the ultra high-sensitivity quantitative method of MIM for rat plasma samples without an internal standard (IS) compound by using simple  ... 
doi:10.1248/bpb.35.698 pmid:22687404 fatcat:3yhhebxbcfhkxcxk75y6s6vbqa
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