Abstract
Background Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Since the calculation of such quantitative representations of molecules may require substantial computational skills and efforts, several tools have been previously developed to make an attempt to ease the process. However, there are still several hurdles for users to overcome to fully harness the power of these tools. First, most of the tools are distributed as standalone software or packages that require necessary configuration or programming efforts of users. Second, many of the tools can only calculate a subset of molecular descriptors, and the results from multiple tools need to be manually merged to generate a comprehensive set of descriptors. Third, some packages only provide application programming interfaces and are implemented in different computer languages, which pose additional challenges to the integration of these tools.Results A freely available web-based platform, named ChemDes, is developed in this study. It integrates multiple state-of-the-art packages (i.e., Pybel, CDK, RDKit, BlueDesc, Chemopy, PaDEL and jCompoundMapper) for computing molecular descriptors and fingerprints. ChemDes not only provides friendly web interfaces to relieve users from burdensome programming work, but also offers three useful and convenient auxiliary tools for format converting, MOPAC optimization and fingerprint similarity calculation. Currently, ChemDes has the capability of computing 3679 molecular descriptors and 59 types of molecular fingerprints.ConclusionChemDes provides users an integrated and friendly tool to calculate various molecular descriptors and fingerprints. It is freely available at http://www.scbdd.com/chemdes. The source code of the project is also available as a supplementary file.Graphical abstract:An overview of ChemDes. A platform for computing various molecular descriptors and fingerprints
Highlights
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes
Besides their extensive usage in the aforementioned regular applications (e.g., QSAR/ QSPR modeling based on machine learning techniques [13,14,15,16]), molecular descriptors and fingerprints are shown to have a significant potential to play a critical role in studies of current scientific interests, such as the identification of biomolecular targets and the network analysis of protein–ligand interactions
We developed a freely-available web-based platform called ChemDes, which provides an online service to the public for calculating a variety of molecular descriptors and fingerprints conveniently and instantly
Summary
Molecular descriptors and fingerprints have been routinely used in QSAR/SAR analysis, virtual drug screening, compound search/ranking, drug ADME/T prediction and other drug discovery processes. Molecular descriptors are experimentally-measured or theoretically-derived properties of a molecule [1] They are quantitative representations of physical, chemical or topological characteristics of molecules that summarize our knowledge and understanding of. Various molecular descriptors and fingerprints have been developed in previous studies for quantitative molecular representation. Besides their extensive usage in the aforementioned regular applications (e.g., QSAR/ QSPR modeling based on machine learning techniques [13,14,15,16]), molecular descriptors and fingerprints are shown to have a significant potential to play a critical role in studies of current scientific interests, such as the identification of biomolecular targets and the network analysis of protein–ligand interactions. Molecular descriptors or fingerprints were used to characterize the structural information of amino acids or nucleotides for developing more effective protein or RNA/DNA descriptors [24,25,26]
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