ReviewJournal of computational chemistry2017
CHARMM-GUI 10 years for biomolecular modeling and simulation.
Review in Journal of computational chemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 181 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
181 citing papers in PubMed, 376 citations in OpenAlex.
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- Molecular dynamics simulations of beta-2-glycoprotein 1 (β2GPI) reveal that post-translational modifications facilitate novel structures.Scientific reports · 2026Article
- Structure and Dynamics of the HIV-1 Envelope Protein on the Virion Envelope.bioRxiv : the preprint server for biology · 2026Article
- Experimental and Computational Analysis of Phenolic Acid Association with PAMAM Dendrimers: Comparing Different Formulation Techniques.Polymers · 2026Article
- Quantifying conformational diversity in protein-ligand ensembles for structure-based virtual screening.Journal of computer-aided molecular design · 2026Article
- Study on the Mechanisms and Key Influencing Factors of Paclitaxel and Indocyanine Green Co-Loading in Lipid Nanoparticles.Pharmaceutics · 2026Article
- Illuminating the pleiotropic effects of bixin-loaded nanoemulsion on glioblastoma cell behavior through an integrated approach.Molecular biology reports · 2026Article
- Deep Learning-Guided Discovery of Dual Inhibitors of SARS-CoV-2 Entry and 3CL Protease.Molecules (Basel, Switzerland) · 2026Article
- ProPrep: An Interactive and Instructional Interface for Proper Protein Preparation with AMBER.bioRxiv : the preprint server for biology · 2026Article
- A conserved salt bridge network stabilizes the hepatic organic anion transporters OATP1B1 and OATP1B3.The Journal of biological chemistry · 2026Article
- Dual-targeting sulfamethoxazole derivatives overcome multidrug resistance in ESKAPE pathogens by inhibiting quorum sensing and efflux pumps.RSC advances · 2026Article
- ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis.bioRxiv : the preprint server for biology · 2026Article
- A Coarse-Grained MARTINI Model for Mucins.Journal of chemical theory and computation · 2026Article
- Complementary GH54 and GH43 α-L-Arabinofuranosidases fromJournal of applied glycoscience · 2026Article
- Combination of Chenpi and Banxia alleviates synovial inflammation in a rat model of rheumatoid arthritis by targeting the JNK/AP-1 signaling pathway.Frontiers in immunology · 2026Article
- Xiaoyao San alleviates emotional distress - induced TNBC growth through augmenting intratumoral CD8Frontiers in immunology · 2026Article
- Molecular dynamics simulation in traditional Chinese medicine research: from molecular mechanisms to multiscale validation.Frontiers in chemistry · 2026Review
- Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness.International journal of molecular sciences · 2025Article
121 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
16 authors at 7 institutions in 2 countries.
Funding
Abstract
CHARMM-GUI, http://www.charmm-gui.org, is a web-based graphical user interface that prepares complex biomolecular systems for molecular simulations. CHARMM-GUI creates input files for a number of programs including CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM. Since its original development in 2006, CHARMM-GUI has been widely adopted for various purposes and now contains a number of different modules designed to set up a broad range of simulations: (1) PDB Reader & Manipulator, Glycan Reader, and Ligand Reader & Modeler for reading and modifying molecules; (2) Quick MD Simulator, Membrane Builder, Nanodisc Builder, HMMM Builder, Monolayer Builder, Micelle Builder, and Hex Phase Builder for building all-atom simulation systems in various environments; (3) PACE CG Builder and Martini Maker for building coarse-grained simulation systems; (4) DEER Facilitator and MDFF/xMDFF Utilizer for experimentally guided simulations; (5) Implicit Solvent Modeler, PBEQ-Solver, and GCMC/BD Ion Simulator for implicit solvent related calculations; (6) Ligand Binder for ligand solvation and binding free energy simulations; and (7) Drude Prepper for preparation of simulations with the CHARMM Drude polarizable force field. Recently, new modules have been integrated into CHARMM-GUI, such as Glycolipid Modeler for generation of various glycolipid structures, and LPS Modeler for generation of lipopolysaccharide structures from various Gram-negative bacteria. These new features together with existing modules are expected to facilitate advanced molecular modeling and simulation thereby leading to an improved understanding of the structure and dynamics of complex biomolecular systems. Here, we briefly review these capabilities and discuss potential future directions in the CHARMM-GUI development project. © 2016 Wiley Periodicals, Inc.
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What OpenQuestion holds
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.