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STITCH 3: zooming in on protein-chemical interactions

M. Kuhn, D. Szklarczyk, A. Franceschini, C. von Mering, L. J. Jensen, P. Bork
2011 Nucleic Acids Research  
To facilitate the study of interactions between proteins and chemicals, we have created STITCH, an aggregated database of interactions connecting over 300 000 chemicals and 2.6 million proteins from 1133  ...  The database can be accessed interactively through a web interface, displaying interactions in an integrated network view.  ...  When a user zooms in on a compound, only those isomers with associations (in any species) are shown.  ... 
doi:10.1093/nar/gkr1011 pmid:22075997 pmcid:PMC3245073 fatcat:dkri4srxl5egbn7ou4wikebg6i

Stitching together a nm thick peptide-based semiconductor sheet using UV light [article]

Alain Bolaño Alvarez, Marcelo Pino, Steffen B. Petersen, Gerardo D. Fidelio
2020 bioRxiv   pre-print
UVB-light induces changes in the lateral conductivity and current-voltage behaviour as well as monolayer heterogeneity monitored by Brewster angle microscopy that depends on the peptide bond backbone orientation  ...  Our results indicate that one may design extended nano-sheets with particular electric properties, reminiscent of semiconductors.  ...  In this connection, but with a different approach, it was recently reported that the conductance in protein-ligand systems is sensitive to the charge and the nature of chemical electrical contact between  ... 
doi:10.1101/2020.07.01.183152 fatcat:t6z5ed7dx5a3jml6pgborpfowi

Stitching together Multiple Data Dimensions Reveals Interacting Metabolomic and Transcriptomic Networks That Modulate Cell Regulation

Jun Zhu, Pavel Sova, Qiuwei Xu, Kenneth M. Dombek, Ethan Y. Xu, Heather Vu, Zhidong Tu, Rachel B. Brem, Roger E. Bumgarner, Eric E. Schadt, Andre Levchenko
2012 PLoS Biology  
, protein-metabolite interaction, and protein-protein interaction data, to construct probabilistic causal networks that elucidate the complexity of cell regulation in a segregating yeast population.  ...  Small-molecule metabolites are one category of critical cellular intermediates that can influence as well as be a target of cellular regulations.  ...  basis of protein-protein interaction data.  ... 
doi:10.1371/journal.pbio.1001301 pmid:22509135 pmcid:PMC3317911 fatcat:l2ihbmv37nck3oyh4fgvzee4em

A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics

Andrew D Southam, Ralf J M Weber, Jasper Engel, Martin R Jones, Mark R Viant
2017 Nature Protocols  
MR 2017, 'A complete workflow for high-resolution spectral-stitching nanoelectrospray direct-infusion mass-spectrometry-based metabolomics and lipidomics ', Nature protocols, vol. 12, no. 2, . https://  ...  As one example, regulatory toxicology is now opening the door to new testing strategies for determining the impacts of chemicals on human health.  ...  single or multiple chemical name(s).  ... 
doi:10.1038/nprot.2016.156 pmid:28079878 fatcat:jyonzbotnfe25hwhsg3ng6zgv4

3DProIN: Protein-Protein Interaction Networks and Structure Visualization

Hui Li, Chunmei Liu
2014 American Journal of Bioinformatics and Computational Biology  
It models protein-protein interactions in a graph and explores the biologically relevant features of the tertiary structures of each protein in the network.  ...  3DProIN is a computational tool to visualize protein-protein interaction networks in both two dimensional (2D) and three dimensional (3D) view.  ...  For example, Medusa (Hooper and Bork, 2005) optimizes proteinprotein interaction data taken from STRING or protein-chemical and chemical-chemical interactions taken from STITCH.  ... 
doi:10.7726/ajbcb.2014.1003 pmid:25664223 pmcid:PMC4316736 fatcat:gxddlnd2mbfntdt7djtervfl7e

3-D Imaging Reveals Participation of Donor Islet Schwann Cells and Pericytes in Islet Transplantation and Graft Neurovascular Regeneration

