ReviewCurrent opinion in structural biology2008
Multiscale methods for macromolecular simulations.
Review in Current opinion in structural biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 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
51 citing papers in PubMed.
- Article
- Computational and Experimental Approaches to Investigate Lipid Nanoparticles as Drug and Gene Delivery Systems.Current topics in medicinal chemistry · 2021Review
- Multiscale simulation unravel the kinetic mechanisms of inflammasome assembly.Biochimica et biophysica acta. Molecular cell research · 2020Article
- Atomic-level reconstruction of biomolecules by a rigid-fragment- and local-frame-based (RF-LF) strategy.Journal of molecular modeling · 2020Article
- A Multiscale Model for the Self-Assembly of Coat Proteins in Bacteriophage MS2.Journal of chemical information and modeling · 2019Article
- Peptides for Infectious Diseases: From Probe Design to Diagnostic Microarrays.Antibodies (Basel, Switzerland) · 2019Review
- Integrating Structural Information to Study the Dynamics of Protein-Protein Interactions in Cells.Structure (London, England : 1993) · 2018Article
- Adaptive QM/MM for Molecular Dynamics Simulations: 5. On the Energy-Conserved Permuted Adaptive-Partitioning Schemes.Molecules (Basel, Switzerland) · 2018Article
- General principles of binding between cell surface receptors and multi-specific ligands: A computational study.PLoS computational biology · 2017Article
- A coarse-grained model for assisting the investigation of structure and dynamics of large nucleic acids by ion mobility spectrometry-mass spectrometry.Physical chemistry chemical physics : PCCP · 2017Article
- Review
- Protocols for Molecular Dynamics Simulations of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2017Article
- Cellular Delivery of RNA Nanoparticles.ACS combinatorial science · 2016Review
- A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds.Molecules (Basel, Switzerland) · 2015Article
- Integrating atomistic molecular dynamics simulations, experiments, and network analysis to study protein dynamics: strength in unity.Frontiers in molecular biosciences · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.Journal of chemical theory and computation · 2014Article
- Web-based computational chemistry education with CHARMMing I: Lessons and tutorial.PLoS computational biology · 2014Article
- Computational and experimental characterization of RNA cubic nanoscaffolds.Methods (San Diego, Calif.) · 2014Article
- Theoretical frameworks for multiscale modeling and simulation.Current opinion in structural biology · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
In this article we review the key modeling tools available for simulating biomolecular systems. We consider recent developments and representative applications of mixed quantum mechanics/molecular mechanics (QM/MM), elastic network models (ENMs), coarse-grained molecular dynamics, and grid-based tools for calculating interactions between essentially rigid protein assemblies. We consider how the different length scales can be coupled, both in a sequential fashion (e.g. a coarse-grained or grid model using parameterization from MD simulations), and via concurrent approaches, where the calculations are performed together and together control the progression of the simulation. We suggest how the concurrent coupling approach familiar in the context of QM/MM calculations can be generalized, and describe how this has been done in the CHARMM macromolecular simulation package.
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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.