ReviewBiochimica et biophysica acta2015
CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.
Review in Biochimica et biophysica acta, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 128 papers, 1 of them a synthesis that pooled it.
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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
128 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review.Journal of infection and public health · 2022Pooled it
- Reverse engineering of BNIP3 identifies a mitochondrial protective peptide.Nature communications · 2026Article
- Structure and organization of AMPA receptor-TARP complexes in the mammalian cerebellum.Science (New York, N.Y.) · 2026Article
- Virtual screening and molecular dynamics simulations for drug repurposing against autophagy to attenuate blast in cereal plants.Scientific reports · 2026Article
- Discovery of hydroxytriazole as a potential glyoxalase-I inhibitor utilizing computer-aided drug design techniques.Scientific reports · 2026Article
- Natural Fatty Acids as Dual ACE2-Inflammatory Modulators: Integrated Computational Framework for Pandemic Preparedness.International journal of molecular sciences · 2025Article
- In Silico Analysis of CMolecules (Basel, Switzerland) · 2025Article
- Dissociation kinetics of G proteins from G protein-coupled receptors and effects of allosteric modulation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- TMC1 and TMC2 are cholesterol-dependent scramblases that regulate membrane homeostasis in auditory hair cells.bioRxiv : the preprint server for biology · 2025Article
- Unraveling the Mechanical Behavior of Softwood Secondary Cell Walls through Atomistic Simulations.Biomacromolecules · 2025Article
- The physics-AI dialogue in drug design.RSC medicinal chemistry · 2025Review
- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- Mechanisms of Peptide Agonist Dissociation and Deactivation of Adhesion G-Protein-Coupled Receptors.Biochemistry · 2025Article
- Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels.eLife · 2025Article
- Polymorphic potential of SRF binding site ofRSC advances · 2024Article
- Article
- Mechanisms of peptide agonist dissociation and deactivation of adhesion G-protein-coupled receptors.bioRxiv : the preprint server for biology · 2024Article
- Ligand Gaussian Accelerated Molecular Dynamics 3 (LiGaMD3): Improved Calculations of Binding Thermodynamics and Kinetics of Both Small Molecules and Flexible Peptides.Journal of chemical theory and computation · 2024Article
- Complexes of vertebrate TMC1/2 and CIB2/3 proteins form hair-cell mechanotransduction cation channels.bioRxiv : the preprint server for biology · 2024Article
- Structure and function of a ligand-free GPCR-Gαβγ intermediate complex.Research square · 2024Article
68 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
2 authors.
Funding
Abstract
backgroundMolecular Mechanics (MM) is the method of choice for computational studies of biomolecular systems owing to its modest computational cost, which makes it possible to routinely perform molecular dynamics (MD) simulations on chemical systems of biophysical and biomedical relevance. SCOPE OF REVIEW: As one of the main factors limiting the accuracy of MD results is the empirical force field used, the present paper offers a review of recent developments in the CHARMM additive force field, one of the most popular biomolecular force fields. Additionally, we present a detailed discussion of the CHARMM Drude polarizable force field, anticipating a growth in the importance and utilization of polarizable force fields in the near future. Throughout the discussion emphasis is placed on the force fields' parametrization philosophy and methodology. MAJOR
conclusionsRecent improvements in the CHARMM additive force field are mostly related to newly found weaknesses in the previous generation of additive force fields. Beyond the additive approximation is the newly available CHARMM Drude polarizable force field, which allows for MD simulations of up to 1μs on proteins, DNA, lipids and carbohydrates. GENERAL SIGNIFICANCE: Addressing the limitations ensures the reliability of the new CHARMM36 additive force field for the types of calculations that are presently coming into routine computational reach while the availability of the Drude polarizable force fields offers an inherently more accurate model of the underlying physical forces driving macromolecular structures and dynamics. This article is part of a Special Issue entitled "Recent developments of molecular dynamics".
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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.