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HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data

Denis Fourches, Maria F. Sassano, Bryan L. Roth, Alexander Tropsha
2013 Computer applications in the biosciences : CABIOS  
We report on the development of the high-throughput screening (HTS) Navigator software to analyze and visualize the results of HTS of chemical libraries.  ...  The software is freely available for academic laboratories.  ...  Network-MLSCN) conducting high-throughput screening (HTS) comes the need for processing HTS results efficiently.  ... 
doi:10.1093/bioinformatics/btt718 pmid:24376084 pmcid:PMC3928525 fatcat:hm3bxz5ug5a45gusenroj5hr7m

HTS navigator: freely accessible cheminformatics software for analyzing high-throughput screening data

Bryan L. Roth, Denis Fourches, Alexander Tropsha, Maria F. Sassano
2014
Summary: We report on the development of the high-throughput screening (HTS) Navigator software to analyze and visualize the results of HTS of chemical libraries.  ...  The software is freely available for academic laboratories.  ...  Network-MLSCN) conducting high-throughput screening (HTS) comes the need for processing HTS results efficiently.  ... 
doi:10.17615/a39s-h534 fatcat:tohssyuxszg2pmopxncoccefty

Fishing out the signal in polypharmacological high-throughput screening data using novel navigator cheminformatics software

Denis Fourches, Alexander Tropsha
2014 Journal of Cheminformatics  
We have developed the freely-accessible HTS Navigator software to enable and facilitate the processing and analysis of polypharmacological HTS data.  ...  Thus, prospective drug discovery studies often start by testing large compound libraries in multiple and diverse High-Throughput Screening (HTS) assays.  ...  We have developed the freely-accessible HTS Navigator software to enable and facilitate the processing and analysis of polypharmacological HTS data.  ... 
doi:10.1186/1758-2946-6-s1-p14 pmcid:PMC3980057 fatcat:wmbwsgudgvgjfovrs3qn7pxh4q

Advances in Cheminformatics Methodologies and Infrastructure to Support the Data Mining of Large, Heterogeneous Chemical Datasets

Rajarshi Guha, Kevin Gilbert, Geoffrey Fox, Marlon Pierce, David Wild, Huapeng Yuan
2010 Current Computer - Aided Drug Design  
Equally important is the ability for non-experts to access and utilize state of the art cheminformatics method and models.  ...  Given that the above work is applicable to arbitrary types of cheminformatics problems, we also present some case studies related to virtual screening for anti-malarials and predictions of anti-cancer  ...  Jean-Claude Bradley for synthesizing the Ugi products identified in our docking procedure and Prof. Philip Rosenthal (UCSF) for performing the assays.  ... 
doi:10.2174/157340910790980115 pmid:20370695 fatcat:5qjtgrpemnbkfjlzmrvgrev5le

Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO)

Uma D. Vempati, Magdalena J. Przydzial, Caty Chung, Saminda Abeyruwan, Ahsan Mir, Kunie Sakurai, Ubbo Visser, Vance P. Lemmon, Stephan C. Schürer, Dermot Cox
2012 PLoS ONE  
Huge amounts of high-throughput screening (HTS) data for probe and drug development projects are being generated in the pharmaceutical industry and more recently in the public sector.  ...  We used BAO to annotate assays from the largest public HTS data repository, PubChem, and demonstrate its utility to categorize and analyze diverse HTS results from numerous experiments.  ...  Introduction High-throughput screening (HTS) has become the most common approach to identify starting points for the development of novel drugs [1] .  ... 
doi:10.1371/journal.pone.0049198 pmid:23155465 pmcid:PMC3498356 fatcat:u5ez2f43fzbkdfw4z62z2gp7cu

The CompTox Chemistry Dashboard: a community data resource for environmental chemistry

Antony J. Williams, Christopher M. Grulke, Jeff Edwards, Andrew D. McEachran, Kamel Mansouri, Nancy C. Baker, Grace Patlewicz, Imran Shah, John F. Wambaugh, Richard S. Judson, Ann M. Richard
2017 Journal of Cheminformatics  
Despite an abundance of online databases providing access to chemical data, there is increasing demand for highquality, structure-curated, open data to meet the various needs of the environmental sciences  ...  This facilitates fast access to available structure, property, toxicity, and bioassay data for collections of chemicals (hundreds to thousands at a time).  ...  of high-throughput and high-content screening (HTS and HCS) assays.  ... 
doi:10.1186/s13321-017-0247-6 pmid:29185060 pmcid:PMC5705535 fatcat:bnea633xifbhbjd7zbsqmxcdku

"Molecular Anatomy": a new multi-dimensional hierarchical scaffold analysis tool

Candida Manelfi, Marica Gemei, Carmine Talarico, Carmen Cerchia, Anna Fava, Filippo Lunghini, Andrea Rosario Beccari
2021 Journal of Cheminformatics  
contributing to perform high quality SAR analysis.  ...  The protocol is freely available as a web interface at https://ma.exscalate.eu.  ...  frameworks identified according to increased values of EF within the cluster analyzed in Abbreviations HTS: High-throughput screening; SAR: Structure activity relationships; MCS: Maximum Common Substructure  ... 
doi:10.1186/s13321-021-00526-y pmid:34301327 pmcid:PMC8299179 fatcat:s4zvgu7z2nbdfp55w6okj7srxm

