The cytoplasm of the gram-negative bacterium Escherichia coli is very densely packed with macromolecules, and this highly crowded environment is expected to have a significant impact on the diffusive and thermodynamic properties of its constituents. Continuing progress in the field of structural biology now allows molecular simulations of the cytoplasm to be performed with structurally detailed models, providing a new, computational view of macromolecular behavior in vivo (see McGuffee, Elcock, doi:10.1371/journal.pcbi.1000694).
Image Credit: Adrian H Elcock (University of Iowa)
Message from ISCB
Getting Started in Gene Orthology and Functional Analysis
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000703
Research Articles
Using Pre-existing Microarray Datasets to Increase Experimental Power: Application to Insulin Resistance
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000718
Specialization Can Drive the Evolution of Modularity
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000719
Drug-Class Specific Impact of Antivirals on the Reproductive Capacity of HIV
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000720
The Impact of Contact Tracing in Clustered Populations
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000721
Investigating Homology between Proteins using Energetic Profiles
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000722
Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000723
A Human-Specific De Novo Protein-Coding Gene Associated with Human Brain Functions
PLOS Computational Biology: published March 26, 2010 | https://doi.org/10.1371/journal.pcbi.1000734
Tumor Growth Rate Determines the Timing of Optimal Chronomodulated Treatment Schedules
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000712
Estimating the Stoichiometry of HIV Neutralization
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000713
Predicting Transmembrane Helix Packing Arrangements using Residue Contacts and a Force-Directed Algorithm
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000714
Patient Referral Patterns and the Spread of Hospital-Acquired Infections through National Health Care Networks
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000715
Emergence of Spatial Structure in Cell Groups and the Evolution of Cooperation
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000716
Predicted Auxiliary Navigation Mechanism of Peritrichously Flagellated Chemotactic Bacteria
PLOS Computational Biology: published March 19, 2010 | https://doi.org/10.1371/journal.pcbi.1000717
Quantitative Comparison of Catalytic Mechanisms and Overall Reactions in Convergently Evolved Enzymes: Implications for Classification of Enzyme Function
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000700
Non-Linear Neuronal Responses as an Emergent Property of Afferent Networks: A Case Study of the Locust Lobula Giant Movement Detector
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000701
Effects of Transcriptional Pausing on Gene Expression Dynamics
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000704
Detailed Simulations of Cell Biology with Smoldyn 2.1
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000705
A Multiscale Model to Investigate Circadian Rhythmicity of Pacemaker Neurons in the Suprachiasmatic Nucleus
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000706
Modeling Co-Expression across Species for Complex Traits: Insights to the Difference of Human and Mouse Embryonic Stem Cells
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000707
Slower Visuomotor Corrections with Unchanged Latency are Consistent with Optimal Adaptation to Increased Endogenous Noise in the Elderly
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000708
Comparing Families of Dynamic Causal Models
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000709
Interplay between Pleiotropy and Secondary Selection Determines Rise and Fall of Mutators in Stress Response
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000710
Neocortical Axon Arbors Trade-off Material and Conduction Delay Conservation
PLOS Computational Biology: published March 12, 2010 | https://doi.org/10.1371/journal.pcbi.1000711
Molecular Structures of Quiescently Grown and Brain-Derived Polymorphic Fibrils of the Alzheimer Amyloid Aβ9-40 Peptide: A Comparison to Agitated Fibrils
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000693
Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000694
Designing Focused Chemical Libraries Enriched in Protein-Protein Interaction Inhibitors using Machine-Learning Methods
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000695
Parameter Estimation and Model Selection in Computational Biology
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000696
Within- and Cross-Modal Distance Information Disambiguate Visual Size-Change Perception
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000697
Systematic Planning of Genome-Scale Experiments in Poorly Studied Species
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000698
Estimating the Stochastic Bifurcation Structure of Cellular Networks
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000699
Related Articles
Mathematical Modelling of Cell-Fate Decision in Response to Death Receptor Engagement
PLOS Computational Biology: published March 5, 2010 | https://doi.org/10.1371/journal.pcbi.1000702