ArticleNature methods2018
NAMD goes quantum: an integrative suite for hybrid simulations.
Article in Nature methods, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 1 of them a synthesis that pooled it.
What it found
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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.
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.
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Who cites it
81 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
- Engineering of fructose-6-phosphate aldolase for one-carbon conversion to mannitol in a designed biotransformation system.Synthetic and systems biotechnology · 2026Article
- Review
- Mapping Strigolactone Hydrolysis in DWARF14 via QM/MM String Method.bioRxiv : the preprint server for biology · 2026Article
- From Atoms to Cells: AI-Based Structure Prediction Fueling Molecular Dynamics Simulations in Computational Structural Biology.Advances in experimental medicine and biology · 2026Review
- Mutation-induced heme pocket destabilization in myoglobinopathy.Frontiers in bioinformatics · 2026Article
- Solar-hybrid biocatalyst for methane hydroxylation to methanol.Nature communications · 2025Article
- Proton Transfer through a Charged Conduit in Respiratory Complex I: Long-Range Effects and Conformational Gating.Journal of chemical information and modeling · 2025Article
- Mechanism for Nucleotidyl Transfer in LINE-1 ORF2p Revealed by QM/MM Simulations.International journal of molecular sciences · 2025Article
- Molecular insights of acarbose metabolization catalyzed by acarbose-preferred glucosidase.Nature communications · 2025Article
- Special Issue: "Advanced Research on Molecular Modeling of Protein Structure and Functions".International journal of molecular sciences · 2025Article
- Effects of Conformational Sampling on Computing Redox Properties Using Linear Response Approach.The journal of physical chemistry. B · 2025Article
- Substrate Activation Efficiency in Active Sites of Hydrolases Determined by QM/MM Molecular Dynamics and Neural Networks.International journal of molecular sciences · 2025Article
- Article
- Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.Nucleic acids research · 2025Article
- Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?Protein science : a publication of the Protein Society · 2024Article
- Article
- Machine Learning Approach to Vertical Energy Gap in Redox Processes.Journal of chemical theory and computation · 2024Article
- Molecular Basis of Influence of A501X Mutations in Penicillin-Binding Protein 2 ofInternational journal of molecular sciences · 2024Article
- Condensed Matter Systems Exposed to Radiation: Multiscale Theory, Simulations, and Experiment.Chemical reviews · 2024Review
21 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
13 authors.
Funding
Abstract
Hybrid methods that combine quantum mechanics (QM) and molecular mechanics (MM) can be applied to studies of reaction mechanisms in locations ranging from active sites of small enzymes to multiple sites in large bioenergetic complexes. By combining the widely used molecular dynamics and visualization programs NAMD and VMD with the quantum chemistry packages ORCA and MOPAC, we created an integrated, comprehensive, customizable, and easy-to-use suite (http://www.ks.uiuc.edu/Research/qmmm). Through the QwikMD interface, setup, execution, visualization, and analysis are streamlined for all levels of expertise.
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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.