TY - JOUR
T1 - ChemDes
T2 - An integrated web-based platform for molecular descriptor and fingerprint computation
AU - Dong, Jie
AU - Cao, Dong Sheng
AU - Miao, Hong Yu
AU - Liu, Shao
AU - Deng, Bai Chuan
AU - Yun, Yong Huan
AU - Wang, Ning Ning
AU - LYU, Aiping
AU - Zeng, Wen Bin
AU - Chen, Alex F.
N1 - Publisher Copyright:
© 2015 Dong et al.
PY - 2015/12/9
Y1 - 2015/12/9
N2 - 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. Conclusion: 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.
AB - 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. Conclusion: 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.
KW - Chemoinformatics
KW - Molecular descriptors
KW - Molecular fingerprints
KW - Molecular representation
KW - Online descriptor calculation
KW - QSAR/QSPR
UR - http://www.scopus.com/inward/record.url?scp=84949646594&partnerID=8YFLogxK
U2 - 10.1186/s13321-015-0109-z
DO - 10.1186/s13321-015-0109-z
M3 - Journal article
AN - SCOPUS:84949646594
SN - 1758-2946
VL - 7
JO - Journal of Cheminformatics
JF - Journal of Cheminformatics
IS - 1
M1 - 60
ER -