Computational Approaches to Understanding the Self-assembly of Peptide-based Nanostructures

Design of nanostructures based on aromatic peptide amphiphiles

(2014) Scott Fleming et al.   CHEMICAL SOCIETY REVIEWS

Peptide-Based Carbohydrate Receptors

(2014) Melanie Rauschenberg et al.   CHEMISTRY-A EUROPEAN JOURNAL

Minimal Model of Self-Assembly: Emergence of Diversity and Complexity

(2014) Bogdan Barz et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of the pH-Controlled Self-Assembly of Nanofibers from Peptide Amphiphiles

(2014) Yoann Cote et al.   Journal of Physical Chemistry C

Supramolecular Assembly of Asymmetric Self-Neutralizing Amphiphilic Peptide Wedges

(2014) Dara Van Gough et al.   LANGMUIR

β Sheets Not Required: Combined Experimental and Computational Studies of Self-Assembly and Gelation of the Ester-Containing Analogue of an Fmoc-Dipeptide Hydrogelator

(2014) Kevin M. Eckes et al.   LANGMUIR

Chirality effects at each amino acid position on tripeptide self-assembly into hydrogel biomaterials

(2014) S. Marchesan et al.   Nanoscale

Triphenylalanine peptides self-assemble into nanospheres and nanorods that are different from the nanovesicles and nanotubes formed by diphenylalanine peptides

(2014) Cong Guo et al.   Nanoscale

Exploring the sequence space for (tri-)peptide self-assembly to design and discover new hydrogels

(2014) Pim W. J. M. Frederix et al.   Nature Chemistry

Effects of hydrophobic interaction strength on the self-assembled structures of model peptides

(2014) Yan Mu et al.   Soft Matter

Molecular characterization of l-phenylalanine terminated poly(l-lactide) conjugates

(2014) Sara K. Murase et al.   RSC Advances

Ion Channel Models Based on Self-Assembling Cyclic Peptide Nanotubes

(2013) Javier Montenegro et al.   ACCOUNTS OF CHEMICAL RESEARCH

Exploring the sequence–structure relationship for amyloid peptides

(2013) Kyle L. Morris et al.   BIOCHEMICAL JOURNAL

Self-assembly of ciprofloxacin and a tripeptide into an antimicrobial nanostructured hydrogel

(2013) Silvia Marchesan et al.   BIOMATERIALS

Effects of mutations in de novo designed synthetic amphiphilic β-sheet peptides on self-assembly of fibrils

(2013) Yoav Raz et al.   CHEMICAL COMMUNICATIONS

Stabilization of α-helices by the self-assembly of macrocyclic peptides on the surface of gold nanoparticles for molecular recognition

(2013) Boram Kim et al.   CHEMICAL COMMUNICATIONS

Tuning of peptide assembly through force balance adjustment

(2013) Meiwen Cao et al.   JOURNAL OF COLLOID AND INTERFACE SCIENCE

Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

(2013) Tao Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Self-Assembly of Arg–Phe Nanostructures via the Solid–Vapor Phase Method

(2013) Michelle S. Liberato et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Free-Energy Landscape for Peptide Amphiphile Self-Assembly: Stepwise versus Continuous Assembly Mechanisms

(2013) Tao Yu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Self-Assembly of Cysteine Dimers at the Gold Surface: A Computational Study of Competing Interactions

(2013) Chris R. L. Chapman et al.   Journal of Physical Chemistry C

Ferrocenoyl Phenylalanine: A New Strategy Toward Supramolecular Hydrogels with Multistimuli Responsive Properties

(2013) Zhifang Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assessing the Utility of Infrared Spectroscopy as a Structural Diagnostic Tool for β-Sheets in Self-Assembling Aromatic Peptide Amphiphiles

(2013) Scott Fleming et al.   LANGMUIR

Tuning the Self-Assembly of Short Peptides via Sequence Variations

(2013) Yurong Zhao et al.   LANGMUIR

Spectroscopic signatures of an Fmoc–tetrapeptide, Fmoc and fluorene

(2013) Yi Zou et al.   RSC Advances

Probing the Self-Assembly Mechanism of Diphenylalanine-Based Peptide Nanovesicles and Nanotubes

(2012) Cong Guo et al.   ACS Nano

Self-Assembling Nanotubes Consisting of Rigid Cyclic γ-Peptides

(2012) Liangchun Li et al.   ADVANCED FUNCTIONAL MATERIALS

Experimental and Computational Studies Reveal an Alternative Supramolecular Structure for Fmoc-Dipeptide Self-Assembly

(2012) Xiaojia Mu et al.   BIOMACROMOLECULES

A molecular dynamics simulation of N-(fluorenyl-9-methoxycarbonyl)-dipeptides supramolecular hydrogel

(2012) Heng Zhang et al.   COLLOIDS AND SURFACES A-PHYSICOCHEMICAL AND ENGINEERING ASPECTS

Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides

(2012) Mikyung Seo et al.   Journal of Chemical Theory and Computation

Driving Forces and Structural Determinants of Steric Zipper Peptide Oligomer Formation Elucidated by Atomistic Simulations

(2012) Dirk Matthes et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular dynamics simulation of β-sheet formation in self-assembled peptide amphiphile fibers

(2012) One-Sun Lee et al.   JOURNAL OF NANOPARTICLE RESEARCH

A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly

(2012) Scott P. Carmichael et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Vibrational spectroscopy of self-assembling aromatic peptide derivates

