A hybrid approach for coarse-graining helical peptoids: Solvation, secondary structure, and assembly

Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets

(2022) Mingfei Zhao et al.   BIOMACROMOLECULES

Interaction energy between neuronal cell receptors and peptoid ligands

(2021) Mohan Yasodharababu et al.   JOURNAL OF BIOMECHANICS

Potent Antiviral Activity against HSV-1 and SARS-CoV-2 by Antimicrobial Peptoids

(2021) Gill Diamond et al.   Pharmaceuticals

Quantifying Polypeptoid Conformational Landscapes through Integrated Experiment and Simulation

(2021) Sally Jiao et al.   MACROMOLECULES

Polypeptoids and Peptoid–Peptide Hybrids by Transition Metal Catalysis

(2021) Zachary S. Clauss et al.   ACS Applied Materials & Interfaces

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

(2021) Akash Banerjee et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

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

Resolving the Morphology of Peptoid Vesicles at the One Nanometer Length-Scale Using Cryogenic Electron Microscopy

(2019) Xi Jiang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptoid microsphere coatings: The effects of helicity, temperature, pH, and ionic strength

(2019) German R. Perez Bakovic et al.   BIOPOLYMERS

A CGenFF‐based force field for simulations of peptoids with both cis and trans peptide bonds

(2019) Laura J. Weiser et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Peptides and peptidomimetics as inhibitors of protein–protein interactions involving β-sheet secondary structures

(2019) José Laxio Arenas et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Universal Relationship between Molecular Structure and Crystal Structure in Peptoid Polymers and Prevalence of the cis Backbone Conformation

(2018) Douglas R. Greer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Conformations of peptoids in nanosheets result from the interplay of backbone energetics and intermolecular interactions

(2018) John R. Edison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Designable and dynamic single-walled stiff nanotubes assembled from sequence-defined peptoids

(2018) Haibao Jin et al.   Nature Communications

Biasing Smarter, Not Harder, by Partitioning Collective Variables into Families in Parallel Bias Metadynamics

(2018) Arushi Prakash et al.   Journal of Chemical Theory and Computation

Precisely tuneable energy transfer system using peptoid helix-based molecular scaffold

(2017) Boyeong Kang et al.   Scientific Reports

Morphology and Proton Transport in Humidified Phosphonated Peptoid Block Copolymers

(2016) Jing Sun et al.   MACROMOLECULES

Development of protein mimics for intracellular delivery

(2015) Brittany M. deRonde et al.   BIOPOLYMERS

Efficient Sampling of High-Dimensional Free-Energy Landscapes with Parallel Bias Metadynamics

(2015) Jim Pfaendtner et al.   Journal of Chemical Theory and Computation

Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential

(2015) Sudipto Mukherjee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Peptoid nanosheets exhibit a new secondary-structure motif

(2015) Ranjan V. Mannige et al.   NATURE

Modeling Sequence-Specific Polymers Using Anisotropic Coarse-Grained Sites Allows Quantitative Comparison with Experiment

(2014) Thomas K. Haxton et al.   Journal of Chemical Theory and Computation

Morphology-Conductivity Relationship in Crystalline and Amorphous Sequence-Defined Peptoid Block Copolymer Electrolytes

(2014) Jing Sun et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assembly and molecular order of two-dimensional peptoid nanosheets through the oil–water interface

(2014) Ellen J. Robertson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Peptoid Polymers: A Highly Designable Bioinspired Material

(2013) Jing Sun 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

Development and use of an atomistic CHARMM-based forcefield for peptoid simulation

(2013) Dina T. Mirijanian et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Tunable peptoid microspheres: effects of side chain chemistry and sequence

(2013) Melissa L. Hebert et al.   ORGANIC & BIOMOLECULAR CHEMISTRY

Improved Parameters for the Martini Coarse-Grained Protein Force Field

(2012) Djurre H. de Jong et al.   Journal of Chemical Theory and Computation

Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral Angles

(2012) Robert B. Best et al.   Journal of Chemical Theory and Computation

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

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

Structure–Conductivity Relationship for Peptoid-Based PEO–Mimetic Polymer Electrolytes

(2012) Jing Sun et al.   MACROMOLECULES

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

(2012) Emiliano Brini et al.   Soft Matter

Structural and Dynamical Characteristics of Peptoid Oligomers with Achiral Aliphatic Side Chains Studied by Molecular Dynamics Simulation

(2011) Sung Hyun Park et al.   JOURNAL OF PHYSICAL CHEMISTRY B

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

Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER

(2010) Vincent A. Voelz et al.   BIOPOLYMERS

Hierarchical Self-Assembly of a Biomimetic Diblock Copolypeptoid into Homochiral Superhelices

(2010) Hannah K. Murnen et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Synthetic mimetics of protein secondary structure domains

(2010) N. T. Ross et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Multiscale Coarse-Graining of the Protein Energy Landscape

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

Versatile Object-Oriented Toolkit for Coarse-Graining Applications

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

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields

(2009) K. Vanommeslaeghe et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

A Preliminary Survey of the Peptoid Folding Landscape

(2009) Glenn L. Butterfoss 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

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

(2009) Christine Peter et al.   Soft Matter

The MARTINI Coarse-Grained Force Field: Extension to Proteins

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

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS