NANOGOLD decorated by pHLIP peptide: comparative force field study

Targeting acidity in diseased tissues: Mechanism and applications of the membrane-inserting peptide, pHLIP

(2015) John C. Deacon et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Lipid Headgroups Modulate Membrane Insertion of pHLIP Peptide

(2015) Alexander Kyrychenko et al.   BIOPHYSICAL JOURNAL

Atomistic Simulations of Coating of Silver Nanoparticles with Poly(vinylpyrrolidone) Oligomers: Effect of Oligomer Chain Length

(2015) Alexander Kyrychenko et al.   Journal of Physical Chemistry C

Atomistic simulations of anionic Au144(SR)60 nanoparticles interacting with asymmetric model lipid membranes

(2014) Elena Heikkilä et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Comparative Study of Materials-Binding Peptide Interactions with Gold and Silver Surfaces and Nanostructures: A Thermodynamic Basis for Biological Selectivity of Inorganic Materials

(2014) J. Pablo Palafox-Hernandez et al.   CHEMISTRY OF MATERIALS

Lanthanide-coated gold nanoparticles for biomedical applications

(2014) David J. Lewis et al.   COORDINATION CHEMISTRY REVIEWS

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Benchmarking of Force Fields for Molecule–Membrane Interactions

(2014) Markéta Paloncýová et al.   Journal of Chemical Theory and Computation

Residue-Specific Force Field Based on the Protein Coil Library. RSFF1: Modification of OPLS-AA/L

(2014) Fan Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

(2014) Grzegorz Nawrocki et al.   Journal of Physical Chemistry C

Folding of Fourteen Small Proteins with a Residue-Specific Force Field and Replica-Exchange Molecular Dynamics

(2014) Fan Jiang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Folding Simulations for Proteins with Diverse Topologies Are Accessible in Days with a Physics-Based Force Field and Implicit Solvent

(2014) Hai Nguyen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Theoretical Description of the Role of Halides, Silver, and Surfactants on the Structure of Gold Nanorods

(2014) Neyvis Almora-Barrios et al.   NANO LETTERS

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

(2014) Oliver Stueker et al.   Small

Are Current Atomistic Force Fields Accurate Enough to Study Proteins in Crowded Environments?

(2014) Drazen Petrov et al.   PLoS Computational Biology

Targeting diseased tissues by pHLIP insertion at low cell surface pH

(2014) Oleg A. Andreev et al.   Frontiers in Physiology

Evidence of energy transfer from tryptophan to BSA/HSA protected gold nanoclusters

(2014) Sangram Raut et al.   Methods and Applications in Fluorescence

Biomolecular Recognition Principles for Bionanocombinatorics: An Integrated Approach To Elucidate Enthalpic and Entropic Factors

(2013) Zhenghua Tang et al.   ACS Nano

Physicochemical Properties of Nanoparticles Regulate Translocation across Pulmonary Surfactant Monolayer and Formation of Lipoprotein Corona

(2013) Guoqing Hu et al.   ACS Nano

Insights into cell entry and intracellular trafficking of peptide and protein drugs provided by electron microscopy

(2013) Helerin Margus et al.   ADVANCED DRUG DELIVERY REVIEWS

A Controlled-Release Nanocarrier with Extracellular pH Value Driven Tumor Targeting and Translocation for Drug Delivery

(2013) Zilong Zhao et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100)

(2013) Louise B. Wright et al.   Journal of Chemical Theory and Computation

Improved Generalized Born Solvent Model Parameters for Protein Simulations

(2013) Hai Nguyen et al.   Journal of Chemical Theory and Computation

CHARMM36 all-atom additive protein force field: Validation based on comparison to NMR data

(2013) Jing Huang et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Conformational Behavior of Genetically-Engineered Dodecapeptides as a Determinant of Binding Affinity for Gold.

(2013) Stefano Corni et al.   Journal of Physical Chemistry C

First-Principles-Based Force Field for the Interaction of Proteins with Au(100)(5 × 1): An Extension of GolP-CHARMM

(2013) Louise B. Wright et al.   Journal of Physical Chemistry C

Engineering Gold Nanoparticle Interaction by PAMAM Dendrimer

(2013) Taraknath Mandal et al.   Journal of Physical Chemistry C

Structure of Mixed-Monolayer-Protected Nanoparticles in Aqueous Salt Solution from Atomistic Molecular Dynamics Simulations

(2013) Reid C. Van Lehn et al.   Journal of Physical Chemistry C

pH dependent transfer of nano-pores into membrane of cancer cells to induce apoptosis

(2013) Dayanjali Wijesinghe et al.   Scientific Reports

pH-Controlled Delivery of Nanoparticles into Tumor Cells

(2013) Liang Han et al.   Advanced Healthcare Materials

Detecting and Destroying Cancer Cells in More than One Way with Noble Metals and Different Confinement Properties on the Nanoscale

(2012) Erik C. Dreaden et al.   ACCOUNTS OF CHEMICAL RESEARCH

Designing Nanoparticle Translocation through Membranes by Computer Simulations

(2012) Hong-ming Ding et al.   ACS Nano

Spectroscopic investigation of the interactions between gold nanoparticles and bovine serum albumin

(2012) XiuJuan Shi et al.   CHINESE SCIENCE BULLETIN

Critical Assessment of Current Force Fields. Short Peptide Test Case

(2012) Jiří Vymětal et al.   Journal of Chemical Theory and Computation

Atomistic Simulations of Functional Au144(SR)60 Gold Nanoparticles in Aqueous Environment

(2012) Elena Heikkilä et al.   Journal of Physical Chemistry C

Supercrystals of DNA-Functionalized Gold Nanoparticles: A Million-Atom Molecular Dynamics Simulation Study

(2012) Van A. Ngo et al.   Journal of Physical Chemistry C

Fluorescence Probing of Thiol-Functionalized Gold Nanoparticles: Is Alkylthiol Coating of a Nanoparticle as Hydrophobic as Expected?