(2012) Wiwat Nuansing et al.   JOURNAL OF RAMAN SPECTROSCOPY

Sequence, Structure, and Function of Peptide Self-Assembled Monolayers

(2012) Ann K. Nowinski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The Rheological and Structural Properties of Fmoc-Peptide-Based Hydrogels: The Effect of Aromatic Molecular Architecture on Self-Assembly and Physical Characteristics

(2012) Ron Orbach et al.   LANGMUIR

Modeling the Self-Assembly of Peptide Amphiphiles into Fibers Using Coarse-Grained Molecular Dynamics

(2012) One-Sun Lee et al.   NANO LETTERS

Unzipping the role of chirality in nanoscale self-assembly of tripeptide hydrogels

(2012) Silvia Marchesan et al.   Nanoscale

Structure and stability of cyclic peptide based nanotubes: a molecular dynamics study of the influence of amino acid composition

(2012) Ramadoss Vijayaraj et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Sequence/structure relationships in aromatic dipeptide hydrogels formed under thermodynamic control by enzyme-assisted self-assembly

(2012) Meghan Hughes et al.   Soft Matter

Tripeptide self-assembled hydrogels: unexpected twists of chirality

(2011) Silvia Marchesan et al.   CHEMICAL COMMUNICATIONS

The effect of polarization on multiple hydrogen-bond formation in models of self-assembling materials

(2011) Yung-Fou Chen et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Direct evaluation of individual hydrogen bond energy in situ in intra- and intermolecular multiple hydrogen bonds system

(2011) Cui Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Virtual Screening for Dipeptide Aggregation: Toward Predictive Tools for Peptide Self-Assembly

(2011) Pim W. J. M. Frederix et al.   Journal of Physical Chemistry Letters

Simulation of Peptide–Surface Recognition

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

Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers

(2011) One-Sun Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Tuning the Self-Assembly of the Bioactive Dipeptidel-Carnosine by Incorporation of a Bulky Aromatic Substituent

(2011) V. Castelletto et al.   LANGMUIR

A Challenge for Peptide Coarse Graining: Transferability of Fragment-Based Models

(2011) Ozge Engin et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Biocatalytic self-assembly of 2D peptide-based nanostructures

(2011) Meghan Hughes et al.   Soft Matter

Coassembly of Oppositely Charged Short Peptides into Well-Defined Supramolecular Hydrogels

(2010) Xiao-Ding Xu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments

(2010) Rebeca García-Fandiño et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hydrogelation Through Self-Assembly of Fmoc-Peptide Functionalized Cationic Amphiphiles: Potent Antibacterial Agent

(2010) Sisir Debnath et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding Cooperativity in Hydrogen-Bond-Induced Supramolecular Polymerization: A Density Functional Theory Study

(2010) Ivo A. W. Filot et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Tuning Supramolecular Rigidity of Peptide Fibers through Molecular Structure

(2010) E. Thomas Pashuck et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Polarization at metal-biomolecular interfaces in solution

(2010) H. Heinz et al.   Journal of the Royal Society Interface

An investigation of the conductivity of peptide nanotube networks prepared by enzyme-triggered self-assembly

(2010) Haixia Xu et al.   Nanoscale

Biocatalytic induction of supramolecular order

(2010) Andrew R. Hirst et al.   Nature Chemistry

Bionanosphere Lithography via Hierarchical Peptide Self-Assembly of Aromatic Triphenylalanine

(2010) Tae Hee Han et al.   Small

Molecular Recognition and Supramolecular Self-Assembly of a Genetically Engineered Gold Binding Peptide on Au{111}

(2009) Christopher R. So et al.   ACS Nano

Introducing chemical functionality in Fmoc-peptide gels for cell culture

(2009) Vineetha Jayawarna et al.   Acta Biomaterialia

Self-Assembly of Phenylalanine Oligopeptides: Insights from Experiments and Simulations

(2009) Phanourios Tamamis et al.   BIOPHYSICAL JOURNAL

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Averaging Semiempirical NMR Chemical Shifts: Dynamic Effects on the Subpicosecond Time Scale†

(2009) Tell Tuttle   JOURNAL OF PHYSICAL CHEMISTRY A

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

Self-assembling dipeptides: including solvent degrees of freedom in a coarse-grained model

(2009) Alessandra Villa et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Self-assembling dipeptides: conformational sampling in solvent-free coarse-grained simulation

(2009) Alessandra Villa et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

A Theoretical Comparison of Self-Assembling α- and β-Peptide Nanostructures: Toward Design of β-Barrel Frameworks

(2008) Tamás Beke et al.   ACS Nano

An Efficient Fmoc-SPPS Approach for the Generation of Thioester Peptide Precursors for Use in Native Chemical Ligation

(2008) Juan B. Blanco-Canosa et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

The MARTINI Coarse-Grained Force Field: Extension to Proteins

(2008) Luca Monticelli et al.   Journal of Chemical Theory and Computation

Molecular Simulation Study of Peptide Amphiphile Self-Assembly

(2008) Yuri S. Velichko et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Probing Peptide Nanotube Self-Assembly at a Liquid−Liquid Interface with Coarse-Grained Molecular Dynamics

(2008) Ekta Khurana et al.   NANO LETTERS

Self-assembling peptide nanotubes

(2008) Shane Scanlon et al.   Nano Today

Enzyme-assisted self-assembly under thermodynamic control

(2008) Richard J. Williams et al.   Nature Nanotechnology

Self-assembly of amphiphiles with terthiophene and tripeptide segments into helical nanostructures

(2008) Wei-Wen Tsai et al.   TETRAHEDRON

Fmoc-Diphenylalanine Self Assembles to a Hydrogel via a Novel Architecture Based on π–π Interlocked β-Sheets

(2007) A. M. Smith et al.   ADVANCED MATERIALS