Efficient conformational sampling of peptides adsorbed onto inorganic surfaces: insights from a quartz binding peptide

Peptide Adsorption on Silica Nanoparticles: Evidence of Hydrophobic Interactions

(2012) Valeria Puddu et al.   ACS Nano

Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

(2012) Galen Collier et al.   Biointerphases

Force-Field Dependence of Chignolin Folding and Misfolding: Comparison with Experiment and Redesign

(2012) Petra Kührová et al.   BIOPHYSICAL JOURNAL

First-principles molecular dynamics simulations of NH 4+ and CH3COO− adsorption at the aqueous quartz interface

(2012) Louise B. Wright et al.   JOURNAL OF CHEMICAL PHYSICS

Replica exchange with nonequilibrium switches: Enhancing equilibrium sampling by increasing replica overlap

(2012) Andrew J. Ballard et al.   JOURNAL OF CHEMICAL PHYSICS

Nanotechnology Meets Biology: Peptide-based Methods for the Fabrication of Functional Materials

(2012) Beverly D. Briggs et al.   Journal of Physical Chemistry Letters

Chemistry of Aqueous Silica Nanoparticle Surfaces and the Mechanism of Selective Peptide Adsorption

(2012) Siddharth V. Patwardhan et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

On achieving high accuracy and reliability in the calculation of relative protein-ligand binding affinities

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

Peptide-directed co-assembly of nanoprobes on multimaterial patterned solid surfaces

(2012) Marketa Hnilova et al.   Soft Matter

Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach

(2012) R. B. Pandey et al.   Soft Matter

Nanotechnology: Emerging Tool for Diagnostics and Therapeutics

(2011) Mainak Chakraborty et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Theranostic Applications of Nanomaterials in Cancer: Drug Delivery, Image-Guided Therapy, and Multifunctional Platforms

(2011) Alicia Fernandez-Fernandez et al.   APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY

Gold nanoparticles functionalized with therapeutic and targeted peptides for cancer treatment

(2011) Anil Kumar et al.   BIOMATERIALS

How Robust Are Protein Folding Simulations with Respect to Force Field Parameterization?

(2011) Stefano Piana et al.   BIOPHYSICAL JOURNAL

Toxicity of Multiwalled Carbon Nanotubes with End Defects Critically Depends on Their Functionalization Density

(2011) Sanyog Jain et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Protein−Nanoparticle Interactions: Opportunities and Challenges

(2011) Morteza Mahmoudi et al.   CHEMICAL REVIEWS

Engineered nanostructural materials for application in cancer biology and medicine

(2011) Meena Mahmood et al.   JOURNAL OF APPLIED TOXICOLOGY

Computing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations

(2011) Yilin Meng et al.   Journal of Chemical Theory and Computation

Single-step fabrication of patterned gold film array by an engineered multi-functional peptide

(2011) Marketa Hnilova et al.   JOURNAL OF COLLOID AND INTERFACE SCIENCE

Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2)

(2011) Lingle Wang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Simulations of Ovocleidin-17 Binding to Calcite Surfaces and Its Implications for Eggshell Formation

(2011) Colin L. Freeman et al.   Journal of Physical Chemistry C

Facet Selectivity of Binding on Quartz Surfaces: Free Energy Calculations of Amino-Acid Analogue Adsorption

(2011) Louise B. Wright et al.   Journal of Physical Chemistry C

Simulation of Peptide–Surface Recognition

(2011) Rosa Di Felice et al.   Journal of Physical Chemistry Letters

Structure of Peptides on Metal Oxide Surfaces Probed by NMR

(2011) Peter A. Mirau et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Crystallographic Recognition Controls Peptide Binding for Bio-Based Nanomaterials

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

Preferential Binding of Peptides to Graphene Edges and Planes

(2011) Sang N. Kim et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Template Engineering Through Epitope Recognition: A Modular, Biomimetic Strategy for Inorganic Nanomaterial Synthesis

(2011) Alia P. Schoen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Specific Material Recognition by Small Peptides Mediated by the Interfacial Solvent Structure

(2011) Julian Schneider et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Adsorption of Homopolypeptides on Gold Investigated Using Atomistic Molecular Dynamics

(2011) Ana Vila Verde et al.   LANGMUIR

Material Binding Peptides for Nanotechnology

(2011) Urartu Ozgur Safak Seker et al.   MOLECULES

Interaction of β-Sheet Folds with a Gold Surface

(2011) Martin Hoefling et al.   PLoS One

Solution Study of Engineered Quartz Binding Peptides Using Replica Exchange Molecular Dynamics

