ReviewJournal of structural biology2007
High performance computing in biology: multimillion atom simulations of nanoscale systems.
Review in Journal of structural biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
35 citing papers in PubMed.
- Identification of Potential Pancreatic Lipase Inhibitors from Traditional Chinese Medicines via Molecular Docking, Molecular Dynamics Simulation and In Vitro Validation.Current issues in molecular biology · 2026Article
- High-Performance Computing in Tandem Mass Spectrometry (MS/MS) Peptide Identification.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Collective mechanical responses of cadherin-based adhesive junctions as predicted by simulations.Biophysical journal · 2022Article
- Elastic versus brittle mechanical responses predicted for dimeric cadherin complexes.Biophysical journal · 2022Article
- Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives.International journal of molecular sciences · 2022Review
- Molecular dynamics simulations reveal the selectivity mechanism of structurally similar agonists to TLR7 and TLR8.PloS one · 2022Article
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
- Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies.BMC bioinformatics · 2017Article
- Designing the Sniper: Improving Targeted Human Cytolytic Fusion Proteins for Anti-Cancer Therapy via Molecular Simulation.Biomedicines · 2017Review
- Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation.BMC bioinformatics · 2017Article
- Ribosome Mechanics Informs about Mechanism.Journal of molecular biology · 2016Review
- Elucidating the fundamental forces in protein crystal formation: the case of crambin.Chemical science · 2016Article
- Recent advances in QM/MM free energy calculations using reference potentials.Biochimica et biophysica acta · 2015Review
- Computational modeling of RNA 3D structures, with the aid of experimental restraints.RNA biology · 2014Review
- A generic force field for protein coarse-grained molecular dynamics simulation.International journal of molecular sciences · 2012Article
- Effect of the thermostat in the molecular dynamics simulation on the folding of the model protein chignolin.Journal of molecular modeling · 2012Article
- Key intermolecular interactions in the E. coli 70S ribosome revealed by coarse-grained analysis.Journal of the American Chemical Society · 2011Article
- Multiscale simulation of microbe structure and dynamics.Progress in biophysics and molecular biology · 2011Article
- RNA and protein 3D structure modeling: similarities and differences.Journal of molecular modeling · 2011Review
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
Computational methods have been used in biology for sequence analysis (bioinformatics), all-atom simulation (molecular dynamics and quantum calculations), and more recently for modeling biological networks (systems biology). Of these three techniques, all-atom simulation is currently the most computationally demanding, in terms of compute load, communication speed, and memory load. Breakthroughs in electrostatic force calculation and dynamic load balancing have enabled molecular dynamics simulations of large biomolecular complexes. Here, we report simulation results for the ribosome, using approximately 2.64 million atoms, the largest all-atom biomolecular simulation published to date. Several other nano-scale systems with different numbers of atoms were studied to measure the performance of the NAMD molecular dynamics simulation program on the Los Alamos National Laboratory Q Machine. We demonstrate that multimillion atom systems represent a 'sweet spot' for the NAMD code on large supercomputers. NAMD displays an unprecedented 85% parallel scaling efficiency for the ribosome system on 1024 CPUs. We also review recent targeted molecular dynamics simulations of the ribosome that prove useful for studying conformational changes of this large biomolecular complex in atomic detail.
Indexed as
Identifiers
What OpenQuestion holds
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.