Low-Resolution Models for the Interaction Dynamics of Coated Gold Nanoparticles with β2-microglobulin

Citrate stabilized gold nanoparticles interfere with amyloid fibril formation: D76N and ΔN6 β2-microglobulin variants

(2018) Giorgia Brancolini et al.   Nanoscale

Multiscale modeling of proteins interaction with functionalized nanoparticles

(2018) Giorgia Brancolini et al.   CURRENT OPINION IN COLLOID & INTERFACE SCIENCE

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

(2017) Paweł Krupa et al.   Journal of Chemical Information and Modeling

Citrate-stabilized gold nanoparticles hinder fibrillogenesis of a pathological variant of β2-microglobulin

(2017) Cristina Cantarutti et al.   Nanoscale

Coarse-Grained Protein Models and Their Applications

(2016) Sebastian Kmiecik et al.   CHEMICAL REVIEWS

Deriving Coarse-Grained Charges from All-Atom Systems: An Analytic Solution

(2016) Peter McCullagh et al.   Journal of Chemical Theory and Computation

Understanding and Designing the Gold-Bio Interface: Insights from Simulations

(2016) Patrick Charchar et al.   Small

Probing the Influence of Citrate-Capped Gold Nanoparticles on an Amyloidogenic Protein

(2015) Giorgia Brancolini et al.   ACS Nano

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

Coarse-grained model of adsorption of blood plasma proteins onto nanoparticles

(2015) Hender Lopez et al.   JOURNAL OF CHEMICAL PHYSICS

SDA 7: A modular and parallel implementation of the simulation of diffusional association software

(2015) Michael Martinez et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Functionalized Gold Nanoparticles: Synthesis, Properties and Applications—A Review

(2015) Saji Alex et al.   JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY

Competitive Binding of Proteins to Gold Nanoparticles Disclosed by Molecular Dynamics Simulations

(2015) Francesco Tavanti et al.   Journal of Physical Chemistry C

A closer look into the ubiquitin corona on gold nanoparticles by computational studies

(2015) Francesco Tavanti et al.   NEW JOURNAL OF CHEMISTRY

Diffusion within the Cytoplasm: A Mesoscale Model of Interacting Macromolecules

(2014) Fabio Trovato et al.   BIOPHYSICAL JOURNAL

Minimalist Model for the Dynamics of Helical Polypeptides: A Statistic-Based Parametrization

(2014) Giulia Lia Beatrice Spampinato et al.   Journal of Chemical Theory and Computation

RESPAC: Method to Determine Partial Charges in Coarse-Grained Protein Model and Its Application to DNA-Binding Proteins

(2014) Tsuyoshi Terakawa et al.   Journal of Chemical Theory and Computation

Surface Effects on Aggregation Kinetics of Amyloidogenic Peptides

(2014) Robert Vácha et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Gold nanoparticles: testbeds for engineered protein–particle interactions

(2014) Daniel F Moyano et al.   Nanomedicine

Can small hydrophobic gold nanoparticles inhibit β2-microglobulin fibrillation?

(2014) Giorgia Brancolini et al.   Nanoscale

Colloidal nanoparticles as advanced biological sensors

(2014) P. D. Howes et al.   SCIENCE

A Minimalist Model of Protein Diffusion and Interactions: The Green Fluorescent Protein within the Cytoplasm

(2013) Fabio Trovato et al.   MACROMOLECULES

The gold–sulfur interface at the nanoscale

(2012) Hannu Häkkinen   Nature Chemistry

Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models

(2011) A. Ortega et al.   BIOPHYSICAL JOURNAL

Rigid body constraints realized in massively-parallel molecular dynamics on graphics processing units

(2011) Trung Dac Nguyen et al.   COMPUTER PHYSICS COMMUNICATIONS

Brownian Dynamics Simulation of Protein Solutions: Structural and Dynamical Properties

(2010) Paolo Mereghetti et al.   BIOPHYSICAL JOURNAL

Minimalist models for proteins: a comparative analysis

(2010) Valentina Tozzini   QUARTERLY REVIEWS OF BIOPHYSICS

Complexes of HIV-1 integrase with HAT proteins: Multiscale models, dynamics, and hypotheses on allosteric sites of inhibition

(2009) Armida Di Fenza et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Fast procedure for reconstruction of full-atom protein models from reduced representations

(2008) Piotr Rotkiewicz et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

GolP: An atomistic force-field to describe the interaction of proteins with Au(111) surfaces in water

(2008) F. Iori et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS