ReviewJournal of structural biology2011
Exploring the spatial and temporal organization of a cell's proteome.
Review in Journal of structural biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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
15 citing papers in PubMed, 35 citations in OpenAlex.
- Spatiotemporal dynamics of self-assembled structures in enzymatically induced agonistic and antagonistic conditions.Chemical science · 2021Article
- EvoSeg: Automated Electron Microscopy Segmentation through Random Forests and Evolutionary Optimization.Biomimetics (Basel, Switzerland) · 2021Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Principles and Overview of Sampling Methods for Modeling Macromolecular Structure and Dynamics.PLoS computational biology · 2016Review
- Experimental detection of short regulatory motifs in eukaryotic proteins: tips for good practice as well as for bad.Cell communication and signaling : CCS · 2015Review
- Combined approaches to flexible fitting and assessment in virus capsids undergoing conformational change.Journal of structural biology · 2014Article
- Computational methods for constructing protein structure models from 3D electron microscopy maps.Journal of structural biology · 2013Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Automated target segmentation and real space fast alignment methods for high-throughput classification and averaging of crowded cryo-electron subtomograms.Bioinformatics (Oxford, England) · 2013Article
- A computational approach to increase time scales in Brownian dynamics-based reaction-diffusion modeling.Journal of computational biology : a journal of computational molecular cell biology · 2012Article
- High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching.Journal of structural biology · 2012Article
- ATTRACT-EM: a new method for the computational assembly of large molecular machines using cryo-EM maps.PloS one · 2012Article
- High precision alignment of cryo-electron subtomograms through gradient-based parallel optimization.BMC systems biology · 2012Article
- Template-free detection of macromolecular complexes in cryo electron tomograms.Bioinformatics (Oxford, England) · 2011Article
- Gradient-based high precision alignment of cryo-electron subtomograms.IEEE International Conference on Systems Biology : [proceedings]. IEEE International Conference on Systems Biology · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 3 institutions in 3 countries.
Funding
Abstract
To increase our current understanding of cellular processes, such as cell signaling and division, knowledge is needed about the spatial and temporal organization of the proteome at different organizational levels. These levels cover a wide range of length and time scales: from the atomic structures of macromolecules for inferring their molecular function, to the quantitative description of their abundance, and spatial distribution in the cell. Emerging new experimental technologies are greatly increasing the availability of such spatial information on the molecular organization in living cells. This review addresses three fields that have significantly contributed to our understanding of the proteome's spatial and temporal organization: first, methods for the structure determination of individual macromolecular assemblies, specifically the fitting of atomic structures into density maps generated from electron microscopy techniques; second, research that visualizes the spatial distributions of these complexes within the cellular context using cryo electron tomography techniques combined with computational image processing; and third, methods for the spatial modeling of the dynamic organization of the proteome, specifically those methods for simulating reaction and diffusion of proteins and complexes in crowded intracellular fluids. The long-term goal is to integrate the varied data about a proteome's organization into a spatially explicit, predictive model of cellular processes.
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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.