ReviewAdvances in protein chemistry and structural biology2014
CHARMM-GUI PDB manipulator for advanced modeling and simulations of proteins containing nonstandard residues.
Review in Advances in protein chemistry and structural biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 201 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
201 citing papers in PubMed.
- Physical confinement modulates the rate-limiting transition in the release of phosphate from actin filaments.Science advances · 2026Article
- Design, synthesis, biological evaluation and computational studies of novel phthalimides as dual COX-2/5-LOX inhibitors.Molecular diversity · 2026Article
- Mechanism of GPR84 allosteric modulation at a helix 8-proximate site.Science advances · 2026Article
- Insights into the structural dynamics and free energy landscapes of Danio rerio RAB1A and RAB1B: a comparative molecular dynamics simulation approach.Journal of molecular modeling · 2026Article
- Evaluation of Camptothecin Through Computational and Experimental Approaches Targeting Membrane Receptors on Breast Cancer Cells for Potential Therapeutic Applications.International journal of molecular sciences · 2026Article
- New Chromene Derivatives as Promising VEGFR-2 Inhibitors: Experimental Cytotoxicity and Comprehensive Computational Characterization.Archiv der Pharmazie · 2026Article
- A GAPlant communications · 2026Article
- Amitriptyline inhibits EAG1 channels by binding to their PAS domains and exerts EAG1-dependent anti-tumorigenic effects.Cancer gene therapy · 2026Article
- Article
- Evaluating Force Matching as a Parametrization Strategy for the CHARMM36m Force Field Using Phosphorylation.The journal of physical chemistry. B · 2026Article
- Molecular dynamics simulations of beta-2-glycoprotein 1 (β2GPI) reveal that post-translational modifications facilitate novel structures.Scientific reports · 2026Article
- Molecular Insights into End-Group Cluster Formation in Natural Rubber Induced by l-Quebrachitol, a Major Component of Natural Rubber Serum Waste.Langmuir : the ACS journal of surfaces and colloids · 2026Article
- Nisin and rutin as potential coating agents for iron oxide nanoparticles for enhanced theranostic applications against cancer.Scientific reports · 2026Article
- Multilevel synergistic mechanisms of a nanocarrier-enabled topramezone herbicide against invasive weeds.Journal of nanobiotechnology · 2026Article
- CHARMM-GUIJournal of chemical information and modeling · 2026Article
- CHARMM-GUI Hybrid ML/MM Builder for Hybrid Machine Learning and Molecular Mechanical Modeling and Simulations.Journal of chemical information and modeling · 2026Article
- Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments.bioRxiv : the preprint server for biology · 2026Article
- Rheb membrane orientation dynamics and functional consequences elucidated by molecular simulations, single-molecule-FRET and signaling assays.bioRxiv : the preprint server for biology · 2026Article
- Induced opening of conformational switch I in GTP-bound Ran GTPase.Protein science : a publication of the Protein Society · 2026Article
- Poliovirus receptor (PVR) expression as a predictor of relapse in colorectal cancer: bioinformatics and virtual screening.Experimental biology and medicine (Maywood, N.J.) · 2026Article
141 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
13 authors.
Funding
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface to prepare molecular simulation systems and input files to facilitate the usage of common and advanced simulation techniques. Since it is originally developed in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to setup a broad range of simulations including free energy calculation and large-scale coarse-grained representation. Here, we describe functionalities that have recently been integrated into CHARMM-GUI PDB Manipulator, such as ligand force field generation, incorporation of methanethiosulfonate spin labels and chemical modifiers, and substitution of amino acids with unnatural amino acids. These new features are expected to be useful in advanced biomolecular modeling and simulation of proteins.
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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.