Gutermuth Torben, Penner Patrick, Sieg Jochen, Dolfus Uschi, Rarey Matthias
ZBH─Center for Bioinformatics, University of Hamburg, Albert Einstein Ring 8-10, 22761 Hamburg, Germany.
J Chem Inf Model. 2025 Sep 8;65(17):9075-9081. doi: 10.1021/acs.jcim.5c00599. Epub 2025 Jun 9.
Communication between collaborators of different (scientific) backgrounds can be difficult in any interdisciplinary work. Frequently used language of different disciplines can be partially unknown or sometimes even contradict each other. One example of this is knowledge about organic chemical nomenclature used by chemists. Although highly efficient, this nomenclature can be challenging to learn and confusing for scientists new to it. Today, interdisciplinary teams in chemistry often consist of a diverse range of experts, including those from biology, pharmacology, medicine, computer science, and mathematics. This can complicate communication regarding chemical structures, impeding a productive work environment and potentially introducing errors. To address this issue, we present a new web tool called SmartChemist. This tool enables users to upload molecular files or enter SMILES of molecules. It then displays the names of identified substructures, including cyclic substructures, functional groups, and common biologically relevant organic molecules. It utilizes a database of over 40,000 patterns that have been carefully generated for this purpose, and it only shows the most specific substructures found while enabling novices to inquire about all substructures found.
在任何跨学科工作中，不同（科学）背景的合作者之间的沟通都可能存在困难。不同学科常用的语言可能部分不为人所知，有时甚至相互矛盾。化学家用的有机化学命名法就是一个例子。尽管这种命名法效率很高，但对于初次接触的科学家来说，学习起来可能具有挑战性且容易混淆。如今，化学领域的跨学科团队通常由来自生物学、药理学、医学、计算机科学和数学等不同领域的专家组成。这可能会使关于化学结构的沟通变得复杂，阻碍高效的工作环境，并可能引入错误。为了解决这个问题，我们推出了一种名为SmartChemist的新型网络工具。该工具允许用户上传分子文件或输入分子的SMILES。然后它会显示已识别的子结构的名称，包括环状子结构、官能团和常见的具有生物学相关性的有机分子。它利用为此精心生成的一个包含40000多种模式的数据库，并且只显示所发现的最具体的子结构，同时允许新手查询所有发现的子结构。
