scholarly journals miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Tomas Barta ◽  
Lucie Peskova ◽  
Ales Hampl
Keyword(s):  
In Silico ◽  
Web Based ◽  
Mirna Sponge

scholarly journals A Web-based Tool for in Silico Biomarker Discovery Based on Tissue-specific Protein Profiles in Normal and Cancer Tissues

2007 ◽  
Vol 7 (5) ◽  
pp. 825-844 ◽  
Author(s):  
Erik Björling ◽  
Cecilia Lindskog ◽  
Per Oksvold ◽  
Jerker Linné ◽  
Caroline Kampf ◽  
...  
Keyword(s):  
In Silico ◽  
Biomarker Discovery ◽  
Specific Protein ◽  
Protein Profiles ◽  
Web Based ◽  
Tissue Specific ◽  
Cancer Tissues

scholarly journals mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes

2010 ◽  
Vol 38 (suppl_2) ◽  
pp. W194-W200 ◽  
Author(s):  
Yucheng Shao ◽  
Xinyi He ◽  
Ewan M. Harrison ◽  
Cui Tai ◽  
Hong-Yu Ou ◽  
...  
Keyword(s):  
In Silico ◽  
Subtractive Hybridization ◽  
Hybridization Analysis ◽  
Bacterial Genomes ◽  
Web Based

scholarly journals A Free Web-Based Protocol to Assist Structure-Based Virtual Screening Experiments

2019 ◽  
Vol 20 (18) ◽  
pp. 4648 ◽  
Author(s):  
Nathalie Lagarde ◽  
Elodie Goldwaser ◽  
Tania Pencheva ◽  
Dessislava Jereva ◽  
Ilza Pajeva ◽  
...  
Keyword(s):  
Drug Discovery ◽  
Virtual Screening ◽  
Web Service ◽  
Molecular Mechanics ◽  
In Silico ◽  
Chemical Biology ◽  
In Silico Screening ◽  
Web Based ◽  
Screening Experiments ◽  
The Web

Chemical biology and drug discovery are complex and costly processes. In silico screening approaches play a key role in the identification and optimization of original bioactive molecules and increase the performance of modern chemical biology and drug discovery endeavors. Here, we describe a free web-based protocol dedicated to small-molecule virtual screening that includes three major steps: ADME-Tox filtering (via the web service FAF-Drugs4), docking-based virtual screening (via the web service MTiOpenScreen), and molecular mechanics optimization (via the web service AMMOS2 [Automatic Molecular Mechanics Optimization for in silico Screening]). The online tools FAF-Drugs4, MTiOpenScreen, and AMMOS2 are implemented in the freely accessible RPBS (Ressource Parisienne en Bioinformatique Structurale) platform. The proposed protocol allows users to screen thousands of small molecules and to download the top 1500 docked molecules that can be further processed online. Users can then decide to purchase a small list of compounds for in vitro validation. To demonstrate the potential of this online-based protocol, we performed virtual screening experiments of 4574 approved drugs against three cancer targets. The results were analyzed in the light of published drugs that have already been repositioned on these targets. We show that our protocol is able to identify active drugs within the top-ranked compounds. The web-based protocol is user-friendly and can successfully guide the identification of new promising molecules for chemical biology and drug discovery purposes.

scholarly journals epiTAD: a web application for visualizing chromosome conformation capture data in the context of genetic epidemiology

2019 ◽  
Vol 35 (21) ◽  
pp. 4462-4464
Author(s):  
Jordan H Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N Monteiro ◽  
Travis A Gerke
Keyword(s):  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Large Scale ◽  
Source Code ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data

Abstract Summary Complementary advances in genomic technology and public data resources have created opportunities for researchers to conduct multifaceted examination of the genome on a large scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic 3D organization and annotations across multiple databases in an interactive manner to facilitate in silico discovery. Availability and implementation epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/ where we have additionally made publicly available the source code and a Docker containerized version of the application.

scholarly journals UBioLab: a web-LABoratory for Ubiquitous in-silico experiments

2012 ◽  
Vol 9 (1) ◽  
pp. 12-31 ◽  
Author(s):  
E. Bartocci ◽  
M. R. Di Berardini ◽  
E. Merelli ◽  
L. Vito
Keyword(s):  
In Silico ◽  
Domain Knowledge ◽  
Semantic Knowledge ◽  
Semantic Heterogeneity ◽  
Web Based ◽  
Agent Based ◽  
Architectural Features ◽  
Physical Laboratory ◽  
Distributed Execution ◽  
Grid Nodes

Summary The huge and dynamic amount of bioinformatic resources (e.g., data and tools) available nowadays in Internet represents a big challenge for biologists -for what concerns their management and visualization- and for bioinformaticians -for what concerns the possibility of rapidly creating and executing in-silico experiments involving resources and activities spread over the WWW hyperspace. Any framework aiming at integrating such resources as in a physical laboratory has imperatively to tackle -and possibly to handle in a transparent and uniform way- aspects concerning physical distribution, semantic heterogeneity, co-existence of different computational paradigms and, as a consequence, of different invocation interfaces (i.e., OGSA for Grid nodes, SOAP for Web Services, Java RMI for Java objects, etc.). The framework UBioLab has been just designed and developed as a prototype following the above objective. Several architectural features -as those ones of being fully Web-based and of combining domain ontologies, Semantic Web and workflow techniques- give evidence of an effort in such a direction.The integration of a semantic knowledge management system for distributed (bioinformatic) resources, a semantic-driven graphic environment for defining and monitoring ubiquitous workflows and an intelligent agent-based technology for their distributed execution allows UBioLab to be a semantic guide for bioinformaticians and biologists providing (i) a flexible environment for visualizing, organizing and inferring any (semantics and computational) “type” of domain knowledge (e.g., resources and activities, expressed in a declarative form), (ii) a powerful engine for defining and storing semantic-driven ubiquitous in-silico experiments on the domain hyperspace, as well as (iii) a transparent, automatic and distributed environment for correct experiment executions.

