MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing

Hilbig, Matthias; Rarey, Matthias

doi:10.1021/acs.jcim.5b00292

Cited by 29 publications

(23 citation statements)

References 29 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Most of the existing tools to analyze drug screening assays through clustering and visualization of compounds and their corresponding bioactivity measurements have been implemented as stand-alone tools requiring local installation, e.g. Scaffold Hunter ( 15 ), ChemTreeMap ( 16 ), Mona 2 ( 17 ) and Data warrior ( 18 ) or as a browser-based tool, e.g. ChemMineTools ( 19 ).…”

Section: Introductionmentioning

confidence: 99%

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

Ravikumar

Alam

Gopalacharyulu

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

The advent of polypharmacology paradigm in drug discovery calls for novel chemoinformatic tools for analyzing compounds’ multi-targeting activities. Such tools should provide an intuitive representation of the chemical space through capturing and visualizing underlying patterns of compound similarities linked to their polypharmacological effects. Most of the existing compound-centric chemoinformatics tools lack interactive options and user interfaces that are critical for the real-time needs of chemical biologists carrying out compound screening experiments. Toward that end, we introduce C-SPADE, an open-source exploratory web-tool for interactive analysis and visualization of drug profiling assays (biochemical, cell-based or cell-free) using compound-centric similarity clustering. C-SPADE allows the users to visually map the chemical diversity of a screening panel, explore investigational compounds in terms of their similarity to the screening panel, perform polypharmacological analyses and guide drug-target interaction predictions. C-SPADE requires only the raw drug profiling data as input, and it automatically retrieves the structural information and constructs the compound clusters in real-time, thereby reducing the time required for manual analysis in drug development or repurposing applications. The web-tool provides a customizable visual workspace that can either be downloaded as figure or Newick tree file or shared as a hyperlink with other users. C-SPADE is freely available at http://cspade.fimm.fi/.

show abstract

Section: Introductionmentioning

confidence: 99%

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

Ravikumar

Alam

Gopalacharyulu

et al. 2017

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…Seed fragments were modelled in SYBYL ® -X v1.1 [5] based on Structure Activity Relationship (SAR) data obtained from the literature [2] and through the generation of 2D topology maps using the software PoseView ® [7] (Figures 4-6). A total of 5 seed structures were generated (Figures 7-9).…”

Section: Methods 1: De Novo Drug Design Approachmentioning

confidence: 99%

Design and Optimisation of Novel Efflux Pump Inhibitors Using P-Glycoprotein as a Target

Bondin¹,

Shoemake²

2017

Drug Des

View full text Add to dashboard Cite

This project utilised Verapamil as a lead molecule for iterative design of novel anti-cancer drugs with the potential to inhibit P-Glycoprotein (P-gp), a target which is overexpressed in malignant cells. The protein data bank crystallographic deposition 4M2S, describing the bound co-ordinates of P-gp bound to the small antagonist molecule QZ59-RRR, was used as a template for this study. Two drug design approaches were employed-de novo design and virtual screening (VS). For the former, the SYBYL

show abstract

“…Recently, tools tailored to the specific needs of life scientists in the chemical biology, medicinal chemistry and pharmaceutical domain were developed. These include MONA 2 [21], Screening Assistant 2 [22], DataWarrior [23], the Chemical Space Mapper (CheS-Mapper) [16, 17] and the High-Throughput Screening Exploration Environment (HiTSEE) [24, 25]. The last two tools complement the workflow environment KNIME with a visualization node.…”

Section: Introductionmentioning

confidence: 99%

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery

et al. 2017

View full text Add to dashboard Cite

The era of big data is influencing the way how rational drug discovery and the development of bioactive molecules is performed and versatile tools are needed to assist in molecular design workflows. Scaffold Hunter is a flexible visual analytics framework for the analysis of chemical compound data and combines techniques from several fields such as data mining and information visualization. The framework allows analyzing high-dimensional chemical compound data in an interactive fashion, combining intuitive visualizations with automated analysis methods including versatile clustering methods. Originally designed to analyze the scaffold tree, Scaffold Hunter is continuously revised and extended. We describe recent extensions that significantly increase the applicability for a variety of tasks.

show abstract

MONA 2: A Light Cheminformatics Platform for Interactive Compound Library Processing

Cited by 29 publications

References 29 publications

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

C-SPADE: a web-tool for interactive analysis and visualization of drug screening experiments through compound-specific bioactivity dendrograms

Design and Optimisation of Novel Efflux Pump Inhibitors Using P-Glycoprotein as a Target

Scaffold Hunter: a comprehensive visual analytics framework for drug discovery

Contact Info

Product

Resources

About