ArticleProceedings of the National Academy of Sciences of the United States of America2014
Trajectories of the ribosome as a Brownian nanomachine.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 122 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
122 citing papers in PubMed.
- Digital twin of biomacromolecular thermodynamics in cryo-EM data.Communications chemistry · 2026Article
- Engineered Cas9 complexes establish an experimentally grounded benchmark for heterogeneous cryoEM reconstruction methods.bioRxiv : the preprint server for biology · 2026Article
- Signal extraction in SWAXS data for the compact X-ray light sources: a machine learning approach.Scientific reports · 2026Article
- Comparing cryo-EM methods and molecular dynamics simulation to investigate heterogeneity in ligand-bound TRPV1.Nature communications · 2025Article
- The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge.bioRxiv : the preprint server for biology · 2025Article
- Elastic analysis bridges structure and dynamics of an AAA+ molecular motor.PLoS computational biology · 2025Article
- Amortized template matching of molecular conformations from cryoelectron microscopy images using simulation-based inference.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Building molecular model series from heterogeneous CryoEM structures using Gaussian mixture models and deep neural networks.Communications biology · 2025Article
- Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN.Nature communications · 2025Article
- Unraveling atomic complexity from frozen samples.Structural dynamics (Melville, N.Y.) · 2025Article
- The role of ribosomal protein networks in ribosome dynamics.Nucleic acids research · 2025Article
- Methods to Study Poxvirus Structures by Cryo-EM Imaging Modalities.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Integration of Experimental and Computational Methods to Characterize Glycoproteins.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Filling data analysis gaps in time-resolved crystallography by machine learning.Structural dynamics (Melville, N.Y.) · 2025Article
- End-to-end Training of Latent Space Diffusion Models for Conformational Heterogeneity in Cryo-EM Reconstruction.International Conference Image and Vision Computing New Zealand : [proceedings]. International Conference Image and Vision Computing New Zealand · 2024Article
- Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions.IUCrJ · 2024Article
- DynaMight: estimating molecular motions with improved reconstruction from cryo-EM images.Nature methods · 2024Article
- CLEAPA: a framework for exploring the conformational landscape of cryo-EM using energy-aware pathfinding algorithm.Bioinformatics (Oxford, England) · 2024Article
- Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes.International journal of molecular sciences · 2024Article
- A unified view on enzyme catalysis by cryo-EM study of a DNA topoisomerase.Communications chemistry · 2024Article
62 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
14 authors.
Funding
Abstract
A Brownian machine, a tiny device buffeted by the random motions of molecules in the environment, is capable of exploiting these thermal motions for many of the conformational changes in its work cycle. Such machines are now thought to be ubiquitous, with the ribosome, a molecular machine responsible for protein synthesis, increasingly regarded as prototypical. Here we present a new analytical approach capable of determining the free-energy landscape and the continuous trajectories of molecular machines from a large number of snapshots obtained by cryogenic electron microscopy. We demonstrate this approach in the context of experimental cryogenic electron microscope images of a large ensemble of nontranslating ribosomes purified from yeast cells. The free-energy landscape is seen to contain a closed path of low energy, along which the ribosome exhibits conformational changes known to be associated with the elongation cycle. Our approach allows model-free quantitative analysis of the degrees of freedom and the energy landscape underlying continuous conformational changes in nanomachines, including those important for biological function.
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.