Jyuhn-Huarng Juang, Chien-Hung Kuo, Shih-Jung Peng, Shiue-Cheng Tang
2015 EBioMedicine  
In this research, we applied 3-dimensional neurovascular histology with cell tracing to reveal the participation of Schwann cells and pericytes in mouse islet transplantation.  ...  Based on the morphological proximity and cellular reactivity, we propose that the new islet microenvironment should include the perigraft Schwann cell sheath and perivascular pericytes as an integral part  ...  interactions.  ... 
doi:10.1016/j.ebiom.2015.01.014 pmid:26137552 pmcid:PMC4485478 fatcat:nqwhq6tu7rca3caq5bxk2vixc4

ChemProt-3.0: a global chemical biology diseases mapping

Jens Kringelum, Sonny Kim Kjaerulff, Søren Brunak, Ole Lund, Tudor I. Oprea, Olivier Taboureau
2016 Database: The Journal of Biological Databases and Curation  
In this third version, ChemProt has been updated to more than 1.7 million compounds with 7.8 million bioactivity measurements for 19 504 proteins.  ...  Abstract ChemProt is a publicly available compilation of chemical-protein-disease annotation resources that enables the study of systems pharmacology for a small molecule across multiple layers of complexity  ...  Large values indicate strong chemical-protein interactions and are represented in orange. Low value (weak interactions) is depicted in blue.  ... 
doi:10.1093/database/bav123 pmid:26876982 pmcid:PMC4752971 fatcat:rvrdyvwbo5eebp3d5zylcvelwu

Tetrahydroquinoline-Derived Macrocyclic Toolbox: The Discovery of Antiangiogenesis Agents in Zebrafish Assay

Shiva Krishna Reddy Guduru, Srinivas Chamakuri, Gayathri Chandrasekar, Satish Srinivas Kitambi, Prabhat Arya
2013 ACS Medicinal Chemistry Letters  
Further, evaluation in a zebrafish screen identified three active small molecules (2.5b, 3.2d, and 4.2) as antiangiogenesis agents at 2.5 μM.  ...  The presence of an amino acid-derived moiety in the macrocyclic skeleton provides an opportunity to modulate the nature of the chiral side chain.  ...  T he growing quest to undertake biological targets that belong to the family of proteinprotein 1,2 and DNA/ RNA−protein 3 interactions in the signaling pathway arena 4,5 is challenging the current thinking  ... 
doi:10.1021/ml400026n pmid:24900727 pmcid:PMC4027127 fatcat:xtwlp2n4zrcclotvltdhx7ub3e

Toxicological Effects of the Different Substances in Tobacco Smoke on Human Embryonic Development by a Systems Chemo-Biology Approach

Bruno César Feltes, Joice de Faria Poloni, Daniel Luis Notari, Diego Bonatto, Michael Schubert
2013 PLoS ONE  
Moreover, we show that the effect of cigarette smoke on the developing fetus could represent systemic and aggressive impacts in the short term, causing malformations during certain stages of development  ...  In this study, we applied interactome data mining tools and small compound interaction networks to elucidate possible molecular pathways associated with the effects of tobacco smoke components during embryonic  ...  To prospect protein-protein and chemical-protein interactions (PPI and CPI, respectively), we entered each TC into the STITCH program.  ... 
doi:10.1371/journal.pone.0061743 pmid:23637898 pmcid:PMC3639264 fatcat:pdfpcdmecjcbzac64nz2yspdfi

Visualizing the drug target landscape

Stephen J. Campbell, Anna Gaulton, Jason Marshall, Dmitri Bichko, Sid Martin, Cory Brouwer, Lee Harland
2010 Drug Discovery Today  
A retrospective on how the application of data integration and visualisation has been used to connect disparate information sources into a drug-discovery focused, decision making environment.  ...  (d)Protein-protein interaction data used to filter the landscape scatter plot to identify chemically tractable proteins not obviously linked to a disease.  ...  FIGURE 3 3 FIGURE 3 Exploring the target landscape in detail. (a) The heat map view, in which quantitative data such as gene expression results can be incorporated.  ... 
doi:10.1016/j.drudis.2009.09.011 pmid:19840866 fatcat:csd4hsaokjgbjjbq4azwdnf24q

