Filters








243 Hits in 5.2 sec

STITCH 5: augmenting protein–chemical interaction networks with tissue and affinity data

Damian Szklarczyk, Alberto Santos, Christian von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn
2015 Nucleic Acids Research  
In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue.  ...  In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network.  ...  Yuan (EMBL) for his outstanding support with the STITCH servers and Rebeca Quiñones (NNF Center for Protein Research) for help with migrating the text-mining pipeline to a high-performance compute centre  ... 
doi:10.1093/nar/gkv1277 pmid:26590256 pmcid:PMC4702904 fatcat:ofgnm7c3t5eizpqshlb7unurle

STITCH 5: augmenting protein-chemical interaction networks with tissue and affinity data

Damian Szklarczyk, Alberto Santos, Christian Von Mering, Lars Juhl Jensen, Peer Bork, Michael Kuhn
2016
In the new, fifth release of STITCH, we have implemented functionality to filter out the proteins and chemicals not associated with a given tissue.  ...  In addition to the increased scope of the database, we have implemented a new network view that gives the user the ability to view binding affinities of chemicals in the interaction network.  ...  Yuan (EMBL) for his outstanding support with the STITCH servers and Rebeca Quiñones (NNF Center for Protein Research) for help with migrating the text-mining pipeline to a high-performance compute centre  ... 
doi:10.5167/uzh-120036 fatcat:7wx4w6jxgfan5dfyvvhqvbq76u

Network Pharmacological Study of Achyranthis bidentatae Radix Effect on Bone Trauma

Liying Wu, Youguo Hao, Chuanqiang Dai, Zhibang Zhang, Munazza Ijaz, Sobhy M. Ibrahim, Ghulam Murtaza, Zhiguang Yao, Thaqif El Khassawna
2021 BioMed Research International  
The protein-protein interaction network was developed by utilizing the STITCH database and gene ontology (GO) enrichment analysis using Cytoscape and ClueGO.  ...  Moreover, docking studies were performed for revealing the affinity of various ingredients with IL6. Results.  ...  Figure 1 denotes the retrieval of the chemical compounds of ABR, and the potential protein targets in Homo sapiens in step 1, followed by the development of a protein-protein interaction network (PPIN  ... 
doi:10.1155/2021/5692039 pmid:33748269 pmcid:PMC7959927 fatcat:2rabq4d7evaubj4htbroufp6tm

A census of P. longum's phytochemicals and their network pharmacological evaluation for identifying novel drug-like molecules against various diseases, with a special focus on neurological disorders

Neha Choudhary, Vikram Singh, Hiroyoshi Ariga
2018 PLoS ONE  
various protein targets by developing high-confidence tripartite networks consisting of phytochemical-protein target-disease association.  ...  with a special focus on neurological disorders.  ...  Acknowledgments N.C. and V.S. thank the Central University of Himachal Pradesh for providing computational infrastructure.  ... 
doi:10.1371/journal.pone.0191006 pmid:29320554 pmcid:PMC5761900 fatcat:bcvcdx5n2zgq3hbe2xrcvh45lu

Analysis and Anticancer Effects of Active Compounds from Spatholobi Caulis in Human Breast Cancer Cells

Hung Manh Phung, Hesol Lee, Sullim Lee, Dongyeop Jang, Chang-Eop Kim, Ki Sung Kang, Chang-Seob Seo, You-Kyung Choi
2020 Processes  
In addition, the network pharmacological analysis pointed out that the p53, mitogen-activated protein kinase (MAPK), estrogen, and Wnt signaling pathways have a great correlation with the targets of gallic  ...  Our data showed that the gallic acid induced apoptotic MCF-7 cell death through both extrinsic and intrinsic pathways, which increased the expression of cleaved caspase-7, -8, and -9, Bax and p53, but  ...  "STITCH 5: Augmenting protein-chemical interaction networks with tissue and affinity data." Nucleic acids research 44.D1 (2016): D380-D384.) .  ... 
doi:10.3390/pr8091193 doaj:17ddb71ce6ac439e86d7f164367ed0f8 fatcat:c7md3x2uerd5hh2bai5pzorqza

