ArticleNature methods2016
Parmbsc1: a refined force field for DNA simulations.
Article in Nature methods, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 534 papers.
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Who cites it
534 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
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- Phosphorylation by CaMKIV regulates the transcriptional repressor activity and half-life of REST/NRSF.Science advances · 2026Article
- Exploring the bistable equilibrium of methylated CpG DNA recognition by the MBD2 protein.Nucleic acids research · 2026Article
- Topology-enforced synthesis of atomically precise silver nanoclusters in 3D DNA lattices.Science advances · 2026Article
- Transposon end recognition and pairing by I-F3 CRISPR-associated transposase.Science advances · 2026Article
- Improving aptamer binding affinity for HN protein of newcastle disease virus: molecular dynamics simulations and MM/GBSA calculations studies.Molecular diversity · 2026Article
- Binding of Anthracyclines Within DNA-Topoisomerase ΙΙ Cleavage Complexes: Thermodynamics and Interactions.Journal of chemical information and modeling · 2026Article
- A dynamically frustrated allosteric checkpoint consistent with conformational proofreading in CRISPR-Cas9.Nucleic acids research · 2026Article
- Integrated Experimental and Computational Investigation of Salicylaldehyde-Derived Imine/Amine Derivatives as Antioxidant and Cytotoxic Agents.Materials (Basel, Switzerland) · 2026Article
- Martini 3 Coarse-Grained Model of DNA for Heterogeneous Molecular Systems.bioRxiv : the preprint server for biology · 2026Article
- Viral nucleosome-like particles show increased dynamic behavior and altered thermodynamic stability.Biophysical journal · 2026Article
- Multivalent cations stabilize DNA duplexes beyond charge neutralization.Chemical science · 2026Article
- The conformation of the complementary strand and the deformation of the DNA groove upon DDB2 binding justifies the different repair rates for cyclobutane pyrimidine dimers.Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology · 2026Article
- Imaging and mechanism of DNA-DNA recognition mediated by divalent ions.Nucleic acids research · 2026Article
- Atomistic Simulations Decode the Mechanisms of DNA and RNA Processing Enzymes: Function through Motion.Accounts of chemical research · 2026Article
- LignAmb25: A comprehensive AMBER force field addressing lignin's structural and chemical diversity.Biophysical journal · 2026Article
- Readout of intrinsic and induced DNA shape by homeodomain transcription factor complexes.Biophysical journal · 2026Article
- CRISPR RNA architecture steers Cas9 catalysis and fidelity via a guide repeat clasp motif.Nucleic acids research · 2026Article
- Can intrinsic loop energetics predict G-Quadruplex topology?PLoS computational biology · 2026Article
474 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
Abstract
We present parmbsc1, a force field for DNA atomistic simulation, which has been parameterized from high-level quantum mechanical data and tested for nearly 100 systems (representing a total simulation time of ∼ 140 μs) covering most of DNA structural space. Parmbsc1 provides high-quality results in diverse systems. Parameters and trajectories are available at http://mmb.irbbarcelona.org/ParmBSC1/.
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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.