PharmaTrek: A Semantic Web Explorer for Open Innovation in Multitarget Drug Discovery

Maria C. Carrascosa, Oriol L. Massaguer, Jordi Mestres
2012 Molecular Informatics  
also an interactive small-size overall viewer that allows you to zoom in and out on different regions of the interaction map.  ...  To do that, simply put the mouse on top of the target name appearing in the labels of the columns (zoom in if necessary) and drag and drop the name into the target profile basket.  ... 
doi:10.1002/minf.201200070 pmid:23548981 pmcid:PMC3573647 fatcat:vvvqswk6kbefzosdk24siwkadm

Simultaneous detection of multiple targets for ultrastructural immunocytochemistry

V. V. Philimonenko, A. A. Philimonenko, I. Šloufová, M. Hrubý, F. Novotný, Z. Halbhuber, M. Krivjanská, J. Nebesářová, M. Šlouf, P. Hozák
2014 Histochemistry and Cell Biology  
For the first time in ultrastructural histochemistry, up to five molecular targets can be identified simultaneously.  ...  Jiří Janáček for modifying the relevant spatial statistics plug-ins for evaluation of the five labeling types.  ...  Open Access This article is distributed under the terms of the Creative Commons attribution license which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ... 
doi:10.1007/s00418-013-1178-6 pmid:24449180 pmcid:PMC3935117 fatcat:5okzkvwzx5alfbpxy7bvfzhwfe

Mapping the genome of Plasmodium falciparum on the drug-like chemical space reveals novel anti-malarial targets and potential drug leads

Kasper Jensen, Damian Plichta, Gianni Panagiotou, Irene Kouskoumvekaki
2012 Molecular Biosystems  
zoomed on the predicted interactions between polyactive GSK compounds and prioritized P. falciparum proteins.  ...  Fig. 3 3 Heatmap with predicted interactions between GSK compounds and P. falciparum experimentally validated essential proteins.  ... 
doi:10.1039/c2mb00008c pmid:22446744 fatcat:s7zlxuafwvhntgoaexldvkic7u

Ribbon scanning confocal for high-speed high-resolution volume imaging of brain

Alan M. Watson, Annika H. Rose, Gregory A. Gibson, Christina L. Gardner, Chengqun Sun, Douglas S. Reed, L. K. Metthew Lam, Claudette M. St. Croix, Peter L. Strick, William B. Klimstra, Simon C. Watkins, Thomas Abraham
2017 PLoS ONE  
PLoS ONE 12(7): e0180486.  ...  We describe the first application of multicolor ribbon scanning confocal methods to collect high-resolution volume images of chemically cleared brains.  ...  Fig 3 . 3 Confocal is more effective than multiphoton at multicolor deep tissue imaging in chemically cleared brains.  ... 
doi:10.1371/journal.pone.0180486 pmid:28686653 pmcid:PMC5501561 fatcat:xhcf5hl4prbgrii6dk3zze7the

Functional scaffold-free 3-D cardiac microtissues: a novel model for the investigation of heart cells

B. R. Desroches, P. Zhang, B.-R. Choi, M. E. King, A. E. Maldonado, W. Li, A. Rago, G. Liu, N. Nath, K. M. Hartmann, B. Yang, G. Koren (+2 others)
2012 American Journal of Physiology. Heart and Circulatory Physiology  
Importantly, Ba 2ϩ -sensitive inward rectifier K ϩ currents and Ca 2ϩ -handling proteins, including sarco(endo)plasmic reticulum Ca 2ϩ -ATPase 2a, were detected in CM-containing microtissues.  ...  Furthermore, cell type-specific adenoviral gene transfer was achieved, with no impact on microtissue formation or cell viability.  ...  interactions in a 3-D environment.  ... 
doi:10.1152/ajpheart.00743.2011 pmid:22427522 pmcid:PMC3362102 fatcat:ovege6hshfdzzmwxjia6vcsxw4
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