Artificial intelligence to deep learning: machine intelligence approach for drug discovery

Rohan Gupta, Devesh Srivastava, Mehar Sahu, Swati Tiwari, Rashmi K Ambasta, Pravir Kumar
2021 Molecular diversity  
structure-activity relationship to drug repositioning, protein misfolding to protein-protein interactions, and molecular pathway identification to polypharmacology.  ...  Drug designing and development is an important area of research for pharmaceutical companies and chemical scientists.  ...  Authors' contribution All authors have read the paper and agreed to submit. PK conceived the idea. RG, DS, MS, ST arranged the data. RG, DS, MS, and ST contributed equally to this work.  ... 
doi:10.1007/s11030-021-10217-3 pmid:33844136 pmcid:PMC8040371 fatcat:yltthjorrvfrjgyrnszpxgpb2q

Introductory Chapter: Multitask Portfolio of Chitin/Chitosan: Biomatrix to Quantum Dot [chapter]

Rajendra Sukhadeorao Dongre
2018 Chitin-Chitosan - Myriad Functionalities in Science and Technology  
Shrilk composite consists of laminar plywood-like layers altered via mechanical and chemical interactions of chitosan/fibroin laminates.  ...  It has myriad therapeutic uses, including fibroplasia-inhibited wound healing/dressing, absorbable stitches, and supports tissue/cell growth and differentiates cells.  ... 
doi:10.5772/intechopen.77218 fatcat:xtgeystrufh73g75r7pjhdzauy

The integration of 'omic' disciplines and systems biology in cattle breeding

D. P. Berry, K. G. Meade, M. P. Mullen, S. Butler, M. G. Diskin, D. Morris, C. J. Creevey
2010 Animal  
A move away from traditional approaches of animal breeding toward systems approaches using integrative analysis of data from the 'omic' disciplines represents a multitude of exciting opportunities for  ...  Harnessing the potential of this paradigm shift also poses some new challenges for animal scientists – and they will also be discussed.  ...  The database STITCH (search tool for interactions of chemicals) (http://stitch.embl.de/; Kuhn et al., 2008) is one such tool, combining information on the interaction of chemicals and proteins from multiple  ... 
doi:10.1017/s1751731110002120 pmid:22439945 fatcat:cwh6ayajfzboljrfgrhmtyap6y

1-Deoxynojirimycin: Occurrence, Extraction, Chemistry, Oral Pharmacokinetics, Biological Activities and In Silico Target Fishing

Kuo Gao, Chenglong Zheng, Tong Wang, Huihui Zhao, Juan Wang, Zhiyong Wang, Xing Zhai, Zijun Jia, Jianxin Chen, Yingwu Zhou, Wei Wang
2016 Molecules  
well as from several bacterial strains such as Bacillus and Streptomyces species.  ...  Deoxynojirimycin possesses antihyperglycemic, anti-obesity, and antiviral features.  ...  Chemical (DNG)-protein associations are found between following couples: DNJ-CALR, DNJ-GANAB, DNJ-MGAM, DNJ-GLA, and DNJ-GAA. Figure 5 . 5 The protein network of DNJ.  ... 
doi:10.3390/molecules21111600 pmid:27886092 fatcat:zgdfqofhv5aapfsbddhbpsuwxi

Combinatorial Drug Screening Identifies Ewing Sarcoma–specific Sensitivities

Branka Radic-Sarikas, Kalliopi P. Tsafou, Kristina B. Emdal, Theodore Papamarkou, Kilian V. M. Huber, Cornelia Mutz, Jeffrey A. Toretsky, Keiryn L. Bennett, Jesper V. Olsen, Søren Brunak, Heinrich Kovar, Giulio Superti-Furga
2016 Molecular Cancer Therapeutics  
We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes.  ...  Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including  ...  Bekker-Jensen, Anna-Kathrine Pedersen, and Dave Aryee for skillful advice and help.  ... 
doi:10.1158/1535-7163.mct-16-0235 pmid:28062706 fatcat:c2lwpykdj5dyrlqex4d6mw7re4

A simple mathematical approach to the analysis of polypharmacology and polyspecificity data

