ReviewStructure (London, England : 1993)2009
Discovery through the computational microscope.
Review in Structure (London, England : 1993), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 137 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
137 citing papers in PubMed.
- A new method to build an initial configuration for molecular modeling.Journal of molecular modeling · 2026Article
- Bayesian-Steered Structure Prediction of Mechanical Biomolecules Using Twisted Diffusion.bioRxiv : the preprint server for biology · 2026Article
- PySteMoDA: An Open-Source Python Package for the Analysis of Steered Molecular Dynamics Simulations Data.bioRxiv : the preprint server for biology · 2026Article
- Computational methods in physical virology: a critical perspective across lengths and timescales.FEMS microbiology reviews · 2026Review
- Bridging Scales: Coarse-Grained Protein Models in Computational Biology.Advances in experimental medicine and biology · 2026Review
- Molecular Modeling and Molecular Dynamics Simulation of a Packed and Intact Bacterial Microcompartment.The journal of physical chemistry. B · 2025Article
- High-Speed Atomic Force Microscopy Reveals the Dynamic Interplay of Membrane Proteins is Lipid-Modulated.Small science · 2025Article
- Combining Fast Exploration with Accurate Reweighting in the OPES-eABF Hybrid Sampling Method.Journal of chemical theory and computation · 2025Article
- In silico analyses of molecular force sensors for mechanical characterization of biological systems.Biophysical journal · 2025Article
- Article
- Structures of Oligomeric States of Tau Protein, Amyloid-β, α-Synuclein and Prion Protein Implicated in Alzheimer's Disease, Parkinson's Disease and Prionopathies.International journal of molecular sciences · 2024Review
- Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning.Biophysical journal · 2024Article
- Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells.ACS omega · 2024Article
- Guidelines for naming and studying plasma membrane domains in plants.Nature plants · 2024Review
- Article
- Interactions of a Novel Anthracycline with Oligonucleotide DNA and Cyclodextrins in an Aqueous Environment.The journal of physical chemistry. B · 2024Article
- Illuminating ligand-induced dynamics in nuclear receptors through MD simulations.Biochimica et biophysica acta. Gene regulatory mechanisms · 2024Review
- Comparative Pore Structure and Dynamics for Bacterial Microcompartment Shell Protein Assemblies in Sheets or Shells.bioRxiv : the preprint server for biology · 2024Article
- AMBERff at Scale: Multimillion-Atom Simulations with AMBER Force Fields in NAMD.Journal of chemical information and modeling · 2024Article
- Mesoscale simulations: An indispensable approach to understand biomembranes.Biophysical journal · 2023Review
77 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
5 authors.
Funding
Abstract
All-atom molecular dynamics simulations have become increasingly popular as a tool to investigate protein function and dynamics. However, researchers are concerned about the short time scales covered by simulations, the apparent impossibility to model large and integral biomolecular systems, and the actual predictive power of the molecular dynamics methodology. Here we review simulations that were in the past both hotly disputed and considered key successes, namely of proteins with mainly mechanical functions (titin, fibrinogen, ankyrin, and cadherin). The simulation work covered shows how state-of-the-art modeling alleviates some of the prior concerns and how unrefuted discoveries are made through the "computational microscope."
Indexed as
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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.