Targeted classification of metal-organic frameworks in the Cambridge structural database (CSD)

Peyman Z Moghadam, Aurelia Li, Xiao-Wei Liu, Rocio Bueno-Perez, Shudong Wang, Seth Wiggin, Peter Andrew Wood, David Fairen-Jimenez
2020 Chemical Science  
We also show the usefulness of these tools with a high-throughput screening for hydrogen storage at room temperature using grand canonical Monte Carlo simulations.  ...  Although high-throughput screening has been widely performed on MOFs for hydrogen storage, very little work published results at these conditions. 72 In addition, the classification presented in this  ... 
doi:10.1039/d0sc01297a pmid:33384860 pmcid:PMC7690317 fatcat:2qozmwowgzapfitp5bzpvkapxi

Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences

Colin L. Bird, Jeremy G. Frey
2013 Chemical Society Reviews  
Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the  ...  , and analysing "big data".  ...  On the other hand, data sets generated by high-throughput screening (HTS), while homogeneous, can be very large.  ... 
doi:10.1039/c3cs60050e pmid:23686012 fatcat:dibiolkg4zgixp6npavea765ze

ChemTreeMap: an interactive map of biochemical similarity in molecular datasets

Jing Lu, Heather A. Carlson
2016 Bioinformatics  
Computational biology often incorporates diverse chemical data to probe a biological question, but the existing tools for chemical data are ill-suited for the very large datasets inherent to bioinformatics  ...  Biologists need an interactive tool for visualizing chemical information in an intuitive, accessible way that facilitates its integration into today's team-based biological research.  ...  Acknowledgements We thank Chemical Computing Group for their generous donation of the MOE software package. J.L. thanks the entire Carlson lab for constructive feedback.  ... 
doi:10.1093/bioinformatics/btw523 pmid:27515740 pmcid:PMC5181537 fatcat:fhf62j5q7bekpkyd43kpaio4xm

QSAR without borders

Eugene N. Muratov, Jürgen Bajorath, Robert P. Sheridan, Igor V. Tetko, Dmitry Filimonov, Vladimir Poroikov, Tudor I. Oprea, Igor I. Baskin, Alexandre Varnek, Adrian Roitberg, Olexandr Isayev, Stefano Curtalolo (+7 others)
2020 Chemical Society Reviews  
QSAR-like approaches in genomics Genomic and HTS (high throughput screening) data have rarely been subjected to QSAR analyses.  ...  However, high throughput driven biomedical knowledge accumulation has created an urgent need for Big Data analytics in genomics and HTS to help with the evaluation, interpretation, and integration of data  ... 
doi:10.1039/d0cs00098a pmid:32356548 fatcat:l456rjoqbzgehkqa63uvqrv2gy

In silico approach in reveal traditional medicine plants pharmacological material basis

Fan Yi, Li Li, Li-jia Xu, Hong Meng, Yin-mao Dong, Hai-bo Liu, Pei-gen Xiao
2018 Chinese Medicine  
We also survey common databases, software programs and website tools that can be used for virtual screening and pharmacological network construction.  ...  In this review, we first provide a detailed research routine for examining traditional medicinal plants by in silico techniques and elaborate on their theoretical principles.  ...  Jun Xu (Research Centerfor Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou) for his valuable suggestions.  ... 
doi:10.1186/s13020-018-0190-0 pmid:29946351 pmcid:PMC6006786 fatcat:btf7nau2wbeyrkrgxvuvvkn26i

The 18th European Symposium on Quantitative Structure–Activity Relationships

Anna Tsantili-Kakoulidou, Dimitris K Agrafiotis
2011 Expert Opinion on Drug Discovery  
The authors are also thankful to Biobyte Corp. and Dr Hansch and Dr Leo for their support and free access to the C-QSAR program.  ...  Acknowledgements: AMBIT software was developed within the framework of CEFIC LRI project EEM-9 and extended under subsequent CEFIC LRI contract for developing AmbitXT.  ...  The data were compiled in an ad hoc application based on the ACCESS software.  ... 
doi:10.1517/17460441.2011.560604 pmid:22646021 fatcat:tb4bhvtnpzahxm4xba7iw4afuy

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
Fernando Palluzzi for numerous discussions regarding the data model. This work was supported by a PRIN awarded to Prof. Stefano Ceri.  ...  Peter Robinson (Charité -Universitätsmedizin Berlin) for the helpful discussions.  ...  In contrast, norfenfluramine exhibited high affinity for 5-HT(2B) and 5-HT(2C) receptors and more moderate affinity for 5-HT(2A) receptors.  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

Eu Us Roadmap Nanoinformatics 2030 [article]

Haase, Klaessig
2018 Zenodo  
At the same time, André Nel and collaborators proposed to employ QSAR-like methods for NM High Throughput Screening Data to assess NM safety [112] .  ...  A data-driven workflow applies new-generation high-throughput, high-content and omics technology in a systematic tiered framework to screen the effects of NMs and provide a comprehensive understanding  ...  Other questions of the survey addressed the main objective(s) of the database, database design and implementation, database availability/accessibility, the use of semantics technology methods, the data  ... 
doi:10.5281/zenodo.1486012 fatcat:yll2tsodjbgmlmyoyjfkcptxja
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