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ACS NANO (2014)
Complementary Co-assembling Peptides: From In Silico Studies to In Vivo Application
Andrea Raspa et al.
ADVANCED FUNCTIONAL MATERIALS (2014)
Biomaterials for Tissue Engineering
Esther J. Lee et al.
ANNALS OF BIOMEDICAL ENGINEERING (2014)
CHARMM All-Atom Additive Force Field for Sphingomyelin: Elucidation of Hydrogen Bonding and of Positive Curvature
Richard M. Venable et al.
BIOPHYSICAL JOURNAL (2014)
Rapid Communication Computational Simulation and Analysis of a Candidate for the Design of a Novel Silk-Based Biopolymer
Ewa I. Golas et al.
BIOPOLYMERS (2014)
The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems
Fabio Sterpone et al.
CHEMICAL SOCIETY REVIEWS (2014)
Modelling and analysis of early aggregation events of BMHP1-derived self-assembling peptides
Gloria Anna Ada Saracino et al.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2014)
Mechanism of Folding and Binding of an Intrinsically Disordered Protein As Revealed by ab Initio Simulations
Mateusz Kurcinski et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
Tsjerk A. Wassenaar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
Lipid14: The Amber Lipid Force Field
Callum J. Dickson et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions
Adam Liwo et al.
JOURNAL OF MOLECULAR MODELING (2014)
Refined OPLS All-Atom Force Field for Saturated Phosphatidylcholine Bilayers at Full Hydration
Arkadiusz Maciejewski et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2014)
Lipid Organization of the Plasma Membrane
Helgi I. Ingolfsson et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2014)
Double-stranded RNA under force and torque: Similarities to and striking differences from double-stranded DNA
Jan Lipfert et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2014)
Synthetic biodegradable functional polymers for tissue engineering: a brief review
Guo BaoLin et al.
SCIENCE CHINA-CHEMISTRY (2014)
DFT optimization and DFT-MD studies of glucose, ten explicit water molecules enclosed by an implicit solvent, COSMO
Frank Momany et al.
COMPUTATIONAL AND THEORETICAL CHEMISTRY (2014)
Molecular dynamics study of DNA oligomers under angled pulling
A. M. Naserian-Nik et al.
RSC ADVANCES (2014)
Hyaluronan and cardiac regeneration
Francesca Bonafe et al.
JOURNAL OF BIOMEDICAL SCIENCE (2014)
Tuning supramolecular mechanics to guide neuron development
Shantanu Sur et al.
BIOMATERIALS (2013)
Perspective on the Martini model
Siewert J. Marrink et al.
CHEMICAL SOCIETY REVIEWS (2013)
Nanomaterials design and tests for neural tissue engineering
Gloria A. A. Saracino et al.
CHEMICAL SOCIETY REVIEWS (2013)
Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION
Nathalie Basdevant et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
PaLaCe: A Coarse-Grain Protein Model for Studying Mechanical Properties
Marco Pasi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
PRIMO: A Transferable Coarse-Grained Force Field for Proteins
Parimal Kar et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Polarizable Atomic Multipole-Based AMOEBA Force Field for Proteins
Yue Shi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)
Steered Molecular Dynamics Studies of the Potential of Mean Force for Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
Tao Yu et al.
JOURNAL OF PHYSICAL CHEMISTRY A (2013)
On the Foldability of Tryptophan-Containing Tetra- and Pentapeptides: An Exhaustive Molecular Dynamics Study
Panagiota S. Georgoulia et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Mixing MARTINI: Electrostatic Coupling in Hybrid Atomistic-Coarse-Grained Biomolecular Simulations
Tsjerk A. Wassenaar et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Coarse-Grained Model for Predicting RNA Folding Thermodynamics
Natalia A. Denesyuk et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2013)
Mechanical Identities of RNA and DNA Double Helices Unveiled at the Single-Molecule Level
Elias Herrero-Galan et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2013)
Assessing the Utility of Infrared Spectroscopy as a Structural Diagnostic Tool for β-Sheets in Self-Assembling Aromatic Peptide Amphiphiles
Scott Fleming et al.
LANGMUIR (2013)
Self-Assembling Peptides Improve the Stability of Glucagon-like Peptide-1 by Forming a Stable and Sustained Complex
Ying Li et al.