(2012) Alexander Kyrychenko et al.   Journal of Physical Chemistry C

Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations

(2012) Ting I.N.G. Li et al.   NANO LETTERS

pH (low) insertion peptide (pHLIP) targets ischemic myocardium

(2012) E. A. Sosunov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pHLIP peptide targets nanogold particles to tumors

(2012) L. Yao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pH-controlled delivery of luminescent europium coated nanoparticles into platelets

(2012) A. Davies et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multifunctional Nanoparticles: Cost Versus Benefit of Adding Targeting and Imaging Capabilities

(2012) Z. Cheng et al.   SCIENCE

Influence of the Shape of Nanostructured Metal Surfaces on Adsorption of Single Peptide Molecules in Aqueous Solution

(2012) Jie Feng et al.   Small

Beating cancer in multiple ways using nanogold

(2011) Erik C. Dreaden et al.   CHEMICAL SOCIETY REVIEWS

The golden age: gold nanoparticles for biomedicine

(2011) Erik C. Dreaden et al.   CHEMICAL SOCIETY REVIEWS

Gold Nanoparticle/Polymer Interfaces: All Atom Structures from Molecular Dynamics Simulations

(2011) G. Milano et al.   Journal of Physical Chemistry C

Simulation Study of Aggregations of Monolayer-Protected Gold Nanoparticles in Solvents

(2011) Jia-Qi Lin et al.   Journal of Physical Chemistry C

Crystallographic Recognition Controls Peptide Binding for Bio-Based Nanomaterials

(2011) Ryan Coppage et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Influence of Amino Acid Sequence and Functionality on the Binding Process of Peptides onto Gold Surfaces

(2011) Jing Yu et al.   LANGMUIR

Preparation, structure, and a coarse-grained molecular dynamics model for dodecanethiol-stabilized gold nanoparticles

(2011) Alexander Kyrychenko et al.   Computational and Theoretical Chemistry

Penetration of Lipid Membranes by Gold Nanoparticles: Insights into Cellular Uptake, Cytotoxicity, and Their Relationship

(2010) Jiaqi Lin et al.   ACS Nano

A Quantitative, Real-Time Assessment of Binding of Peptides and Proteins to Gold Surfaces

(2010) Ori Cohavi et al.   CHEMISTRY-A EUROPEAN JOURNAL

The Conformations of Amino Acids on a Gold(111) Surface

(2010) Martin Hoefling et al.   CHEMPHYSCHEM

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models

(2010) Pär Bjelkmar et al.   Journal of Chemical Theory and Computation

Atomistic Simulation Study of Striped Phase Separation in Mixed-Ligand Self-Assembled Monolayer Coated Nanoparticles

(2010) Pradip Kr. Ghorai et al.   Journal of Physical Chemistry C

Using DNA to Link Gold Nanoparticles, Polymers, and Molecules: A Theoretical Perspective

(2010) One-Sun Lee et al.   Journal of Physical Chemistry Letters

Nuclear Targeting of Gold Nanoparticles in Cancer Cells Induces DNA Damage, Causing Cytokinesis Arrest and Apoptosis

(2010) Bin Kang et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Interaction of Amino Acids with the Au(111) Surface: Adsorption Free Energies from Molecular Dynamics Simulations

(2010) Martin Hoefling et al.   LANGMUIR

Challenges in protein-folding simulations

(2010) Peter L. Freddolino et al.   Nature Physics

pH (low) insertion peptide (pHLIP) inserts across a lipid bilayer as a helix and exits by a different path

(2010) O. A. Andreev et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Molecular Dynamics Simulation of the Stability-Limited Growth Mechanism of Peptide-Mediated Gold-Nanoparticle Synthesis

(2010) Jing Yu et al.   Small

Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations

(2009) Ana Vila Verde et al.   BIOMACROMOLECULES

Bilayer Interactions of pHLIP, a Peptide that Can Deliver Drugs and Target Tumors

(2008) Manuela Zoonens et al.   BIOPHYSICAL JOURNAL

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

Accurate Simulation of Surfaces and Interfaces of Face-Centered Cubic Metals Using 12−6 and 9−6 Lennard-Jones Potentials

(2008) Hendrik Heinz et al.   Journal of Physical Chemistry C

Competing Adsorption between Hydrated Peptides and Water onto Metal Surfaces: From Electronic to Conformational Properties

(2008) Luca M. Ghiringhelli et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Energetics of peptide (pHLIP) binding to and folding across a lipid bilayer membrane

(2008) Y. K. Reshetnyak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2007) Berk Hess   Journal of Chemical Theory and Computation