Understanding Interactions of Functionalized Nanoparticles with Proteins: A Case Study on Lactate Dehydrogenase

Exploring the essential collective dynamics of interacting proteins: Application to prion protein dimers

(2013) Bilkiss B. Issack et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Molecular Mechanisms in the Activation of Abscisic Acid Receptor PYR1

(2013) Lyudmyla Dorosh et al.   PLoS Computational Biology

Docking of Ubiquitin to Gold Nanoparticles

(2012) Giorgia Brancolini et al.   ACS Nano

Conformational modes in biomolecules: Dynamics and approximate invariance

(2012) Alex Potapov et al.   PHYSICAL REVIEW E

Protein−Nanoparticle Interactions: Opportunities and Challenges

(2011) Morteza Mahmoudi et al.   CHEMICAL REVIEWS

Understanding and controlling the interaction of nanomaterials with proteins in a physiological environment

(2011) Carl D. Walkey et al.   CHEMICAL SOCIETY REVIEWS

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Binding Ligands and Cofactor toL-Lactate Dehydrogenase from Human Skeletal and Heart Muscles

(2011) Katarzyna Świderek et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Inhibition of enzyme activity by nanomaterials: Potential mechanisms and implications for nanotoxicity testing

(2011) Tyson J. MacCormack et al.   Nanotoxicology

Effects of Temperature on the p53-DNA Binding Interactions and Their Dynamical Behavior: Comparing the Wild Type to the R248Q Mutant

(2011) Khaled Barakat et al.   PLoS One

Comparative analysis of essential collective dynamics and NMR-derived flexibility profiles in evolutionarily diverse prion proteins

(2011) Kolattukudy P Santo et al.   Prion

Soft Hedgehogs on Coarse Carpets: A Molecular Simulation Study of Capped Nanocrystals Interacting with Self-Assembled Monolayers of Alkylthiols on a Gold (111) Surface

(2010) Philipp Schapotschnikow et al.   Journal of Physical Chemistry C

Debunking Some Misconceptions about Nanotoxicology

(2010) David B. Warheit   NANO LETTERS

Structural Domains and Main-Chain Flexibility in Prion Proteins†

(2009) N. Blinov et al.   BIOCHEMISTRY

Understanding interactions between capped nanocrystals: Three-body and chain packing effects

(2009) Philipp Schapotschnikow et al.   JOURNAL OF CHEMICAL PHYSICS

Identification of dynamic structural domains in proteins, analysis of local bond flexibility and application for interpretation of NMR experiments

(2009) Maria Stepanova   MOLECULAR SIMULATION

Understanding biophysicochemical interactions at the nano–bio interface

(2009) Andre E. Nel et al.   NATURE MATERIALS

Site-directed nanoparticle labeling of cytochrome c

(2009) M.-E. Aubin-Tam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

(2008) Berk Hess et al.   Journal of Chemical Theory and Computation

Including image charge effects in the molecular dynamics simulations of molecules on metal surfaces

(2008) F. Iori 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

Molecular Simulations of Interacting Nanocrystals

(2008) Philipp Schapotschnikow et al.   NANO LETTERS

P-LINCS:  A Parallel Linear Constraint Solver for Molecular Simulation

(2007) Berk Hess   Journal of Chemical Theory and Computation