Chemical space visualization using ViFrame

Abstract

Exploration of the chemical space is an important component of drug discovery process and its importance grows with the increase in the computation power which allows to explore larger areas of the chemical space. Recently, there emerged new algorithms proposed to automatically generate and search for compounds (objects in the chemical space) with desired properties. Although these approaches can be a big help, human interaction is usually still inevitable in the end. Visualization of the space can help make sense of the generated data and therefore visualization techniques are usually an integral part of any task related to chemical space exploration. Currently, there exist methods dealing with visualization of the chemical space but there is no framework supporting simple development of new methods. The purpose of this paper is to introduce such a modular framework called ViFrame. ViFrame offers the possibility to implement every single part of the visualization pipeline consisting of steps such as reading and merging molecules from multiple data sources, applying transformations and, of course, visualization of the data set in 2D space. The advantage of the framework consists in providing an environment where the user can focus on the development of the previously mentioned tasks while the framework supports seamless integration of the developed components. The framework also incorporates an application that provides the user with graphical interface for modules manipulation and presentation of the visualization results. For simple utilization of the application without the necessity of implementation of one's own module, several visualization methods have been implemented.