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. 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. ChemDes 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.

中文翻译：

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ChemDes：用于分子描述符和指纹计算的基于Web的集成平台。

分子描述符和指纹已常规用于QSAR / SAR分析，虚拟药物筛选，化合物搜索/排序，药物ADME / T预测和其他药物发现过程。由于分子的这种定量表示的计算可能需要大量的计算技能和精力，因此先前已经开发了几种工具来尝试简化该过程。但是，要充分利用这些工具的功能，用户仍需克服几个障碍。首先，大多数工具作为独立软件或软件包分发，需要用户进行必要的配置或编程工作。其次，许多工具只能计算分子描述符的子集，并且需要手动合并来自多个工具的结果以生成一组全面的描述符。第三，一些软件包仅提供应用程序编程接口，并以不同的计算机语言实现，这给这些工具的集成带来了额外的挑战。这项研究开发了一个免费的基于Web的平台，名为ChemDes。它集成了多个最新的软件包（即，Pybel，CDK，RDKit，BlueDesc，Chemopy，PaDEL和jCompoundMapper），用于计算分子描述符和指纹。ChemDes不仅提供友好的Web界面以减轻用户的繁琐编程工作，而且还提供了三个有用且方便的辅助工具，用于格式转换，MOPAC优化和指纹相似度计算。目前，ChemDes能够计算3679个分子描述符和59种类型的分子指纹。ChemDes为用户提供了一个集成的友好工具，可以计算各种分子描述符和指纹。可从http://www.scbdd.com/chemdes免费获得。该项目的源代码也可以作为补充文件使用。