A hybrid coarse-grained model for structure, solvation and assembly of lipid-like peptides

A MARTINI-Compatible Coarse-Grained Model for the Mesoscale Simulation of Peptoids

(2020) Mingfei Zhao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Backmapping from Multiresolution Coarse-Grained Models to Atomic Structures of Large Biomolecules by Restrained Molecular Dynamics Simulations using Bayesian Inference

(2019) Junhui Peng et al.   Journal of Chemical Theory and Computation

Transferable Coarse-Grained Models of Liquid–Liquid Equilibrium Using Local Density Potentials Optimized with the Relative Entropy

(2018) Tanmoy Sanyal et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Designing phenylalanine-based hybrid biological materials: controlling morphology via molecular composition

(2018) Srinivas Mushnoori et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Molecular Dynamics Simulation for All

(2018) Scott A. Hollingsworth et al.   NEURON

Coarse-Grained Molecular Simulation of the Hierarchical Self-Assembly of π-Conjugated Optoelectronic Peptides

(2017) Rachael A. Mansbach et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Control of the hierarchical assembly of π-conjugated optoelectronic peptides by pH and flow

(2017) Rachael A. Mansbach et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Coarse-grained models using local-density potentials optimized with the relative entropy: Application to implicit solvation

(2016) Tanmoy Sanyal et al.   JOURNAL OF CHEMICAL PHYSICS

Sodium chloride's effect on self-assembly of diphenylalanine bilayer

(2016) Junpyo Kwon et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Tripeptide Emulsifiers

(2015) Gary G. Scott et al.   ADVANCED MATERIALS

Amphiphilic Peptides A6K and V6K Display Distinct Oligomeric Structures and Self-Assembly Dynamics: A Combined All-Atom and Coarse-Grained Simulation Study

(2015) Yunxiang Sun et al.   BIOMACROMOLECULES

The design of shape-tunable hairy vesicles

(2015) Fikret Aydin et al.   COLLOIDS AND SURFACES B-BIOINTERFACES

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

Molecular insights into the self-assembly of short amphiphilic peptides FmDn and FmKn

(2014) Naresh Thota et al.   RSC Advances

Nanofiber-Based Delivery of Therapeutic Peptides to the Brain

(2013) Mariarosa Mazza et al.   ACS Nano

Perspective on the Martini model

(2013) Siewert J. Marrink et al.   CHEMICAL SOCIETY REVIEWS

Perspective: Coarse-grained models for biomolecular systems

(2013) W. G. Noid   JOURNAL OF CHEMICAL PHYSICS

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models

(2013) Tsjerk A. Wassenaar et al.   Journal of Chemical Theory and Computation

Self-Assembly of Amphiphilic Peptide (AF)6H5K15: Coarse-Grained Molecular Dynamics Simulation

(2013) Naresh Thota et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mechanism of IAPP amyloid fibril formation involves an intermediate with a transient  -sheet

(2013) L. E. Buchanan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Cong Guo et al.   ACS Nano

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

The multiscale coarse-graining method. IX. A general method for construction of three body coarse-grained force fields

(2012) Avisek Das et al.   JOURNAL OF CHEMICAL PHYSICS

Multiscale simulation of small peptides: Consistent conformational sampling in atomistic and coarse-grained models

(2012) Olga Bezkorovaynaya et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

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

Tunable Self-Assembled Peptide Amphiphile Nanostructures

(2012) Qingbin Meng 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

Systematic coarse-graining methods for soft matter simulations – a review

(2012) Emiliano Brini et al.   Soft Matter

Modeling the Self-Assembly of Lipids and Nanotubes in Solution: Forming Vesicles and Bicelles with Transmembrane Nanotube Channels

(2011) Meenakshi Dutt et al.   ACS Nano

Toward a Molecular Theory of Early and Late Events in Monomer to Amyloid Fibril Formation

(2011) John E. Straub et al.   Annual Review of Physical Chemistry

Coarse-grained models for protein aggregation

(2011) Chun Wu et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

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

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

Hybrid Approaches to Coarse-Graining using the VOTCA Package: Liquid Hexane

(2011) Victor Rühle et al.   MACROMOLECULAR THEORY AND SIMULATIONS

Multiscale modeling of soft matter: scaling of dynamics

(2011) Dominik Fritz et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Self-assembly of amphiphilic peptides

(2011) I. W. Hamley   Soft Matter

The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials

(2010) Luca Larini et al.   JOURNAL OF CHEMICAL PHYSICS

Forming transmembrane channels using end-functionalized nanotubes

(2010) Meenakshi Dutt et al.   Nanoscale

Designer Amphiphilic Short Peptides Enhance Thermal Stability of Isolated Photosystem-I

(2010) Baosheng Ge et al.   PLoS One

Multiscale Coarse-Graining of the Protein Energy Landscape

(2010) Ronald D. Hills et al.   PLoS Computational Biology

Association of Helical β-Peptides and their Aggregation Behavior from the Potential of Mean Force in Explicit Solvent

(2009) Clark A. Miller et al.   BIOPHYSICAL JOURNAL

Simulations of nucleation and elongation of amyloid fibrils

(2009) Jianing Zhang et al.   JOURNAL OF CHEMICAL PHYSICS

Isothermal-isobaric molecular dynamics using stochastic velocity rescaling

(2009) Giovanni Bussi et al.   JOURNAL OF CHEMICAL PHYSICS

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

(2009) Victor Rühle et al.   Journal of Chemical Theory and Computation

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

Multiscale simulation of soft matter systems – from the atomistic to the coarse-grained level and back

(2009) Christine Peter et al.   Soft Matter

The relative entropy is fundamental to multiscale and inverse thermodynamic problems

(2008) M. Scott Shell   JOURNAL OF CHEMICAL PHYSICS

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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

Designer Peptide Surfactants Stabilize Functional Photosystem-I Membrane Complex in Aqueous Solution for Extended Time⊥

(2008) Kazuya Matsumoto et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Understanding Self-Assembled Amphiphilic Peptide Supramolecular Structures from Primary Structure Helix Propensity

(2008) Martina K. Baumann et al.   LANGMUIR