MOLECULAR PHARMACEUTICS (2013)
Synthesis and characterization of designed BMHP1-derived self-assembling peptides for tissue engineering applications
Diego Silva et al.
NANOSCALE (2013)
Persistence length and stochastic fragmentation of supramolecular nanotubes under mechanical force
L. Ruiz et al.
NANOTECHNOLOGY (2013)
A novel bioactive peptide: assessing its activity over murine neural stem cells and its potential for neural tissue engineering
Andrea Caprini et al.
NEW BIOTECHNOLOGY (2013)
An in situ cross-linking hybrid hydrogel for controlled release of proteins
Hila Epstein-Barash et al.
ACTA BIOMATERIALIA (2012)
Self-Assembling Nanotubes Consisting of Rigid Cyclic γ-Peptides
Liangchun Li et al.
ADVANCED FUNCTIONAL MATERIALS (2012)
First-principles study of the adsorption of lysine on hydroxyapatite (100) surface
Zhaoyang Lou et al.
APPLIED SURFACE SCIENCE (2012)
Sustained delivery of VEGF from designer self-assembling peptides improves cardiac function after myocardial infarction
Hai-dong Guo et al.
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2012)
Chitosan-based scaffolds for the support of smooth muscle constructs in intestinal tissue engineering
Elie Zakhem et al.
BIOMATERIALS (2012)
Controlled release of urea from chitosan microspheres prepared by emulsification and cross-linking method
Md. Rabiul Hussain et al.
IRANIAN POLYMER JOURNAL (2012)
Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides
Mikyung Seo et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
GROMOS 53A6GLYC, an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates
Laercio Pol-Fachin et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Reference Simulations of Noncanonical Nucleic Acids with Different χ Variants of the AMBER Force Field: Quadruplex DNA, Quadruplex RNA, and Z-DNA
Miroslav Krepl et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Toward Quantitative Coarse-Grained Models of Lipids with Fluids Density Functional Theory
Laura J. Douglas Frink et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
Membrane Protein Simulations Using AMBER Force Field and Berger Lipid Parameters
Arnau Cordomi et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2012)
A New Multiscale Algorithm and Its Application to Coarse-Grained Peptide Models for Self-Assembly
Scott P. Carmichael et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
LIPID11: A Modular Framework for Lipid Simulations Using Amber
Age A. Skjevik et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
Aram Davtyan et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2012)
Insights into Intrastrand Cross-Link Lesions of DNA from QM/MM Molecular Dynamics Simulations
Julian Garrec et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)
Modeling the Self-Assembly of Peptide Amphiphiles into Fibers Using Coarse-Grained Molecular Dynamics
One-Sun Lee et al.
NANO LETTERS (2012)
New bioactive motifs and their use in functionalized self-assembling peptides for NSC differentiation and neural tissue engineering
F. Gelain et al.
NANOSCALE (2012)
REACTIVE MOLECULAR DYNAMICS: NUMERICAL METHODS AND ALGORITHMIC TECHNIQUES
Hasan Metin Aktulga et al.
SIAM JOURNAL ON SCIENTIFIC COMPUTING (2012)
Fast-Degradable Microbeads Encapsulating Human Umbilical Cord Stem Cells in Alginate for Muscle Tissue Engineering
Jun Liu et al.
TISSUE ENGINEERING PART A (2012)
Hyaluronic acid-based scaffold for central neural tissue engineering
Xiumei Wang et al.
INTERFACE FOCUS (2012)
Assembly of MreB Filaments on Liposome Membranes: A Synthetic Biology Approach
Yusuke T. Maeda et al.
ACS SYNTHETIC BIOLOGY (2012)
RNA Folding Pathways and the Self-Assembly of Ribosomes
Sarah A. Woodson
ACCOUNTS OF CHEMICAL RESEARCH (2011)
Physical Properties of Polymorphic Yeast Prion Amyloid Fibers
Carlos E. Castro et al.
BIOPHYSICAL JOURNAL (2011)
Definition and testing of the GROMOS force-field versions 54A7 and 54B7
Nathan Schmid et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2011)
Validation of the GROMOS 54A7 Force Field with Respect to β-Peptide Folding
Wei Huang et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2011)
Electrospun Collagen: A Tissue Engineering Scaffold with Unique Functional Properties in a Wide Variety of Applications
Balendu Shekhar Jha et al.
JOURNAL OF NANOMATERIALS (2011)
Biomaterial-Biomolecule Interaction: DFT-D Study of Glycine Adsorption on Cr2O3
P-A Garrain et al.
JOURNAL OF PHYSICAL CHEMISTRY C (2011)
Simulation of Chaperonin Effect on Protein Folding: A Shift from Nucleation-Condensation to Framework Mechanism
Sebastian Kmiecik et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Morphology and Persistence Length of Amyloid Fibrils Are Correlated to Peptide Molecular Structure
Corianne C. vandenAkker et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2011)
Molecular simulations predict novel collagen conformations during cross-link loading
Jonathan W. Bourne et al.
MATRIX BIOLOGY (2011)
Evaluation of Early and Late Effects into the Acute Spinal Cord Injury of an Injectable Functionalized Self-Assembling Scaffold
Daniela Cigognini et al.
PLOS ONE (2011)
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite
Sarel J. Fleishman et al.
PLOS ONE (2011)
Steered Molecular Dynamics Study of Mechanical Response of Full Length and Short Collagen Molecules
Shashindra M. Pradhan et al.
JOURNAL OF NANOMECHANICS AND MICROMECHANICS (2011)
DNA Self-assembly for Nanomedicine
Rahul Chhabra et al.
ADVANCED DRUG DELIVERY REVIEWS (2010)
Density functional theory calculations and molecular dynamics simulations of the adsorption of biomolecules on graphene surfaces
Wu Qin et al.
BIOMATERIALS (2010)
Self-Assembly of Peptide Amphiphiles: From Molecules to Nanostructures to Biomaterials
Honggang Cui et al.
BIOPOLYMERS (2010)
Molecular simulations of carbohydrates and protein-carbohydrate interactions: motivation, issues and prospects
Elisa Fadda et al.
DRUG DISCOVERY TODAY (2010)
Coarse-Grained Model of Collagen Molecules Using an Extended MARTINI Force Field
Alfonso Gautieri et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2010)
CHARMM General Force Field: A Force Field for Drug-Like Molecules Compatible with the CHARMM All-Atom Additive Biological Force Fields
K. Vanommeslaeghe et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2010)
DFT molecular dynamics (DFTMD) simulations of carbohydrates: COSMO solvated α-maltose
Frank A. Momany et al.
JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM (2010)
Current Status of the AMOEBA Polarizable Force Field
Jay W. Ponder et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2010)
Lipid microdomains and the regulation of ion channel function
Caroline Dart
JOURNAL OF PHYSIOLOGY-LONDON (2010)
Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity
Tristan Bereau et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)
Application of collagen-chitosan/fibrin glue asymmetric scaffolds in skin tissue engineering
Chun-mao Han et al.
JOURNAL OF ZHEJIANG UNIVERSITY-SCIENCE B (2010)
Nanoconfinement controls stiffness, strength and mechanical toughness of β-sheet crystals in silk
Sinan Keten et al.
NATURE MATERIALS (2010)
Hydroxyapatite as a key biomaterial: quantum-mechanical simulation of its surfaces in interaction with biomolecules
Marta Corno et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2010)
PRIMO/PRIMONA: A coarse-grained model for proteins and nucleic acids that preserves near-atomistic accuracy
Srinivasa M. Gopal et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2010)
Modeling of loops in proteins: a multi-method approach
Michal Jamroz et al.
BMC STRUCTURAL BIOLOGY (2010)
QM/MM Methods for Biomolecular Systems
Hans Martin Senn et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2009)
Self-Assembly of Multidomain Peptides: Sequence Variation Allows Control over Cross-Linking and Viscoelasticity
Lorenzo Aulisa et al.
BIOMACROMOLECULES (2009)
REACH Coarse-Grained Normal Mode Analysis of Protein Dimer Interaction Dynamics
Kei Moritsugu et al.
BIOPHYSICAL JOURNAL (2009)
Synthetic biology of minimal systems
Petra Schwille et al.
CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2009)
Generic coarse-grained model for protein folding and aggregation
Tristan Bereau et al.
JOURNAL OF CHEMICAL PHYSICS (2009)
Martini Coarse-Grained Force Field: Extension to Carbohydrates
Cesar A. Lopez et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2009)
Production of self-assembling biomaterials for tissue engineering
Stuart Kyle et al.
TRENDS IN BIOTECHNOLOGY (2009)
Folding pathway of the B1 domain of protein G explored by multiscale modeling
Sebastian Kmiecik et al.
BIOPHYSICAL JOURNAL (2008)
Systematic Multiscale Parameterization of Heterogeneous Elastic Network Models of Proteins
Edward Lyman et al.
BIOPHYSICAL JOURNAL (2008)
Mechanical properties of physiological and pathological models of collagen peptides investigated via steered molecular dynamics simulations
Alfonso Gautieri et al.
JOURNAL OF BIOMECHANICS (2008)
The MARTINI coarse-grained force field: Extension to proteins
Luca Monticelli et al.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2008)
Dynamic charge interactions create surprising rigidity in the ER/K α-helical protein motif
Sivaraj Sivaramakrishnan et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
GLYCAM06: A generalizable Biomolecular force field. Carbohydrates
Karl N. Kirschner et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2008)
Beyond the code: the mechanical properties of DNA as they relate to mitosis
Kerry S. Bloom
CHROMOSOMA (2008)
The MARTINI force field: Coarse grained model for biomolecular simulations
Siewert J. Marrink et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2007)
Improved residue contact prediction using support vector machines and a large feature set
Jianlin Cheng et al.
BMC BIOINFORMATICS (2007)
Multiscale modeling of biomolecular systems: in serial and in parallel
Gary S. Ayton et al.
CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)
Biological Designer Self-Assembling Peptide Nanofiber Scaffolds Significantly Enhance Osteoblast Proliferation, Differentiation and 3-D Migration
Akihiro Horii et al.
PLOS ONE (2007)
Designer Self-Assembling Peptide Nanofiber Scaffolds for Adult Mouse Neural Stem Cell 3-Dimensional Cultures
Fabrizio Gelain et al.
PLOS ONE (2006)
Self-assembly and applications of biomimetic and bioactive peptide-amphiphiles
Efrosini Kokkoli et al.
SOFT MATTER (2006)
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
P Jurecka et al.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS (2006)
Molecular designer self-assembling peptides
Xiaojun Zhao et al.
CHEMICAL SOCIETY REVIEWS (2006)
Measurement of the elastic modulus of single bacterial cellulose fibers using atomic force microscopy
G Guhados et al.
LANGMUIR (2005)
Validation of the 53A6 GROMOS force field
C Oostenbrink et al.
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS (2005)
A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid
M Bathe et al.
BIOPHYSICAL JOURNAL (2005)
Mechanical unfolding of RNA hairpins
C Hyeon et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)
Single-molecule measurements of the persistence length of double- stranded RNA
JA Abels et al.
BIOPHYSICAL JOURNAL (2005)
NMR solution structure of a peptide from the mdm-2 binding domain of the p53 protein that is selectively cytotoxic to cancer cells
R Rosal et al.
BIOCHEMISTRY (2004)
M3B: A coarse grain force field for molecular simulations of malto-oligosaccharides and their water mixtures
V Molinero et al.
JOURNAL OF PHYSICAL CHEMISTRY B (2004)
A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force-field parameter sets 53A5 and 53A6
C Oostenbrink et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Fabrication of novel biomaterials through molecular self-assembly
SG Zhang
NATURE BIOTECHNOLOGY (2003)
A reactive molecular dynamics model of thermal decomposition in polymers: 1. Poly(methyl methacrylate)
SI Stoliarov et al.
POLYMER (2003)
Characterization of polylactic acid polyglycolic acid composites for cartilage tissue engineering
JM Moran et al.
TISSUE ENGINEERING (2003)
An improved OPLS-AA force field for carbohydrates
D Kony et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2002)
Anisotropy of fluctuation dynamics of proteins with an elastic network model
AR Atilgan et al.
BIOPHYSICAL JOURNAL (2001)