BioTriangle: A web-accessible platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions

Jie Dong, Zhi Jiang Yao, Ming Wen, Min Feng Zhu, Ning Ning Wang, Hong Yu Miao, Aiping LYU, Wen Bin Zeng, Dong Sheng Cao*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

23 Citations (Scopus)

Abstract

Background: More and more evidences from network biology indicate that most cellular components exert their functions through interactions with other cellular components, such as proteins, DNAs, RNAs and small molecules. The rapidly increasing amount of publicly available data in biology and chemistry enables researchers to revisit interaction problems by systematic integration and analysis of heterogeneous data. Currently, some tools have been developed to represent these components. However, they have some limitations and only focus on the analysis of either small molecules or proteins or DNAs/RNAs. To the best of our knowledge, there is still a lack of freely-available, easy-to-use and integrated platforms for generating molecular descriptors of DNAs/RNAs, proteins, small molecules and their interactions. Results: Herein, we developed a comprehensive molecular representation platform, called BioTriangle, to emphasize the integration of cheminformatics and bioinformatics into a molecular informatics platform for computational biology study. It contains a feature-rich toolkit used for the characterization of various biological molecules and complex interaction samples including chemicals, proteins, DNAs/RNAs and even their interactions. By using BioTriangle, users are able to start a full pipelining from getting molecular data, molecular representation to constructing machine learning models conveniently. Conclusion: BioTriangle provides a user-friendly interface to calculate various features of biological molecules and complex interaction samples conveniently. The computing tasks can be submitted and performed simply in a browser without any sophisticated installation and configuration process. BioTriangle is freely available at http://biotriangle.scbdd.com. Graphical abstract An overview of BioTriangle. A platform for generating various molecular representations for chemicals, proteins, DNAs/RNAs and their interactions.

Original languageEnglish
Article number34
JournalJournal of Cheminformatics
Volume8
Issue number1
DOIs
Publication statusPublished - 21 Jun 2016

Scopus Subject Areas

  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Computer Graphics and Computer-Aided Design
  • Library and Information Sciences

User-Defined Keywords

  • Cheminformatics
  • Interaction features
  • Molecular descriptors
  • Molecular representation
  • Online descriptor calculation
  • QSAR/QSPR

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