Platform for Unified Molecular Analysis: PUMA

We introduce a free
platform for chemoinformatic-based diversity
analysis and visualization of chemical space of user supplied data
sets. Platform for Unified Molecular Analysis (PUMA) integrates metrics
used to characterize compound databases including visualization of
chemical space, scaffold content, and analysis of chemical diversity.
The user’s input is a file with SMILES, database names, and
compound IDs. PUMA computes molecular properties of pharmaceutical
relevance, Murcko scaffolds, and diversity analysis. The user can
interactively navigate through the graphs and export image files and
the raw data of the diversity calculations. The platform links two
public online resources: Consensus Diversity Plots for the assessment of global diversity and Activity Landscape
Plotter to analyze structure–activity relationships.
Herein, we describe the functionalities of PUMA and exemplify its
use through the analysis of compound databases of general interest.
PUMA is freely accessible at the authors web-site https://www.difacquim.com/d-tools/.

本研究介绍一款免费平台，可针对用户提供的数据集开展基于化学信息学（chemoinformatics）的多样性分析与化学空间可视化工作。统一分子分析平台（Platform for Unified Molecular Analysis，简称PUMA）整合了用于表征化合物数据库的多项指标，涵盖化学空间可视化、分子骨架组成分析以及化学多样性分析等内容。用户的输入为包含简化分子线性输入规范（SMILES）、数据库名称以及化合物ID的文件。PUMA可计算与药物研发相关的分子性质、默克骨架（Murcko scaffolds），并开展多样性分析。用户可交互式浏览各类图表，并导出多样性计算所得的图像文件与原始数据。该平台整合了两款公开在线资源：用于评估全局多样性的共识多样性图（Consensus Diversity Plots），以及用于分析构效关系（structure–activity relationships）的活性景观绘图器（Activity Landscape Plotter）。本文详述了PUMA的各项功能，并通过分析通用型化合物数据库示例展示其应用场景。用户可通过作者团队的官方网站https://www.difacquim.com/d-tools/免费访问该平台。