ReviewJournal of molecular graphics & modelling2013
Reaching new levels of realism in modeling biological macromolecules in cellular environments.
Review in Journal of molecular graphics & modelling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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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.
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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
27 citing papers in PubMed.
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- Review
- Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.PLoS computational biology · 2023Article
- Crowding within synaptic junctions influences the degradation of nucleotides by CD39 and CD73 ectonucleotidases.Biophysical journal · 2022Article
- Computer-Aided Whole-Cell Design: Taking a Holistic Approach by Integrating Synthetic With Systems Biology.Frontiers in bioengineering and biotechnology · 2020Article
- Recent Advances in Coarse-Grained Models for Biomolecules and Their Applications.International journal of molecular sciences · 2019Review
- Particle-Based Simulation Reveals Macromolecular Crowding Effects on the Michaelis-Menten Mechanism.Biophysical journal · 2019Article
- Dynamic cluster formation determines viscosity and diffusion in dense protein solutions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- Toward an understanding of biochemical equilibria within living cells.Biophysical reviews · 2018Review
- High-Performance Data Analysis on the Big Trajectory Data of Cellular Scale All-atom Molecular Dynamics Simulations.Journal of physics. Conference series · 2018Article
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
- Crowding in Cellular Environments at an Atomistic Level from Computer Simulations.The journal of physical chemistry. B · 2017Article
- Explicit Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Protein Mixtures. 2. Effects of Varying Hard and Soft Interactions upon Prototypical Chemical Equilibria.The journal of physical chemistry. B · 2017Article
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Article
- Challenges in structural approaches to cell modeling.Journal of molecular biology · 2016Review
- GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations.Wiley interdisciplinary reviews. Computational molecular science · 2015Article
- Complete atomistic model of a bacterial cytoplasm for integrating physics, biochemistry, and systems biology.Journal of molecular graphics & modelling · 2015Article
- Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.Journal of chemical theory and computation · 2015Article
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
An increasing number of studies are aimed at modeling cellular environments in a comprehensive and realistic fashion. A major challenge in these efforts is how to bridge spatial and temporal scales over many orders of magnitude. Furthermore, there are additional challenges in integrating different aspects ranging from questions about biomolecular stability in crowded environments to the description of reactive processes on cellular scales. In this review, recent studies with models of biomolecules in cellular environments at different levels of detail are discussed in terms of their strengths and weaknesses. In particular, atomistic models, implicit representations of cellular environments, coarse-grained and spheroidal models of biomolecules, as well as the inclusion of reactive processes via reaction-diffusion models are described. Furthermore, strategies for integrating the different models into a comprehensive description of cellular environments are discussed.
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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.