Development and current status of the CHARMM force field for nucleic acids

2000/01/01 by Alexander D. MacKerell, Nilesh Banavali, Nilesh K. Banavali +1 · 30 citations
Biochemistry, Genetics and Molecular Biology · Materials Science · #DNA and Nucleic Acid Chemistry #Protein Structure and Dynamics #Enzyme Structure and Function

paper · doi:10.1002/1097-0282(2000)56:4<257::aid-bip10029>3.0.co;2-w

Abstract

The CHARMM27 all-atom force field for nucleic acids represents a highly optimized model for investigations of nucleic acids via empirical force field calculations. The force field satisfactorily treats the A, B, and Z forms of DNA as well as RNA, and it also useful for nucleosides and nucleotides. In addition, it is compatible with the CHARMM force fields for proteins and lipids, allowing for simulation studies of heterogeneous systems.

Citations

• Die Berechnung optischer und elektrostatischer Gitterpotentiale

Cited by

• Charge Transfer in Classical Molecular Dynamics Simulations of Met-enkephalin: Improving Traditional Force Field with Data Driven Models
• Extended <scp>tight‐binding</scp> quantum chemistry methods
• Physics-Inspired All-Pair Interaction Learning for 3D Dynamics Modeling
• Web interface for brownian dynamics simulation of ion transport and its applications to beta‐barrel pores
• FlowBack-Adjoint: Physics-Aware and Energy-Guided Conditional Flow-Matching for All-Atom Protein Backmapping
• Ensemble refinement of protein crystal structures: validation and application. [europepmc]
• Docking to RNA via root-mean-square-deviation-driven energy minimization with flexible ligands and flexible targets. [europepmc]
• CHARMM: the biomolecular simulation program. [europepmc]
• Coarse-grained model for simulation of RNA three-dimensional structures. [europepmc]
• Transient Hoogsteen base pairs in canonical duplex DNA. [europepmc]
• Recent Developments and Applications of the CHARMM force fields. [europepmc]
• Twenty-five years of nucleic acid simulations. [europepmc]
• Advances in the determination of nucleic acid conformational ensembles. [europepmc]
• Protein-guided RNA dynamics during early ribosome assembly. [europepmc]
• Molecular mechanism of Aurora A kinase autophosphorylation and its allosteric activation by TPX2. [europepmc]
• The energy landscape of adenylate kinase during catalysis. [europepmc]
• Combined covalent-electrostatic model of hydrogen bonding improves structure prediction with Rosetta. [europepmc]
• Mechanism of eIF6 release from the nascent 60S ribosomal subunit. [europepmc]
• Metal Ion Modeling Using Classical Mechanics. [europepmc]
• Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. [europepmc]
• Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs. [europepmc]
• RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. [europepmc]
• AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids. [europepmc]
• IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding. [europepmc]
• Sensitive and frequent identification of high avidity neo-epitope specific CD8 + T cells in immunotherapy-naive ovarian cancer. [europepmc]
• Improving the Performance of the Amber RNA Force Field by Tuning the Hydrogen-Bonding Interactions. [europepmc]
• Robust Atomistic Modeling of Materials, Organometallic, and Biochemical Systems. [europepmc]
• Atazanavir, Alone or in Combination with Ritonavir, Inhibits SARS-CoV-2 Replication and Proinflammatory Cytokine Production. [europepmc]
• RLDOCK: A New Method for Predicting RNA-Ligand Interactions. [europepmc]
• SOD1 mutations associated with amyotrophic lateral sclerosis analysis of variant severity. [europepmc]

Related

• Modern theory of nuclear forces
• Nuclear Forces from Lattice Quantum Chromodynamics
• Exploring medium mass nuclei using effective chiral nucleon-nucleon interactions
• Three-Body Forces and Proton-Rich Nuclei
• Towards high-precision nuclear forces from chiral effective field theory