BioTriangle:a web service for computing various descriptors of small molecules,proteins,DNAs/RNAs and their interactions
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- 英文论文题名：BioTriangle:a web service for computing various descriptors of small molecules,proteins,DNAs/RNAs and their interactions
- 论文作者：Jie dong ; Zhi-Jiang Yao ; Ming Wen ; Min-Feng Zhu ; Ning-Ning Wang ; Hong-Yu Miao ; Dong-Sheng Cao
- 英文论文作者：Jie dong ; Zhi-Jiang Yao ; Ming Wen ; Min-Feng Zhu ; Ning-Ning Wang ; Hong-Yu Miao ; Dong-Sheng Cao ; School of Pharmaceutical Sciences ; Central South University ; College of Chemistry and Chemical Engineering ; Central South University ; School of Mathematics and Statistics ; Central South University ; Department of Biostatistics ; School of Public Health ; University of Texas Health Science Center at Houston
- 年：2016
- 作者机构：School of Pharmaceutical Sciences,Central South University;College of Chemistry and Chemical Engineering,Central South University;School of Mathematics and Statistics,Central South University;Department of Biostatistics,School of Public Health,University of Texas Health Science Center at Houston;
- 英文论文关键词：Molecular descriptors ; molecular representation ; interaction features ; QSAR/QSPR ; chemoinformatics
- 会议召开时间：2016-07-01
- 会议录名称：中国化学会第30届学术年会摘要集-第二十五分会：化学信息学与化学计量学
- 语种：英文
- 分类号：O629.7
- 学会代码：ZGHY
- 会议名称：中国化学会第30届学术年会-第二十五分会 ; 化学信息学与化学计量学
- 会议地点：中国辽宁大连
- 主办单位：中国化学会
- 学会名称：中国化学会
- 页数：1
- 文件大小：139k
- 原文格式：D
- 会议级别：全国
摘要
Rapid advances in network biology indicate that most cellular components exert their functions through interactions with other cellular components,such as proteins,DNA,RNA and small molecules~([1-3]).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~([4-6]).Herein,we developed a comprehensive molecular representation tool,called BioTriangle,to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for computational biology study.BioTriangle is a feature-rich toolkit used for the characterization of various complex biological molecules and interaction samples,such as chemicals,proteins,DNA/RNA,and their interactions.BioTriangle calculates nine types of features including chemical descriptors or molecular fingerprints,structural and physicochemical features of proteins and peptides from amino acid sequence,composition and physicochemical features of DNA/RNA from their primary sequences,chemical-chemical interaction features,chemical-protein interaction features,chemical-DNA/RNA interaction features,protein-protein interaction features,protein-DNA/RNA interaction features,and DNA/RNA-DNA/RNA interaction features.We recommend BioTriangle to analyze and represent various complex molecular data under investigation.We hope that the web service will be helpful when exploring questions concerning structures,functions and interactions of various molecular data in the context of computational biology~([7-9]).
Rapid advances in network biology indicate that most cellular components exert their functions through interactions with other cellular components,such as proteins,DNA,RNA and small molecules~([1-3]).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~([4-6]).Herein,we developed a comprehensive molecular representation tool,called BioTriangle,to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for computational biology study.BioTriangle is a feature-rich toolkit used for the characterization of various complex biological molecules and interaction samples,such as chemicals,proteins,DNA/RNA,and their interactions.BioTriangle calculates nine types of features including chemical descriptors or molecular fingerprints,structural and physicochemical features of proteins and peptides from amino acid sequence,composition and physicochemical features of DNA/RNA from their primary sequences,chemical-chemical interaction features,chemical-protein interaction features,chemical-DNA/RNA interaction features,protein-protein interaction features,protein-DNA/RNA interaction features,and DNA/RNA-DNA/RNA interaction features.We recommend BioTriangle to analyze and represent various complex molecular data under investigation.We hope that the web service will be helpful when exploring questions concerning structures,functions and interactions of various molecular data in the context of computational biology~([7-9]).
Rapid advances in network biology indicate that most cellular components exert their functions through interactions with other cellular components,such as proteins,DNA,RNA and small molecules~([1-3]).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~([4-6]).Herein,we developed a comprehensive molecular representation tool,called BioTriangle,to emphasize the integration of chemoinformatics and bioinformatics into a molecular informatics platform for computational biology study.BioTriangle is a feature-rich toolkit used for the characterization of various complex biological molecules and interaction samples,such as chemicals,proteins,DNA/RNA,and their interactions.BioTriangle calculates nine types of features including chemical descriptors or molecular fingerprints,structural and physicochemical features of proteins and peptides from amino acid sequence,composition and physicochemical features of DNA/RNA from their primary sequences,chemical-chemical interaction features,chemical-protein interaction features,chemical-DNA/RNA interaction features,protein-protein interaction features,protein-DNA/RNA interaction features,and DNA/RNA-DNA/RNA interaction features.We recommend BioTriangle to analyze and represent various complex molecular data under investigation.We hope that the web service will be helpful when exploring questions concerning structures,functions and interactions of various molecular data in the context of computational biology~([7-9]).
引文
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[2].Brodland GW,Semin Cell Dev Biol 2015,47-48:62-73.
[3].Barabasi AL,Oltvai ZN,Nat Rev Genet 2004,5(2):101-115.
[4].Kuhn M,Szklarczyk D,Pletscher-Frankild S,Blicher TH,von Mering C,Jensen LJ,Bork P,Nucleic Acids Res2014,42(D1):D401-D407.
[5].Chen X,Ji ZL,Chen YZ,Nucleic Acids Res 2002,30(1):412-415.
[6].Gaulton A,Bellis LJ,Bento AP,Chambers J,Davies M,Hersey A,Light Y,McGlinchey S,Michalovich D,Al-Lazikani B,Overington JP,Nucleic Acids Res 2012,40(D1):D1100-D1107.
[7].Rognan D,Brit J Pharmacol 2007,152(1):38-52.
[8].Huang J,Cao D,Yan J,Xu Q,Hu Q,Liang Y,Biochimie 2012,94(8):1697-1704.
[9].van Westen GJP,Wegner JK,IJzerman AP,van Vlijmen HWT,Bender A,Medchemcomm 2011,2(1):16-30.