Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F16%3A10336781" target="_blank" >RIV/00216208:11320/16:10336781 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1186/s13321-016-0186-7" target="_blank" >http://dx.doi.org/10.1186/s13321-016-0186-7</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1186/s13321-016-0186-7" target="_blank" >10.1186/s13321-016-0186-7</a>

Result language

angličtina

Original language name

Scaffold analysis of PubChem database as background for hierarchical scaffold-based visualization

Original language description

Background Visualization of large molecular datasets is a challenging yet important topic utilised in diverse fields of chemistry ranging from material engineering to drug design. Especially in drug design, modern methods of high-throughput screening generate large amounts of molecular data that call for methods enabling their analysis. One such method is classification of compounds based on their molecular scaffolds, a concept widely used by medicinal chemists to group molecules of similar properties. This classification can then be utilized for intuitive visualization of compounds. Results In this paper, we propose a scaffold hierarchy as a result of large-scale analysis of the PubChem Compound database. The analysis not only provided insights into scaffold diversity of the PubChem Compound database, but also enables scaffold-based hierarchical visualization of user compound data sets on the background of empirical chemical space, as defined by the PubChem data, or on the background of any other user-defined data set. The visualization is performed by a web based client-server application called Scaffvis. It provides an interactive zoomable tree map visualization of data sets up to hundreds of thousands molecules. Scaffvis is free to use and its source codes have been published under an open source license.

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

IN - Informatics

OECD FORD branch

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Project

<a href="/en/project/GP14-29032P" target="_blank" >GP14-29032P: Efficient chemical space exploration using multi-objective optimization</a><br>

Continuities

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Publication year

2016

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Cheminformatics

ISSN

1758-2946

e-ISSN

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Volume of the periodical

8

Issue of the periodical within the volume

12

Country of publishing house

GB - UNITED KINGDOM

Number of pages

14

Pages from-to

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UT code for WoS article

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EID of the result in the Scopus database

2-s2.0-85007505718