HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation

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• 作者：Tianhong Zhang ; Hongli Li ; Hualin Xi ; Robert V. Stanton ; Sergio H. Rotstein
• 刊名：Journal of Chemical Information and Modeling
• 出版年：2012
• 出版时间：October 22, 2012
• 年：2012
• 卷：52
• 期：10
• 页码：2796-2806
• 全文大小：587K
• 年卷期：v.52,no.10(October 22, 2012)
• ISSN：1549-960X

文摘

When biological macromolecules are used as therapeutic agents, it is often necessary to introduce non-natural chemical modifications to improve their pharmaceutical properties. The final products are complex structures where entities such as proteins, peptides, oligonucleotides, and small molecule drugs may be covalently linked to each other, or may include chemically modified biological moieties. An accurate in silico representation of these complex structures is essential, as it forms the basis for their electronic registration, storage, analysis, and visualization. The size of these molecules (henceforth referred to as 鈥渂iomolecules鈥? often makes them too unwieldy and impractical to represent at the atomic level, while the presence of non-natural chemical modifications makes it impossible to represent them by sequence alone. Here we describe the Hierarchical Editing Language for Macromolecules (鈥淗ELM鈥? and demonstrate its utility in the representation of structures such as antisense oligonucleotides, short interference RNAs, peptides, proteins, and antibody drug conjugates.