Discovery of Surface Target Proteins Linking Drugs, Molecular Markers, Gene Regulation, Protein Networks, and Disease by Using a Web-Based Platform Targets-search

2017 ◽  
pp. 331-344
Author(s):  
Bin Yan ◽  
Panwen Wang ◽  
Junwen Wang ◽  
Kenneth R. Boheler
Keyword(s):  
Gene Regulation ◽  
Molecular Markers ◽  
Protein Networks ◽  
Web Based ◽  
Target Proteins

Modern Paradigm Towards Potential Target Identification for Antiviral (SARS-nCoV-2) and Anticancer Lipopeptides: A Pharmacophore-Based Approach

2022 ◽  
Author(s):  
Manisha Yadav ◽  
J. Satya Eswari
Keyword(s):  
Drug Discovery ◽  
Target Identification ◽  
Target Prediction ◽  
Cost Effective ◽  
Time Saving ◽  
Web Based ◽  
Target Proteins ◽  
Lead Compounds ◽  
Potential Target ◽  
Biopharmaceutical Properties

Background: Lipopeptides are potential microbial metabolites that are abandoned with broad spectrum biopharmaceutical properties ranging from antimicrobial, antiviral and anticancer, etc. Clinical studies are not much explored beyond the experimental methods to understand drug mechanisms on target proteins at the molecular level for large molecules. Due to the less available studies on potential target proteins of lipopeptide based drugs, their potential inhibitory role for more obvious treatment on disease have not been explored in the direction of lead optimization. However, Computational approaches need to be utilized to explore drug discovery aspects on lipopeptide based drugs, which are time saving and cost-effective techniques. Methods: Here a ligand-based drug discovery approach is coupled with reverse pharmacophore-mapping for the prediction of potential targets for antiviral (SARS-nCoV-2) and anticancer lipopeptides. Web-based servers PharmMapper and Swiss Target Prediction are used for the identification of target proteins for lipopeptides surfactin and iturin produced by Bacillus subtilis. Results: The studies have given the insight to treat the diseases with next-generation large molecule therapeutics. Results also indicate the affinity for Angiotensin-Converting Enzymes (ACE) and proteases as the potential viral targets for these categories of peptide therapeutics. A target protein for the Human Papilloma Virus (HPV) has also been mapped. Conclusion: The work will further help in exploring computer-aided drug designing of novel compounds with greater efficiency where the structure of the target proteins and lead compounds are known.  

scholarly journals Identifying Interacting Proteins of Arabidopsis Cyclophilin38 (AtCYP38), a Key Factor for PSII Assembly/Repair, via Multiple Screening Approaches

2020 ◽  
Author(s):  
Yaqi Hao ◽  
Jiashu Chu ◽  
Lujing Shi ◽  
Cong Ma ◽  
Liangliang Hui ◽  
...  
Keyword(s):  
Membrane Proteins ◽  
Thylakoid Membrane ◽  
Interacting Proteins ◽  
Yeast Two Hybrid ◽  
Working Mechanism ◽  
Web Based ◽  
Thylakoid Lumen ◽  
Target Proteins ◽  
Thylakoid Membrane Proteins ◽  
Two Hybrid

Abstract BackgroundAtCYP38, a thylakoid lumen localized immunophilin, is essential for photosystem II (PSII) assembly and maintenance, but how AtCYP38 functions in chloroplast remains unknown. Based on previous functional studies and its crystal structure, we hypothesize that AtCYP38 should function via binding its targets or cofactors in the thylakoid lumen to influence PSII performance. Therefore, identifying its target proteins and cofactors would be a key step to understand the working mechanism of AtCYP38.ResultsTo identify potential interacting proteins of AtCYP38, we first adopted two web-based tools, ATTED-II and STRING, and found 15 proteins functionally related to AtCYP38. We then screened a yeast two-hybrid library including an Arabidopsis genome wide cDNA with the N-terminal domain, the C-terminal domain, and the full-length mature protein of AtCYP38. 25 positive targets were identified, but a very limited number of target proteins were localized in the thylakoid lumen. In order to specifically search interacting proteins of AtCYP38 in the thylakoid lumen, we created a yeast two-hybrid mini library including the thylakoid lumenal proteins and lumen fractions of thylakoid membrane proteins. After screening the mini library with 3 different forms of AtCYP38, we obtained 6 thylakoid membrane proteins and 9 thylakoid lumenal proteins as interacting proteins of AtCYP38. We further confirmed the localization of several identified proteins and their interaction between AtCYP38.ConclusionsAfter analysis with two web-based tools and yeast two-hybrid screenings against two different libraries, we identified a couple of potential interacting proteins, which could be functionally related to AtCYP38. We believe that the results will lay a foundation for unveiling the working mechanism of AtCYP38 in photosynthesis.

scholarly journals Plant microRNAs: biogenesis, gene silencing, web-based analysis tools and their use as molecular markers

3 Biotech ◽  
2019 ◽  
Vol 9 (11) ◽  
Author(s):  
Sandhya Tyagi ◽  
Sandeep Sharma ◽  
Showkat Ahmad Ganie ◽  
Mohd. Tahir ◽  
Reyazul Rouf Mir ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Gene Silencing ◽  
Web Based ◽  
Analysis Tools

scholarly journals Web-based tools and approaches to study long-range gene regulation in Metazoa

2009 ◽  
Vol 8 (4) ◽  
pp. 231-242 ◽  
Author(s):  
D. Fredman ◽  
P. G. Engstrom ◽  
B. Lenhard
Keyword(s):  
Gene Regulation ◽  
Long Range ◽  
Web Based ◽  
Approaches To Study

scholarly journals Web based algorithms EvoPrinter and cis-Decoder reveal functional sequences in enhancers and complex networks of transcription factor interactions required for gene regulation

2011 ◽  
Vol 356 (1) ◽  
pp. 110
Author(s):  
Thomas Brody ◽  
Alexander Kuzin ◽  
Mukta Kundu ◽  
Jermaine Ross ◽  
Leonard Tyson ◽  
...  
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Complex Networks ◽  
Web Based ◽  
Factor Interactions

The PBL-Evaluator: a web-based tool for assessment in tutorials

1998 ◽  
Vol 62 (9) ◽  
pp. 671-674
Author(s):  
JF Chaves ◽  
JA Chaves ◽  
MS Lantz
Keyword(s):  
Web Based

Using Popular Mobile Devices in Voice Therapy

2013 ◽  
Vol 23 (3) ◽  
pp. 82-87 ◽  
Author(s):  
Eva van Leer
Keyword(s):  
Exercise Behavior ◽  
Voice Therapy ◽  
Pure Oxygen ◽  
Mobile Platforms ◽  
Self Monitoring ◽  
Web Based ◽  
Motivational Messages ◽  
Related Information ◽  
Health Related ◽  
Tailored Approach

Mobile tools are increasingly available to help individuals monitor their progress toward health behavior goals. Commonly known commercial products for health and fitness self-monitoring include wearable devices such as the Fitbit© and Nike + Pedometer© that work independently or in conjunction with mobile platforms (e.g., smartphones, media players) as well as web-based interfaces. These tools track and graph exercise behavior, provide motivational messages, offer health-related information, and allow users to share their accomplishments via social media. Approximately 2 million software programs or “apps” have been designed for mobile platforms (Pure Oxygen Mobile, 2013), many of which are health-related. The development of mobile health devices and applications is advancing so quickly that the Food and Drug Administration issued a Guidance statement with the purpose of defining mobile medical applications and describing a tailored approach to their regulation.

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