Gerry Maggiora, Vijay Gokhale
2017 F1000Research  
Szklarczyk D, Santos A, von Mering C, et al.: STITCH 5: augmenting proteinchemical interaction networks with tissue and affinity data. Nucleic Acids Res. 2016; 44(D1): D380-D384.  ...  There many possible types of drug-target interactions, because there are a surprising number of ways in which drugs and their targets can associate with one another.  ...  Acknowledgments GM wishes to thank Professor Jürgen Bajorath and Dr.  ... 
doi:10.12688/f1000research.11517.1 pmid:28690829 pmcid:PMC5482344 fatcat:c3sz3e2m3fhzndkwzyclhjufnm

Systems Biology in Immunology: A Computational Modeling Perspective

Ronald N. Germain, Martin Meier-Schellersheim, Aleksandra Nita-Lazar, Iain D.C. Fraser
2011 Annual Review of Immunology  
generate the quantitative and qualitative data required for such modeling and simulation and summarize the progress to date in applying these tools and techniques to questions of immunological interest  ...  Systems biology is an emerging discipline that combines high-content, multiplexed measurements with informatic and computational modeling methods to better understand biological function at various scales  ...  Acknowledgments The authors wish to thank many colleagues, especially Gregoire Altan-Bonnet, or discussions and research interactions that were critical to our developing the perspective espoused in this  ... 
doi:10.1146/annurev-immunol-030409-101317 pmid:21219182 pmcid:PMC3164774 fatcat:my2czdrjajd5ldhrm52k2fzd5a

A critical overview of computational approaches employed for COVID-19 drug discovery

Eugene N. Muratov, Rommie Amaro, Carolina H. Andrade, Nathan Brown, Sean Ekins, Denis Fourches, Olexandr Isayev, Dima Kozakov, José L. Medina-Franco, Kenneth M. Merz, Tudor I. Oprea, Vladimir Poroikov (+7 others)
2021 Chemical Society Reviews  
We cover diverse methodologies, computational approaches, and case studies illustrating the ongoing efforts to develop viable drug candidates for treatment of COVID-19.  ...  Human PPIs were Recon2 (PMID: 23455439), obtained using SpidermiR human PPI network from tool (PMID: 28134831) STRING (https://string-db. org) Source of Drug-target interactions were STITCH (http://stitch  ...  with essential ingredients such as virus-host proteinprotein interactions (VHPPIs), human protein-protein interactions (hPPIs), and drug-target interactions (DTIs).  ... 
doi:10.1039/d0cs01065k pmid:34212944 pmcid:PMC8371861 fatcat:n6dxyyjxifh6hoehd7myapjtwu

Identification of Steroidogenic Components Derived From Gardenia jasminoides Ellis Potentially Useful for Treating Postmenopausal Syndrome

Xueyu Wang, Guo-Cai Wang, Jianhui Rong, Shi Wei Wang, Tzi Bun Ng, Yan Bo Zhang, Kai Fai Lee, Lin Zheng, Hei-Kiu Wong, Ken Kin Lam Yung, Stephen Cho Wing Sze
2018 Frontiers in Pharmacology  
In STITCH and CTD database, confidence score and gene frequency indicate the strength of the chemical-target interaction.  ...  For the identification of GJE associated proteins and genes, STITCH ("search tool for interactions of chemicals") database 4.0 (http://stitch.embl.de/) was used to explore the compoundprotein interactions  ... 
doi:10.3389/fphar.2018.00390 pmid:29899696 pmcid:PMC5989419 fatcat:rxgh3hl5vbcyrav4tl7hwcbf3u

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.  ...  Acknowledgements The authors acknowledge the guidance of Enoch Huang and substantial input from Robert Hernandez, Markella Skempri, Dave  ...  Augmenting a mechanism hypothesis From a protein that is known to be involved in a disease, researchers can use in-house and external protein-protein interaction data to navigate to an alternative point  ... 
doi:10.1016/j.drudis.2009.09.011 pmid:19840866 fatcat:csd4hsaokjgbjjbq4azwdnf24q
« Previous Showing results 1 — 15 out of 243 results