CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biom-olecular Modeling and Simulation

SJ Park and N Kern and T Brown and J Lee and W Im, JOURNAL OF MOLECULAR BIOLOGY, 435, 167995 (2023).

DOI: 10.1016/j.jmb.2023.167995

Molecular modeling and simulation play important roles in biomedical research as they provide molecularlevel insight into the underlying mechanisms of biological functions that are difficult to elucidate only with experiments. CHARMM-GUI ( 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 CHARMMGUI. 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. & COPY; 2023 Elsevier Ltd. All rights reserved.

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