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

Overview

Journal J Mol Biol

Publisher Elsevier

Specialties Microbiology
Molecular Biology

Date 2023 Jun 25

PMID 37356910

Authors

Sang-Jun Park

Nathan Kern

Turner Brown

Jumin Lee

Wonpil Im

Affiliations

Soon will be listed here.

Abstract

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.

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