ArticleJournal of molecular biology2024
CHARMM-GUI PDB Reader and Manipulator: Covalent Ligand Modeling and Simulation.
Article in Journal of molecular biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
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- Genome-Wide Analysis ofInternational journal of molecular sciences · 2026Article
- Quantum mechanical investigation and environmental engineering of LinB for enhanced polyvinyl chloride degradation.Molecular diversity · 2026Article
- CHARMM-GUIbioRxiv : the preprint server for biology · 2026Article
- Structure-guided reprogramming of DELLA turnover for a sustainable Green Revolution in rice.Nature communications · 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
- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 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
- Ligand Versatility and Resistance Mechanism of Monotherapy-Grade HIV-1 Protease Inhibitor GRL-142 Binding the Multidrug Resistant Variant p51: Insights from 1 μs MD Simulations.Journal of chemical information and modeling · 2026Article
- Dynamic domain interactions encode possible CheA autophosphorylation mechanisms revealed by coarse-grained simulations.Biophysical journal · 2026Article
- Theoretical study of KRAS G12C secondary mutations influencing inhibitor resistance.Biophysics and physicobiology · 2026Article
- Dynamic domain interactions encode possible CheA autophosphorylation mechanisms revealed by coarse-grained simulations.bioRxiv : the preprint server for biology · 2025Article
- βInternational journal of molecular sciences · 2025Article
- Minimalistic Peptide Nanocarriers for Multiple Cancer Drugs.ACS applied bio materials · 2025Article
- Investigating the Chemical-Biological Link inFood science & nutrition · 2025Article
- Molecular dynamics study of differential effects of serotonin-2A-receptor (5-HT2AR) modulators.PLoS computational biology · 2025Article
- Structure-based rational design of covalent probes.Communications chemistry · 2025Review
- CHARMM-GUIJournal of chemical information and modeling · 2025Article
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Authors and funding
3 authors.
Funding
Abstract
Molecular modeling and simulation serve an important role in exploring biological functions of proteins at the molecular level, which is complementary to experiments. CHARMM-GUI (https://www.charmm-gui.org) is a web-based graphical user interface that generates complex molecular simulation systems and input files, and we have been continuously developing and expanding its functionalities to facilitate various complex molecular modeling and make molecular dynamics simulations more accessible to the scientific community. Currently, covalent drug discovery emerges as a popular and important field. Covalent drug forms a chemical bond with specific residues on the target protein, and it has advantages in potency for its prolonged inhibition effects. Even though there are higher demands in modeling PDB protein structures with various covalent ligand types, proper modeling of covalent ligands remains challenging. This work presents a new functionality in CHARMM-GUI PDB Reader & Manipulator that can handle a diversity of ligand-amino acid linkage types, which is validated by a careful benchmark study using over 1,000 covalent ligand structures in RCSB PDB. We hope that this new functionality can boost the modeling and simulation study of covalent ligands.
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Registered trials
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