(2010) Rebecca Notman et al.   BIOMACROMOLECULES

Molecular biomimetics: GEPI-based biological routes to technology

(2010) Candan Tamerler et al.   BIOPOLYMERS

Applications of peptide and protein-based materials in bionanotechnology

(2010) Roberto de la Rica et al.   CHEMICAL SOCIETY REVIEWS

Exchange Often and Properly in Replica Exchange Molecular Dynamics

(2010) Daniel J. Sindhikara et al.   Journal of Chemical Theory and Computation

Improved Replica Exchange Method for Native-State Protein Sampling

(2010) Samuel L. C. Moors et al.   Journal of Chemical Theory and Computation

The temperature intervals with global exchange of replicas empirical accelerated sampling method: Parameter sensitivity and extension to a complex molecular system

(2010) Xianfeng Li et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

On easy implementation of a variant of the replica exchange with solute tempering in GROMACS

(2010) Tsuyoshi Terakawa et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Enhanced Conformational Sampling of Peptides via Reduced Side-Chain and Solvent Masses

(2010) I-Chun Lin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Nacre Protein Fragment Templates Lamellar Aragonite Growth

(2010) Rebecca A. Metzler et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

What the Cell “Sees” in Bionanoscience

(2010) Dorota Walczyk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Probing the Molecular Mechanisms of Quartz-Binding Peptides

(2010) Ersin Emre Oren et al.   LANGMUIR

Investigation of the influence of surface defects on peptide adsorption onto carbon nanotubes

(2010) T. R. Walsh et al.   Molecular BioSystems

Interplay of Sequence, Conformation, and Binding at the Peptide−Titania Interface as Mediated by Water

(2009) Adam A. Skelton et al.   ACS Applied Materials & Interfaces

Genetically Designed Peptide-Based Molecular Materials

(2009) Candan Tamerler et al.   ACS Nano

Molecular simulation of protein-surface interactions: Benefits, problems, solutions, and future directions (Review)

(2009) Robert A. Latour   Biointerphases

Improving replica exchange using driven scaling

(2009) Alexis J. Lee et al.   JOURNAL OF CHEMICAL PHYSICS

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

(2009) Xianfeng Li et al.   JOURNAL OF CHEMICAL PHYSICS

Optimized Molecular Dynamics Force Fields Applied to the Helix−Coil Transition of Polypeptides

(2009) Robert B. Best et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Modeling the Binding Affinity of Peptides for Graphitic Surfaces. Influences of Aromatic Content and Interfacial Shape

(2009) Susana M. Tomásio et al.   Journal of Physical Chemistry C

Adsorption of Ionic Peptides on Inorganic Supports

(2009) Susanna Monti et al.   Journal of Physical Chemistry C

Nature of Molecular Interactions of Peptides with Gold, Palladium, and Pd−Au Bimetal Surfaces in Aqueous Solution

(2009) Hendrik Heinz et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Molecular Dynamics Studies of the Interactions of Water and Amino Acid Analogues with Quartz Surfaces

(2009) Rebecca Notman et al.   LANGMUIR

Molecular dynamics simulations of peptides on calcite surface

(2009) Mingjun Yang et al.   MOLECULAR SIMULATION

Replica exchange with nonequilibrium switches

(2009) A. J. Ballard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Are Current Molecular Dynamics Force Fields too Helical?

(2008) Robert B. Best et al.   BIOPHYSICAL JOURNAL

Silica Biomineralisation in Diatoms: The Model Organism Thalassiosira pseudonana

(2008) Manfred Sumper et al.   CHEMBIOCHEM

Biological Control on Calcite Crystallization by Polysaccharides

(2008) Mingjun Yang et al.   CRYSTAL GROWTH & DESIGN

Exchange frequency in replica exchange molecular dynamics

(2008) Daniel Sindhikara et al.   JOURNAL OF CHEMICAL PHYSICS

Hamiltonian replica exchange molecular dynamics using soft-core interactions

(2008) Jozef Hritz et al.   JOURNAL OF CHEMICAL PHYSICS

Implicit Solvent Models and the Energy Landscape for Aggregation of the Amyloidogenic KFFE Peptide

(2008) Birgit Strodel et al.   Journal of Chemical Theory and Computation

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

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

A temperature predictor for parallel tempering simulations

(2008) Alexandra Patriksson et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Functionalized Carbon Nanotubes in Drug Design and Discovery

(2007) Maurizio Prato et al.   ACCOUNTS OF CHEMICAL RESEARCH