A New View of the Bacterial Cytosol Environment

Mobility of Cytoplasmic, Membrane, and DNA-Binding Proteins in Escherichia coli

(2010) Mohit Kumar et al.   BIOPHYSICAL JOURNAL

Measuring enzyme activities under standardized in vivo-like conditions for systems biology

(2010) Karen van Eunen et al.   FEBS Journal

Size Dependence of Protein Diffusion in the Cytoplasm of Escherichia coli

(2010) A. Nenninger et al.   JOURNAL OF BACTERIOLOGY

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field

(2010) Devleena Shivakumar et al.   Journal of Chemical Theory and Computation

Crowding and hydrodynamic interactions likely dominate in vivo macromolecular motion

(2010) T. Ando et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anchors Away for Ubiquitin Chains

(2010) K. Parvatiyar et al.   SCIENCE

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Influence of uncertainties in pH, pMg, activity coefficients, metabolite concentrations, and other factors on the analysis of the thermodynamic feasibility of metabolic pathways

(2009) Vojislav Vojinović et al.   BIOTECHNOLOGY AND BIOENGINEERING

Hydrogen Bonding and π-Stacking: How Reliable are Force Fields? A Critical Evaluation of Force Field Descriptions of Nonbonded Interactions

(2009) Robert S. Paton et al.   Journal of Chemical Information and Modeling

The ubiquitin system

(2009) Deepa Nath et al.   NATURE

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

Coarse-Grained Molecular Simulation of Diffusion and Reaction Kinetics in a Crowded Virtual Cytoplasm

(2008) Douglas Ridgway et al.   BIOPHYSICAL JOURNAL

Stochastic thermostats: comparison of local and global schemes

(2008) Giovanni Bussi et al.   COMPUTER PHYSICS COMMUNICATIONS

Effect of Salt on the Dynamics of Aqueous Solution of Hydrophobic Solutes: A Molecular Dynamics Simulation Study†

(2008) Niharendu Choudhury   JOURNAL OF CHEMICAL AND ENGINEERING DATA

A comparative study of two classical force fields on statics and dynamics of [EMIM][BF4] investigated via molecular dynamics simulations

(2008) Florian Dommert et al.   JOURNAL OF CHEMICAL PHYSICS

On the computation and contribution of conductivity in molecular ionic liquids

(2008) C. Schröder et al.   JOURNAL OF CHEMICAL PHYSICS

Reconstruction of biochemical networks in microorganisms

(2008) Adam M. Feist et al.   NATURE REVIEWS MICROBIOLOGY