Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
PLoS One. 2012;7(9):e44480. doi: 10.1371/journal.pone.0044480. Epub 2012 Sep 18.
Near linear scaling fragment based quantum chemical calculations are becoming increasingly popular for treating large systems with high accuracy and is an active field of research. However, it remains difficult to set up these calculations without expert knowledge. To facilitate the use of such methods, software tools need to be available to support these methods and help to set up reasonable input files which will lower the barrier of entry for usage by non-experts. Previous tools relies on specific annotations in structure files for automatic and successful fragmentation such as residues in PDB files. We present a general fragmentation methodology and accompanying tools called FragIt to help setup these calculations. FragIt uses the SMARTS language to locate chemically appropriate fragments in large structures and is applicable to fragmentation of any molecular system given suitable SMARTS patterns. We present SMARTS patterns of fragmentation for proteins, DNA and polysaccharides, specifically for D-galactopyranose for use in cyclodextrins. FragIt is used to prepare input files for the Fragment Molecular Orbital method in the GAMESS program package, but can be extended to other computational methods easily.
基于片段的近线性标度量子化学计算方法在处理具有高精度的大型系统时越来越受欢迎，是一个活跃的研究领域。然而，如果没有专业知识，这些计算的设置仍然很困难。为了方便使用这些方法，需要提供软件工具来支持这些方法，并帮助设置合理的输入文件，从而降低非专家使用的门槛。以前的工具依赖于结构文件中的特定注释来进行自动和成功的片段化，例如 PDB 文件中的残基。我们提出了一种通用的片段化方法和配套的工具，称为 FragIt，用于帮助设置这些计算。FragIt 使用 SMARTS 语言在大型结构中定位化学上合适的片段，并且适用于任何分子系统的片段化，只要有合适的 SMARTS 模式。我们为蛋白质、DNA 和多糖，特别是用于环糊精的 D-吡喃半乳糖提供了片段化的 SMARTS 模式。FragIt 用于为 GAMESS 程序包中的分子轨道片段方法准备输入文件，但可以轻松扩展到其他计算方法。