scholarly journals epiTAD: a web application for visualizing high throughput chromosome conformation capture data in the context of genetic epidemiology

2018 ◽  
Author(s):  
Jordan H. Creed ◽  
Garrick Aden-Buie ◽  
Alvaro N. Monteiro ◽  
Travis A. Gerke
Keyword(s):  
High Throughput ◽  
Genetic Epidemiology ◽  
In Silico ◽  
Web Application ◽  
Chromosome Conformation Capture ◽  
Chromosome Conformation ◽  
Web Based ◽  
Genome Wide ◽  
Public Data ◽  
Complex Scale

AbstractThe increasing availability of public data resources coupled with advancements in genomic technology has created greater opportunities for researchers to examine the genome on a large and complex scale. To meet the need for integrative genome wide exploration, we present epiTAD. This web-based tool enables researchers to compare genomic structures and annotations across multiple databases and platforms in an interactive manner in order to facilitate in silico discovery. epiTAD can be accessed at https://apps.gerkelab.com/epiTAD/.

scholarly journals In Silico Design of PCR Primers to Amplify the Salt Tolerance Gene in Soybean

2018 ◽  
Vol 6 (6) ◽  
Author(s):  
Florentina Kusmiyati ◽  
Sutarno Sutarno ◽  
Bagus Herwibawa
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
In Silico ◽  
Pcr Primers ◽  
Significant Similarity ◽  
Web Based ◽  
Conserved Region ◽  
Tolerance Gene ◽  
Salt Tolerance Gene ◽  
Primer Sequence

Soybean yield is decreased because of many stresses such as salt stress. Ionic and osmotic stresses are the effects of salt stress. An effective way of maintaining sustainable production in salt-affected soil is through breeding high salt tolerance soybean, which can be detected by PCR. The optimal PCR plays an important role in gene expression analysis. The success of a PCR-based method largely depends on the optimal primer sequence analysis in silico prior to a wet-bench experiment. Here we described designing of primer using web-based tools. Many types of online primer design software are available, which can be used free of charge to design desirable primers. The objective was to design of PCR primers to amplify the salt tolerance gene in soybean. A highly conserved region of 411 bases was detected by Clustal Omega. Primers were predicted using Primer3 based on conserved region, considering ideal conditions for primer length, hairpin, dimer, Tm, and GC%. The predicted forward and reverse primers were validated using NetPrimer. Both forward and reverse primers have shown significant similarity with salt tolerance gene and recommended to be used to amplify the salt tolerance gene in soybean.

scholarly journals The CombineArchiveWeb application – A web based tool to handle files associated with modelling results

2014 ◽  
Author(s):  
Martin Scharm ◽  
Florian Wendland ◽  
Martin Peters ◽  
Markus Wolfien ◽  
Tom Theile ◽  
...  
Keyword(s):  
Computational Biology ◽  
In Silico ◽  
Simulation Studies ◽  
Meta Data ◽  
Web Based ◽  
Manual Handling ◽  
The Web

Sharing in silico experiments is essential for the advance of research in computational biology. Consequently, the COMBINE archive was designed as a digital container format. It eases the management of files related to a modelling result, fosters collaboration, and ultimately enables the exchange of reproducible simulation studies. However, manual handling of COMBINE archives is tedious and error prone. We therefore developed the CombineArchiveWeb application to support scientists in promoting and publishing their research by means of creating, exploring, modifying, and sharing archives. All files are equipped with meta data and can be distributed over the Web through shareable workspaces.

In vivo analgesic effect of different extracts of Hopea odorata leaves in mice and in silico molecular docking and ADME/T property analysis of some isolated compounds from this plant

2018 ◽  
Vol 30 (1) ◽  
pp. 121-130 ◽  
Author(s):  
Md. Sajjad Ul Hoque ◽  
Mohammed Sohel Chowdhury ◽  
Arkajyoti Paul ◽  
Jackie Barua ◽  
Syeda Sakiatuz Zannat ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Analgesic Activity ◽  
In Silico ◽  
Analgesic Effect ◽  
Ethanolic Extract ◽  
Web Based ◽  
Lipinski’S Rule ◽  
In Silico Molecular Docking ◽  
Hopea Odorata

AbstractBackgroundThe current study evaluates the analgesic effect of different extracts ofHopea odorataleaves in mice followed by molecular docking and absorption, distribution, metabolism, excretion, and toxicity (ADME/T) analysis of isolated compounds derived from the plant with the COX-1 enzyme.MethodsIn the present study, the dried leaves ofH. odoratawere subjected to extraction using methanol, ethanol, and water.In vivoanalgesic activity was evaluated by using the acetic acid-induced writhing test and formalin-induced paw licking test, andin silicomolecular docking and ADME/T study were performed using Schrödinger Maestro (version 11.1) and online-based tools, respectively, on eight isolated compounds.ResultsThe results showed that the methanolic extract of leaves has highest significant dose-dependent analgesic activity at both 200 and 400 mg/kg followed by ethanolic extract of leaves. Among all the compounds, ampelopsin showed the best docking score of −7.055, ensuring strong binding affinity between the ligand and the receptor, and ADME/T analysis using Web-based tools ensures the compound has not violated Lipinski’s rule of five indicating its safety consumption.ConclusionsThe result confirms the analgesic activity ofH. odorataleaves in bothin vivoandin silicoassays. The data support ampelopsin to be a potent analgesic compound worthy of future clinical trials and its “drug-likeliness”

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