Efficient Construction of Atomic-Resolution Models of Non-Sulfated Chondroitin Glycosaminoglycan Using Molecular Dynamics Data

Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations

(2019) Irfan Alibay et al.   Journal of Chemical Information and Modeling

Comparison of Carbohydrate Force Fields Using Gaussian Accelerated Molecular Dynamics Simulations and Development of Force Field Parameters for Heparin-Analogue Pentasaccharides

(2019) Gábor Balogh et al.   Journal of Chemical Information and Modeling

Specificity of glycosaminoglycan–protein interactions

(2018) Lena Kjellén et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

MatrixDB: integration of new data with a focus on glycosaminoglycan interactions

(2018) Olivier Clerc et al.   NUCLEIC ACIDS RESEARCH

Chondroitin sulfates and their binding molecules in the central nervous system

(2017) L Djerbal et al.   GLYCOCONJUGATE JOURNAL

Rigidity and flexibility in the tetrasaccharide linker of proteoglycans from atomic-resolution molecular simulation

(2017) Cathy Ng et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Antibody recognizing 4-sulfated chondroitin sulfate proteoglycans restores memory in tauopathy-induced neurodegeneration

(2017) Sujeong Yang et al.   NEUROBIOLOGY OF AGING

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

(2017) Peter Eastman et al.   PLoS Computational Biology

Urinary Glycosaminoglycans Predict Outcomes in Septic Shock and Acute Respiratory Distress Syndrome

(2016) Eric P. Schmidt et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

CarbBuilder: Software for building molecular models of complex oligo- and polysaccharide structures

(2016) Michelle M. Kuttel et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHST14/D4ST1 deficiency: New form of Ehlers-Danlos syndrome

(2016) Tomoki Kosho   PEDIATRICS INTERNATIONAL

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design

(2015) K. Vanommeslaeghe et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

Proteoglycans and Their Heterogeneous Glycosaminoglycans at the Atomic Scale

(2015) Benedict M. Sattelle et al.   BIOMACROMOLECULES

Fell-Muir Lecture: Heparan sulphate and the art of cell regulation: a polymer chain conducts the protein orchestra

(2015) John Gallagher   INTERNATIONAL JOURNAL OF EXPERIMENTAL PATHOLOGY

Sulfation and Cation Effects on the Conformational Properties of the Glycan Backbone of Chondroitin Sulfate Disaccharides

(2015) Christina E. Faller et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Revealing the Mechanisms of Protein Disorder and N-Glycosylation in CD44-Hyaluronan Binding Using Molecular Simulation

(2015) Olgun Guvench   Frontiers in Immunology

Flexibility and Explicit Solvent in Molecular-Dynamics-Based Docking of Protein–Glycosaminoglycan Systems

(2014) Sergey A. Samsonov et al.   Journal of Chemical Information and Modeling

Efficient Handling of Gaussian Charge Distributions: An Application to Polarizable Molecular Models

(2014) Péter T. Kiss et al.   Journal of Chemical Theory and Computation

CD44 Receptor Unfolding Enhances Binding by Freeing Basic Amino Acids to Contact Carbohydrate Ligand

(2013) Amanda J. Favreau et al.   BIOPHYSICAL JOURNAL

POLYS 2.0: An open source software package for building three-dimensional structures of polysaccharides

(2013) Søren B. Engelsen et al.   BIOPOLYMERS

The power of coarse graining in biomolecular simulations

(2013) Helgi I. Ingólfsson et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Interaction of chondroitin sulfate and dermatan sulfate from various biological sources with heparin-binding growth factors and cytokines

(2012) Shuji Mizumoto et al.   GLYCOCONJUGATE JOURNAL

OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation

(2012) Peter Eastman et al.   Journal of Chemical Theory and Computation

A Solvent-Free Coarse Grain Model for Crystalline and Amorphous Cellulose Fibrils

(2011) Goundla Srinivas et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling

(2011) Olgun Guvench et al.   Journal of Chemical Theory and Computation

CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates

(2011) Sairam S. Mallajosyula et al.   Journal of Chemical Theory and Computation

On the Ewald summation of Gaussian charges for the simulation of metallic surfaces

(2010) Todd R. Gingrich et al.   CHEMICAL PHYSICS LETTERS

OpenMM: A Hardware-Independent Framework for Molecular Simulations

(2010) Peter Eastman et al.   COMPUTING IN SCIENCE & ENGINEERING

Constant Constraint Matrix Approximation: A Robust, Parallelizable Constraint Method for Molecular Simulations

(2010) Peter Eastman et al.   Journal of Chemical Theory and Computation

Free Energy Landscapes of Iduronic Acid and Related Monosaccharides

(2010) Benedict M. Sattelle et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A 3D-structural model of unsulfated chondroitin from high-field NMR: 4-sulfation has little effect on backbone conformation

(2009) Benedict M. Sattelle et al.   CARBOHYDRATE RESEARCH

Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study

(2009) Neha S. Gandhi et al.   CARBOHYDRATE RESEARCH

Glycosyltransferase and sulfotransferase gene expression profiles in human monocytes, dendritic cells and macrophages

(2009) François Trottein et al.   GLYCOCONJUGATE JOURNAL

CHARMM Additive All-Atom Force Field for Glycosidic Linkages between Hexopyranoses

(2009) Olgun Guvench et al.   Journal of Chemical Theory and Computation

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

(2009) Peter Eastman et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Accelerating molecular dynamic simulation on graphics processing units

(2009) Mark S. Friedrichs et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

CHARMM: The biomolecular simulation program

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

Control of Growth Factor Networks by Heparan Sulfate Proteoglycans

(2008) Kimberly Forsten-Williams et al.   ANNALS OF BIOMEDICAL ENGINEERING

The Structure of Glycosaminoglycans and their Interactions with Proteins

(2008) Neha S. Gandhi et al.   Chemical Biology & Drug Design

Additive empirical force field for hexopyranose monosaccharides

(2008) Olgun Guvench et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

The Crystal and Molecular Structures of a Cathepsin K:Chondroitin Sulfate Complex

(2008) Zhenqiang Li et al.   JOURNAL OF MOLECULAR BIOLOGY

Conformational Analysis of a Dermatan Sulfate-Derived Tetrasaccharide by NMR, Molecular Modeling, and Residual Dipolar Couplings

(2007) Alba Silipo et al.   CHEMBIOCHEM