ArticleJournal of computational chemistry2007
CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.
Article in Journal of computational chemistry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 51 citations in OpenAlex.
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties in SPC/E, TIP3P-fb, TIP4P/2005, TIP4P-Ew, and TIP4P-D.Journal of chemical theory and computation · 2022Article
- Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties.Journal of chemical theory and computation · 2021Article
- Phe-140 Determines the Catalytic Efficiency of Arylacetonitrilase fromInternational journal of molecular sciences · 2020Article
- Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Self-assembly Controls Self-cleavage of HHR from ASBVd (-): a Combined SANS and Modeling Study.Scientific reports · 2016Article
- A Two-Metal-Ion-Mediated Conformational Switching Pathway for HDV Ribozyme Activation.ACS catalysis · 2016Article
- Comparison of structural, thermodynamic, kinetic and mass transport properties of Mg(2+) ion models commonly used in biomolecular simulations.Journal of computational chemistry · 2015Article
- Bridging the gap between theory and experiment to derive a detailed understanding of hammerhead ribozyme catalysis.Progress in molecular biology and translational science · 2013Review
- An abridged transition state model to derive structure, dynamics, and energy components of DNA polymerase β fidelity.Biochemistry · 2011Article
- R.E.D. Server: a web service for deriving RESP and ESP charges and building force field libraries for new molecules and molecular fragments.Nucleic acids research · 2011Article
- The R.E.D. tools: advances in RESP and ESP charge derivation and force field library building.Physical chemistry chemical physics : PCCP · 2010Article
- Molecular dynamics simulation of bovine pancreatic ribonuclease A-CpA and transition state-like complexes.The journal of physical chemistry. B · 2010Article
- Targeting a novel N-terminal epitope of death receptor 5 triggers tumor cell death.The Journal of biological chemistry · 2010Article
- A computational study of a recreated G protein-GEF reaction intermediate competent for nucleotide exchange: fate of the Mg ion.PloS one · 2010Article
- RNA in motion.Current opinion in chemical biology · 2008Review
- Extension of adaptive tree code and fast multipole methods to high angular momentum particle charge densities.Journal of computational chemistry · 2008Article
- Solvent structure and hammerhead ribozyme catalysis.Chemistry & biology · 2008Article
- Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.Journal of the American Chemical Society · 2008Article
- Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.Journal of chemical theory and computation · 2007Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Force field parameters specifically optimized for residues important in the study of RNA catalysis are derived from density-functional calculations, in a fashion consistent with the CHARMM27 all-atom empirical force field. Parameters are presented for residues that model reactive RNA intermediates and transition state analogs, thio-substituted phosphates and phosphoranes, and bound Mg(2+) and di-metal bridge complexes. Target data was generated via density-functional calculations at the B3LYP/6-311++G(3df,2p)// B3LYP/6-31++G(d,p) level. Partial atomic charges were initially derived from CHelpG electrostatic potential fitting and subsequently adjusted to be consistent with the CHARMM27 charges. Lennard-Jones parameters were determined to reproduce interaction energies with water molecules. Bond, angle, and torsion parameters were derived from the density-functional calculations and renormalized to maintain compatibility with the existing CHARMM27 parameters for standard residues. The extension of the CHARMM27 force field parameters for the nonstandard biological residues presented here will have considerable use in simulations of ribozymes, including the study of freeze-trapped catalytic intermediates, metal ion binding and occupation, and thio effects.
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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.