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ChemDes specifications

Information


Unique identifier OMICS_12100
Name ChemDes
Interface Web user interface
Restrictions to use None
Programming languages Java, Javascript, Python
Computer skills Basic
Version 15.11.11
Stability Stable
Requirements
HTML5
Maintained Yes

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Maintainer


  • person_outline Wen Bin Zeng

Publication for ChemDes

ChemDes citations

 (6)
library_books

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

2018
J Cheminform
PMCID: 5861255
PMID: 29556758
DOI: 10.1186/s13321-018-0270-2

[…] es and other drug discovery processes []. In terms of molecular representation importance, some web servers and stand-alone programs, such as RDKit [], CDK [], rcdk, PaDEL [], Cinfony [], Chemopy [], ChemDes [], BioJava [], BioTriangle [], bioclipse [], propy [], PyDPI [], Biopython, repDNA [], CDK-Taverna [], protr/protrWeb [], ChemmineR [], and Rcpi [] have been established to calculate such des […]

library_books

In Silico Prediction of Chemical Toxicity for Drug Design Using Machine Learning Methods and Structural Alerts

2018
PMCID: 5826228
PMID: 29515993
DOI: 10.3389/fchem.2018.00030

[…] cs toolkits such as PaDEL-Descriptor (Yap, ), OpenBabel (O'Boyle et al., ), CDKit (Steinbeck et al., ), RDKit (Landrum, ), or web servers like E-Dragon (Tetko et al., ), ChemBCPP (Dong et al., ), and ChemDes (Dong et al., ). Using numeric features may result in overfitting when the size of training set is small (Xue et al., ). Hence, feature selection should be done before model building, to reduc […]

library_books

Mordred: a molecular descriptor calculator

2018
J Cheminform
PMCID: 5801138
PMID: 29411163
DOI: 10.1186/s13321-018-0258-y

[…] tor calculation programs do not have a user-friendly interface and/or it is difficult to set up the environment. Thus, several web-based descriptor calculation interfaces have been developed, such as ChemDes [] and BioTriangle []. ChemDes can calculate all descriptors that can be calculated by ChemoPy, CDK, RDKit, Open Babel, BlueDesc, and PaDEL. Moreover, BioTriangle can manipulate not only small […]

call_split

Multi Target Screening and Experimental Validation of Natural Products from Selaginella Plants against Alzheimer's Disease

2017
Front Pharmacol
PMCID: 5574911
PMID: 28890698
DOI: 10.3389/fphar.2017.00539
call_split See protocol

[…] the model (Cao et al., ,; Yun et al., ). RFs were trained using the RF library in the statistical computing environment, R. All the fingerprints were calculated by some tools developed by our group: ChemDes, BioTriangle webserver and ChemoPy package (Cao et al., ; Dong et al., , ). To improve the prediction ability of the SAR model, we assembled all fingerprint models to obtain the consensus mode […]

library_books

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

2017
J Cheminform
PMCID: 5461230
DOI: 10.1186/s13321-017-0220-4

[…] functionality available in larger systems, a number of projects have employed the CDK as a general cheminformatics toolkit. Examples include jCompoundMapper [], ScaffoldHunter [, ], OMG [], PaDEL [], ChemDes [], ReactPRED [], SMSD [–], WhichCyp [], MetaPrint2D [], MetFrag [], and the IUPHAR/BPS Guide to Pharmacology [], BRENDA [] and QSAR DataBank [] databases. A number of such tools were initiall […]

call_split

Dataset of curcumin derivatives for QSAR modeling of anti cancer against P388 cell line

2016
PMCID: 5061127
PMID: 27752528
DOI: 10.1016/j.dib.2016.09.036
call_split See protocol

[…] f the dataset were sketched using Chemdraw 6.0 software and converted using ChemBio 3D ultra and then followed by energy minimization using MM2 force field .Molecular descriptors were generated using ChemDes software package for each compound for then these descriptors were reduced to a set of descriptors which is as small as possible but are rich information. Correlation matrix was then applied […]

Citations

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ChemDes institution(s)
School of Pharmaceutical Sciences, Central South University, Changsha, China; Department of Biostatistics, School of Public Health, University of Texas Health Science Center at Houston, Houston, USA; Xiangya Hospital, Central South University, Changsha, China; College of Chemistry and Chemical Engineering, Central South University, Changsha, China; Institute of Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tong, Hong Kong People's China
ChemDes funding source(s)
This work is financially supported by grants from the Project of Innovationdriven Plan in Central South University, the National Natural Science Founda tion of China (Grants No. 81402853), and the Postdoctoral Science Foundation of Central South University, the Chinese Postdoctoral Science Foundation (2014T70794, 2014M562142).

ChemDes reviews

 (2)
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changfulu

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Web
A good platform that can be used to calculate different types of molecular descriptors and fingerprints. So far it is the most comprehensive tool.
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Anonymous user #5405

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Web
It's a useful web server.