Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA.
Departments of Biological Sciences, Chemistry, Bioengineering, and Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA.
J Mol Biol. 2023 Jul 15;435(14):167995. doi: 10.1016/j.jmb.2023.167995. Epub 2023 Feb 2.
Molecular modeling and simulation play important roles in biomedical research as they provide molecular-level insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI (https://charmm-gui.org) is a web-based cyberinfrastructure that is widely used to generate various molecular simulation system and input files and thus facilitates and standardizes the usage of common and advanced simulation techniques. In particular, PDB Manipulator provides various chemical modification options as the starting point for most input generation modules in CHARMM-GUI. Here, we discuss recent additions to PDB Manipulator, such as non-standard amino acids/RNA substitutions, ubiquitylation and SUMOylation, Lys/Arg post-translational modifications, lipidation, peptide stapling, and improved parameterization options of small molecules. These additional features are expected to make complex PDB modifications easy for biomolecular modeling and simulation.
分子建模和模拟在生物医学研究中发挥着重要作用，因为它们提供了分子水平的见解，使我们能够理解仅通过实验难以阐明的生物学功能的潜在机制。CHARMM-GUI（https://charmm-gui.org）是一个基于网络的网络基础设施，广泛用于生成各种分子模拟系统和输入文件，从而促进和标准化了常见和高级模拟技术的使用。特别是，PDB 操作器（PDB Manipulator）提供了各种化学修饰选项，作为 CHARMM-GUI 中大多数输入生成模块的起点。在这里，我们讨论了 PDB 操作器的最新添加功能，例如非标准氨基酸/RNA 替换、泛素化和 SUMO 化、Lys/Arg 翻译后修饰、脂化、肽键稳定以及小分子的改进参数化选项。这些附加功能有望使复杂的 PDB 修饰变得易于进行生物分子建模和模拟。
