ArticleJournal of molecular biology2023
CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation.
Article in Journal of molecular biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 87 papers.
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Who cites it
87 citing papers in PubMed, 140 citations in OpenAlex.
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- Lipid Oxidation Effect on Membrane Properties in Phosphatidylinositol- and Phosphatidylserine-Enriched Neuronal Biomimetic Models.The journal of physical chemistry. B · 2026Article
- Synthesis of new sulfonamides from sulfamethizole: in vitro antitubercular and antimicrobial activities supported by molecular docking, molecular dynamics, and ADME studies.Molecular diversity · 2026Article
- Design of a metabolically-stable peptide therapeutic with triple-hormone-receptor agonist activity.Journal of computer-aided molecular design · 2026Article
- FDA-Approved Drug Repurposing as p53 Mutants Rescue Candidates Using Structure-Based Virtual Screening and Molecular Simulations.International journal of molecular sciences · 2026Article
- CHARMM-GUIbioRxiv : the preprint server for biology · 2026Article
- Collective fluctuations underlying nanobody inhibitory activity targetingbioRxiv : the preprint server for biology · 2026Article
- Amitriptyline inhibits EAG1 channels by binding to their PAS domains and exerts EAG1-dependent anti-tumorigenic effects.Cancer gene therapy · 2026Article
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- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 2026Article
- Genome-guided antimicrobial potential of Bacillus stercoris from coastal sand with activity against multidrug-resistant bacteria, including MRSA.International microbiology : the official journal of the Spanish Society for Microbiology · 2026Article
- ARumenamides as Multitarget Ion Channel Modulators: Insights from Fenestration-Focused Docking, ADMET Profiling, and Molecular Dynamics.International journal of molecular sciences · 2026Article
- Mixed-Solvent MD suite: modular tools for building and analyzing mixed-solvent molecular dynamics systems.Journal of computer-aided molecular design · 2026Article
- CHARMM-GUIJournal of chemical information and modeling · 2026Article
- A Bilingual Computational Workflow for Identifying Potential PLK1 Inhibitors in American Sign Language and English.Journal of visualized experiments : JoVE · 2026Article
- Probing the Interaction Between Thioacetamide Fungicide and Bovine Serum Albumin Through Fluorescence, Electrochemical, and Docking Analyses.Luminescence : the journal of biological and chemical luminescence · 2026Article
27 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
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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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.