CHARMM36m: an improved force field for folded and intrinsically disordered proteins

Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, +5

Nature Methods

Protein AssemblyProtein FoldingNatural SciencesImproved Force FieldMolecular Biology +5

Crowding in Cellular Environments at an Atomistic Level from Computer Simulations

Michael Feig, Isseki Yu, Po-Hung Wang, +2

The Journal of Physical Chemistry B

Conformational DynamicsCrowd SimulationBiophysical ModelingEngineeringSimulation +19

CHARMM36: An Improved Force Field for Folded and Intrinsically Disordered Proteins

Jing Huang, Sarah Rauscher, Grzegorz Nawrocki, +5

Biophysical Journal

Protein AssemblyIntrinsically Disordered ProteinsProtein FoldingNatural SciencesImproved Force Field +6

Slow-Down in Diffusion in Crowded Protein Solutions Correlates with Transient Cluster Formation

Grzegorz Nawrocki, Po-Hung Wang, Isseki Yu, +2

The Journal of Physical Chemistry B

Biophysical ModelingEngineeringLong TimeProtein FoldingDiffusion Process +12

Clustering and dynamics of crowded proteins near membranes and their influence on membrane bending

Grzegorz Nawrocki, Wonpil Im, Yuji Sugita, +1

Proceedings of the National Academy of Sciences

Effect of protein–protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments

Grzegorz Nawrocki, Alp Karaboga, Yuji Sugita, +1

Physical Chemistry Chemical Physics

Protein ChemistryProtein–protein InteractionsBiophysical ModelingBiochemistryProtein Crowder Molecules +11

Accurate determination of solvation free energies of neutral organic compounds from first principles

Leonid Pereyaslavets, Ganesh Kamath, Oleg Butin, +21

Nature Communications

Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields

Grzegorz Nawrocki, Marek Cieplak

The Journal of Physical Chemistry C

EngineeringPeptide EngineeringProtein Phase SeparationProtein RefoldingMolecular Dynamics +21

Reduced efficacy of a Src kinase inhibitor in crowded protein solution

Kento Kasahara, Suyong Re, Grzegorz Nawrocki, +8

Nature Communications

Combining Force Fields and Neural Networks for an Accurate Representation of Chemically Diverse Molecular Interactions

Alexey Illarionov, Serzhan Sakipov, Leonid Pereyaslavets, +17

Journal of the American Chemical Society

EngineeringMolecular BiologyComputational ChemistryChemistryForce Fields +19