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STITCH 3: zooming in on protein-chemical interactions
2011
Nucleic Acids Research
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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]
2020
bioRxiv
pre-print
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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
2012
PLoS Biology
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, 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
2017
Nature Protocols
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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
2014
American Journal of Bioinformatics and Computational Biology
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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
2015
EBioMedicine
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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
2016
Database: The Journal of Biological Databases and Curation
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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
2013
ACS Medicinal Chemistry Letters
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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 protein−protein 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
2013
PLoS ONE
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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
2010
Drug Discovery Today
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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
2012
Molecular Informatics
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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
2014
Histochemistry and Cell Biology
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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
2012
Molecular Biosystems
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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
2017
PLoS ONE
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PLoS ONE 12(7): e0180486. https://doi.org/10. ...
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
2012
American Journal of Physiology. Heart and Circulatory Physiology
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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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