ChemDes: an integrated web-based platform for molecular descriptor and fingerprint computation

By Jie Dong, Dongsheng Cao, Hongyu Miao, Shao Liu, Bai-Chuan Deng, Yong-Huan Yun, Ning-Ning Wang, Aiping Lu, Wenbin Zeng, Alex F. Chen. 2015

349 citations recorded by the source corpus.

AbstractBackground 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.

Subfields: Computational Theory and Mathematics, Molecular Biology, Safety Research

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Citations in the corpus

Mordred: a molecular descriptor calculator (2018, methodology): “Thus, several web-based descriptor calculation interfaces have been developed, such as ChemDes [25] and BioTriangle [26].”
ADMETlab: a platform for systematic ADMET evaluation based on a comprehensively collected ADMET database (2018, methodology): “We use Python - RDKit [15], Pybel to wrap molecules; [16] use Chemopy [17] ChemDes [18] and BioTriangle [19] to calculate molecular descriptors and fingerprints; use Scikit - learn to build models of different algorithms; [20] use Numpy [21], Pandas to wrap calculating results into numeric values…”
The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching (2017, methodology): “Examples include jCompoundMapper [11], ScaffoldHunter [12, 13], OMG [14], PaDEL [15], ChemDes [16], ReactPRED [17], SMSD [18–20], WhichCyp [21], MetaPrint2D [22], MetFrag [23], and the IUPHAR/BPS Guide to Pharmacology [24], BRENDA [25] and QSAR DataBank [26] databases.”