Recent Advances in the Open Access Cheminformatics Toolkits, Software Tools, Workflow Environments, and Databases
Pravin Sundarao Ambure, Rahul Balasaheb Aher, Kunal Roy · Methods in pharmacology and toxicology · 2014
Cheminformatics utilizes various computational techniques to solve a wide variety of drug discovery problems, including drug design and predictive toxicology. These computational exercises employ various toolkits/libraries, workflows, databases, etc. for their applications in lead optimization, virtual screening, chemical database mining, structure-activity/toxicity studies, etc. It is therefore important for such techniques to be freely available. Open-access resources permit free use and redistribution of a product via a free license, while open-source resources also provide source code that can be utilized to modify the product. In order to extract the knowledge from enormous amount of data that accumulates at a staggering rate, open-access or open-source cheminformatics packages also need to be efficient and user-friendly. In this chapter, we record the recent advances in freely available (including both open access and open source) cheminformatics toolkits, software (stand-alone and online applications), workflow environment, and databases. The objective of this chapter is to get the readers acquainted with the freely available resources, so that they can utilize those tools for solving different drug discovery challenges. We will start with the toolkit/libraries such as Chemistry Development Kit (CDK), Open Babel, RDKit, ChemmineR, Indigo, chem f , etc., which provide various functionalities that can aid researchers to develop their own cheminformatics software/applications. Next we will discuss various cheminformatics software tools, including iDrug, PharmDock, DecoyFinder, DemQSAR, Chembench, etc. which have recently been developed with a wide variety of applications. We will further discuss workflow environments, including Konstanz Information Miner (KNIME), Taverna, recent combinations, i.e., CDK-KNIME or CDK-Taverna and their contributions in the cheminformatics field. At the end, we will briefly touch various recent databases, such as QSAR DataBank, VAMMPIRE, CREDO, PubChem3D, MMsINC, etc., and their applications. The open-access resources covered in this chapter would enable the medicinal chemists and cheminformaticians to solve various problems encountered during their research.